Daily Papers

Gathering histopathology slides from over 100 publicly available cohorts, we compile a diverse dataset of 460 million pathology tiles covering more than 30 cancer sites. Using this dataset, we train a large self-supervised vision transformer using DINOv2 and publicly release one iteration of this model for further experimentation, coined Phikon-v2. While trained on publicly available histology slides, Phikon-v2 surpasses our previously released model (Phikon) and performs on par with other histopathology foundation models (FM) trained on proprietary data. Our benchmarks include eight slide-level tasks with results reported on external validation cohorts avoiding any data contamination between pre-training and evaluation datasets. Our downstream training procedure follows a simple yet robust ensembling strategy yielding a +1.75 AUC increase across tasks and models compared to one-shot retraining (p<0.001). We compare Phikon (ViT-B) and Phikon-v2 (ViT-L) against 14 different histology feature extractors, making our evaluation the most comprehensive to date. Our result support evidences that DINOv2 handles joint model and data scaling better than iBOT. Also, we show that recent scaling efforts are overall beneficial to downstream performance in the context of biomarker prediction with GigaPath and H-Optimus-0 (two ViT-g with 1.1B parameters each) standing out. However, the statistical margins between the latest top-performing FMs remain mostly non-significant; some even underperform on specific indications or tasks such as MSI prediction - deposed by a 13x smaller model developed internally. While latest foundation models may exhibit limitations for clinical deployment, they nonetheless offer excellent grounds for the development of more specialized and cost-efficient histology encoders fueling AI-guided diagnostic tools.

Radiology reporting generative AI holds significant potential to alleviate clinical workloads and streamline medical care. However, achieving high clinical accuracy is challenging, as radiological images often feature subtle lesions and intricate structures. Existing systems often fall short, largely due to their reliance on fixed size, patch-level image features and insufficient incorporation of pathological information. This can result in the neglect of such subtle patterns and inconsistent descriptions of crucial pathologies. To address these challenges, we propose an innovative approach that leverages pathology-aware regional prompts to explicitly integrate anatomical and pathological information of various scales, significantly enhancing the precision and clinical relevance of generated reports. We develop an anatomical region detector that extracts features from distinct anatomical areas, coupled with a novel multi-label lesion detector that identifies global pathologies. Our approach emulates the diagnostic process of radiologists, producing clinically accurate reports with comprehensive diagnostic capabilities. Experimental results show that our model outperforms previous state-of-the-art methods on most natural language generation and clinical efficacy metrics, with formal expert evaluations affirming its potential to enhance radiology practice.

At the heart of medicine lies the physician-patient dialogue, where skillful history-taking paves the way for accurate diagnosis, effective management, and enduring trust. Artificial Intelligence (AI) systems capable of diagnostic dialogue could increase accessibility, consistency, and quality of care. However, approximating clinicians' expertise is an outstanding grand challenge. Here, we introduce AMIE (Articulate Medical Intelligence Explorer), a Large Language Model (LLM) based AI system optimized for diagnostic dialogue. AMIE uses a novel self-play based simulated environment with automated feedback mechanisms for scaling learning across diverse disease conditions, specialties, and contexts. We designed a framework for evaluating clinically-meaningful axes of performance including history-taking, diagnostic accuracy, management reasoning, communication skills, and empathy. We compared AMIE's performance to that of primary care physicians (PCPs) in a randomized, double-blind crossover study of text-based consultations with validated patient actors in the style of an Objective Structured Clinical Examination (OSCE). The study included 149 case scenarios from clinical providers in Canada, the UK, and India, 20 PCPs for comparison with AMIE, and evaluations by specialist physicians and patient actors. AMIE demonstrated greater diagnostic accuracy and superior performance on 28 of 32 axes according to specialist physicians and 24 of 26 axes according to patient actors. Our research has several limitations and should be interpreted with appropriate caution. Clinicians were limited to unfamiliar synchronous text-chat which permits large-scale LLM-patient interactions but is not representative of usual clinical practice. While further research is required before AMIE could be translated to real-world settings, the results represent a milestone towards conversational diagnostic AI.

As machine learning models become increasingly prevalent in medical diagnostics, the need for interpretability and transparency becomes paramount. The XAI Renaissance signifies a significant shift in the field, aiming to redefine the interpretability of medical diagnostic models. This paper explores the innovative approaches and methodologies within the realm of Explainable AI (XAI) that are revolutionizing the interpretability of medical diagnostic models. By shedding light on the underlying decision-making process, XAI techniques empower healthcare professionals to understand, trust, and effectively utilize these models for accurate and reliable medical diagnoses. This review highlights the key advancements in XAI for medical diagnostics and their potential to transform the healthcare landscape, ultimately improving patient outcomes and fostering trust in AI-driven diagnostic systems.

As the field of artificial intelligence progresses, assistive technologies are becoming more widely used across all industries. The healthcare industry is no different, with numerous studies being done to develop assistive tools for healthcare professionals. Automatic diagnostic systems are one such beneficial tool that can assist with a variety of tasks, including collecting patient information, analyzing test results, and diagnosing patients. However, the idea of developing systems that can provide a differential diagnosis has been largely overlooked in most of these research studies. In this study, we propose a transformer-based approach for providing differential diagnoses based on a patient's age, sex, medical history, and symptoms. We use the DDXPlus dataset, which provides differential diagnosis information for patients based on 49 disease types. Firstly, we propose a method to process the tabular patient data from the dataset and engineer them into patient reports to make them suitable for our research. In addition, we introduce two data modification modules to diversify the training data and consequently improve the robustness of the models. We approach the task as a multi-label classification problem and conduct extensive experiments using four transformer models. All the models displayed promising results by achieving over 97% F1 score on the held-out test set. Moreover, we design additional behavioral tests to get a broader understanding of the models. In particular, for one of our test cases, we prepared a custom test set of 100 samples with the assistance of a doctor. The results on the custom set showed that our proposed data modification modules improved the model's generalization capabilities. We hope our findings will provide future researchers with valuable insights and inspire them to develop reliable systems for automatic differential diagnosis.

Recently, Computer-Aided Diagnosis (CAD) systems have emerged as indispensable tools in clinical diagnostic workflows, significantly alleviating the burden on radiologists. Nevertheless, despite their integration into clinical settings, CAD systems encounter limitations. Specifically, while CAD systems can achieve high performance in the detection of lung nodules, they face challenges in accurately predicting multiple cancer types. This limitation can be attributed to the scarcity of publicly available datasets annotated with expert-level cancer type information. This research aims to bridge this gap by providing publicly accessible datasets and reliable tools for medical diagnosis, facilitating a finer categorization of different types of lung diseases so as to offer precise treatment recommendations. To achieve this objective, we curated a diverse dataset of lung Computed Tomography (CT) images, comprising 330 annotated nodules (nodules are labeled as bounding boxes) from 95 distinct patients. The quality of the dataset was evaluated using a variety of classical classification and detection models, and these promising results demonstrate that the dataset has a feasible application and further facilitate intelligent auxiliary diagnosis.

Quantitative tools are increasingly appealing for decision support in healthcare, driven by the growing capabilities of advanced AI systems. However, understanding the predictive uncertainties surrounding a tool's output is crucial for decision-makers to ensure reliable and transparent decisions. In this paper, we present a case study on pulmonary nodule detection for lung cancer screening, enhancing an advanced detection model with an uncertainty quantification technique called conformal risk control (CRC). We demonstrate that prediction sets with conformal guarantees are attractive measures of predictive uncertainty in the safety-critical healthcare domain, allowing end-users to achieve arbitrary validity by trading off false positives and providing formal statistical guarantees on model performance. Among ground-truth nodules annotated by at least three radiologists, our model achieves a sensitivity that is competitive with that generally achieved by individual radiologists, with a slight increase in false positives. Furthermore, we illustrate the risks of using off-the-shelve prediction models when faced with ontological uncertainty, such as when radiologists disagree on what constitutes the ground truth on pulmonary nodules.

Biomedical data is inherently multimodal, consisting of electronic health records, medical imaging, digital pathology, genome sequencing, wearable sensors, and more. The application of artificial intelligence tools to these multifaceted sensing technologies has the potential to revolutionize the prognosis, diagnosis, and management of human health and disease. However, current approaches to biomedical AI typically only train and evaluate with one or a small set of medical modalities and tasks. This limitation hampers the development of comprehensive tools that can leverage the rich interconnected information across many heterogeneous biomedical sensors. To address this challenge, we present MultiMed, a benchmark designed to evaluate and enable large-scale learning across a wide spectrum of medical modalities and tasks. MultiMed consists of 2.56 million samples across ten medical modalities such as medical reports, pathology, genomics, and protein data, and is structured into eleven challenging tasks, including disease prognosis, protein structure prediction, and medical question answering. Using MultiMed, we conduct comprehensive experiments benchmarking state-of-the-art unimodal, multimodal, and multitask models. Our analysis highlights the advantages of training large-scale medical models across many related modalities and tasks. Moreover, MultiMed enables studies of generalization across related medical concepts, robustness to real-world noisy data and distribution shifts, and novel modality combinations to improve prediction performance. MultiMed will be publicly available and regularly updated and welcomes inputs from the community.

The integration of Artificial Intelligence (AI), especially Large Language Models (LLMs), into the clinical diagnosis process offers significant potential to improve the efficiency and accessibility of medical care. While LLMs have shown some promise in the medical domain, their application in clinical diagnosis remains underexplored, especially in real-world clinical practice, where highly sophisticated, patient-specific decisions need to be made. Current evaluations of LLMs in this field are often narrow in scope, focusing on specific diseases or specialties and employing simplified diagnostic tasks. To bridge this gap, we introduce CliBench, a novel benchmark developed from the MIMIC IV dataset, offering a comprehensive and realistic assessment of LLMs' capabilities in clinical diagnosis. This benchmark not only covers diagnoses from a diverse range of medical cases across various specialties but also incorporates tasks of clinical significance: treatment procedure identification, lab test ordering and medication prescriptions. Supported by structured output ontologies, CliBench enables a precise and multi-granular evaluation, offering an in-depth understanding of LLM's capability on diverse clinical tasks of desired granularity. We conduct a zero-shot evaluation of leading LLMs to assess their proficiency in clinical decision-making. Our preliminary results shed light on the potential and limitations of current LLMs in clinical settings, providing valuable insights for future advancements in LLM-powered healthcare.

Large language models (LLMs) have shown remarkable progress in encoding clinical knowledge and responding to complex medical queries with appropriate clinical reasoning. However, their applicability in subspecialist or complex medical settings remains underexplored. In this work, we probe the performance of AMIE, a research conversational diagnostic AI system, in the subspecialist domain of breast oncology care without specific fine-tuning to this challenging domain. To perform this evaluation, we curated a set of 50 synthetic breast cancer vignettes representing a range of treatment-naive and treatment-refractory cases and mirroring the key information available to a multidisciplinary tumor board for decision-making (openly released with this work). We developed a detailed clinical rubric for evaluating management plans, including axes such as the quality of case summarization, safety of the proposed care plan, and recommendations for chemotherapy, radiotherapy, surgery and hormonal therapy. To improve performance, we enhanced AMIE with the inference-time ability to perform web search retrieval to gather relevant and up-to-date clinical knowledge and refine its responses with a multi-stage self-critique pipeline. We compare response quality of AMIE with internal medicine trainees, oncology fellows, and general oncology attendings under both automated and specialist clinician evaluations. In our evaluations, AMIE outperformed trainees and fellows demonstrating the potential of the system in this challenging and important domain. We further demonstrate through qualitative examples, how systems such as AMIE might facilitate conversational interactions to assist clinicians in their decision making. However, AMIE's performance was overall inferior to attending oncologists suggesting that further research is needed prior to consideration of prospective uses.

Artificial Intelligence (AI) has the potential to revolutionize diagnosis and segmentation in medical imaging. However, development and clinical implementation face multiple challenges including limited data availability, lack of generalizability, and the necessity to incorporate multi-modal data effectively. A foundation model, which is a large-scale pre-trained AI model, offers a versatile base that can be adapted to a variety of specific tasks and contexts. Here, we present a novel foundation model, VISION-MAE, specifically designed for medical imaging. Specifically, VISION-MAE is trained on a dataset of 2.5 million unlabeled images from various modalities (CT, MR, PET, X-rays, and ultrasound), using self-supervised learning techniques. It is then adapted to classification and segmentation tasks using explicit labels. VISION-MAE has high label efficiency, outperforming several benchmark models in both in-domain and out-of-domain applications, and achieves high performance even with reduced availability of labeled data. This model represents a significant advancement in medical imaging AI, offering a generalizable and robust solution for improving segmentation and classification tasks while reducing the data annotation workload.

As advances in large language models (LLMs) and multimodal techniques continue to mature, the development of general-purpose multimodal large language models (MLLMs) has surged, offering significant applications in interpreting natural images. However, the field of pathology has largely remained untapped, particularly in gathering high-quality data and designing comprehensive model frameworks. To bridge the gap in pathology MLLMs, we present PathAsst, a multimodal generative foundation AI assistant to revolutionize diagnostic and predictive analytics in pathology. The development of PathAsst involves three pivotal steps: data acquisition, CLIP model adaptation, and the training of PathAsst's multimodal generative capabilities. Firstly, we collect over 207K high-quality pathology image-text pairs from authoritative sources. Leveraging the advanced power of ChatGPT, we generate over 180K instruction-following samples. Furthermore, we devise additional instruction-following data specifically tailored for invoking eight pathology-specific sub-models we prepared, allowing the PathAsst to effectively collaborate with these models, enhancing its diagnostic ability. Secondly, by leveraging the collected data, we construct PathCLIP, a pathology-dedicated CLIP, to enhance PathAsst's capabilities in interpreting pathology images. Finally, we integrate PathCLIP with the Vicuna-13b and utilize pathology-specific instruction-tuning data to enhance the multimodal generation capacity of PathAsst and bolster its synergistic interactions with sub-models. The experimental results of PathAsst show the potential of harnessing AI-powered generative foundation model to improve pathology diagnosis and treatment processes.

Conversational AI tools that can generate and discuss clinically correct radiology reports for a given medical image have the potential to transform radiology. Such a human-in-the-loop radiology assistant could facilitate a collaborative diagnostic process, thus saving time and improving the quality of reports. Towards this goal, we introduce RaDialog, the first thoroughly evaluated and publicly available large vision-language model for radiology report generation and interactive dialog. RaDialog effectively integrates visual image features and structured pathology findings with a large language model (LLM) while simultaneously adapting it to a specialized domain using parameter-efficient fine-tuning. To keep the conversational abilities of the underlying LLM, we propose a comprehensive, semi-automatically labeled, image-grounded instruct dataset for chest X-ray radiology tasks. By training with this dataset, our method achieves state-of-the-art clinical correctness in report generation and shows impressive abilities in interactive tasks such as correcting reports and answering questions, serving as a foundational step toward clinical dialog systems. Our code is available on github: https://github.com/ChantalMP/RaDialog.

In the light of the COVID-19 pandemic, deep learning methods have been widely investigated in detecting COVID-19 from chest X-rays. However, a more pragmatic approach to applying AI methods to a medical diagnosis is designing a framework that facilitates human-machine interaction and expert decision making. Studies have shown that categorization can play an essential rule in accelerating real-world decision making. Inspired by descriptive document clustering, we propose a domain-independent explanatory clustering framework to group contextually related instances and support radiologists' decision making. While most descriptive clustering approaches employ domain-specific characteristics to form meaningful clusters, we focus on model-level explanation as a more general-purpose element of every learning process to achieve cluster homogeneity. We employ DeepSHAP to generate homogeneous clusters in terms of disease severity and describe the clusters using favorable and unfavorable saliency maps, which visualize the class discriminating regions of an image. These human-interpretable maps complement radiologist knowledge to investigate the whole cluster at once. Besides, as part of this study, we evaluate a model based on VGG-19, which can identify COVID and pneumonia cases with a positive predictive value of 95% and 97%, respectively, comparable to the recent explainable approaches for COVID diagnosis.

Artificial Intelligence (AI) has demonstrated significant potential in healthcare, particularly in disease diagnosis and treatment planning. Recent progress in Medical Large Vision-Language Models (Med-LVLMs) has opened up new possibilities for interactive diagnostic tools. However, these models often suffer from factual hallucination, which can lead to incorrect diagnoses. Fine-tuning and retrieval-augmented generation (RAG) have emerged as methods to address these issues. However, the amount of high-quality data and distribution shifts between training data and deployment data limit the application of fine-tuning methods. Although RAG is lightweight and effective, existing RAG-based approaches are not sufficiently general to different medical domains and can potentially cause misalignment issues, both between modalities and between the model and the ground truth. In this paper, we propose a versatile multimodal RAG system, MMed-RAG, designed to enhance the factuality of Med-LVLMs. Our approach introduces a domain-aware retrieval mechanism, an adaptive retrieved contexts selection method, and a provable RAG-based preference fine-tuning strategy. These innovations make the RAG process sufficiently general and reliable, significantly improving alignment when introducing retrieved contexts. Experimental results across five medical datasets (involving radiology, ophthalmology, pathology) on medical VQA and report generation demonstrate that MMed-RAG can achieve an average improvement of 43.8% in the factual accuracy of Med-LVLMs. Our data and code are available in https://github.com/richard-peng-xia/MMed-RAG.

Chest X-rays (CXRs) play an integral role in driving critical decisions in disease management and patient care. While recent innovations have led to specialized models for various CXR interpretation tasks, these solutions often operate in isolation, limiting their practical utility in clinical practice. We present MedRAX, the first versatile AI agent that seamlessly integrates state-of-the-art CXR analysis tools and multimodal large language models into a unified framework. MedRAX dynamically leverages these models to address complex medical queries without requiring additional training. To rigorously evaluate its capabilities, we introduce ChestAgentBench, a comprehensive benchmark containing 2,500 complex medical queries across 7 diverse categories. Our experiments demonstrate that MedRAX achieves state-of-the-art performance compared to both open-source and proprietary models, representing a significant step toward the practical deployment of automated CXR interpretation systems. Data and code have been publicly available at https://github.com/bowang-lab/MedRAX

Clinical diagnosis is critical in medical practice, typically requiring a continuous and evolving process that includes primary diagnosis, differential diagnosis, and final diagnosis. However, most existing clinical diagnostic tasks are single-step processes, which does not align with the complex multi-step diagnostic procedures found in real-world clinical settings. In this paper, we propose a multi-step diagnostic task and annotate a clinical diagnostic dataset (MSDiagnosis). This dataset includes primary diagnosis, differential diagnosis, and final diagnosis questions. Additionally, we propose a novel and effective framework. This framework combines forward inference, backward inference, reflection, and refinement, enabling the LLM to self-evaluate and adjust its diagnostic results. To assess the effectiveness of our proposed method, we design and conduct extensive experiments. The experimental results demonstrate the effectiveness of the proposed method. We also provide a comprehensive experimental analysis and suggest future research directions for this task.

Human readers or radiologists routinely perform full-body multi-organ multi-disease detection and diagnosis in clinical practice, while most medical AI systems are built to focus on single organs with a narrow list of a few diseases. This might severely limit AI's clinical adoption. A certain number of AI models need to be assembled non-trivially to match the diagnostic process of a human reading a CT scan. In this paper, we construct a Unified Tumor Transformer (UniT) model to detect (tumor existence and location) and diagnose (tumor characteristics) eight major cancer-prevalent organs in CT scans. UniT is a query-based Mask Transformer model with the output of multi-organ and multi-tumor semantic segmentation. We decouple the object queries into organ queries, detection queries and diagnosis queries, and further establish hierarchical relationships among the three groups. This clinically-inspired architecture effectively assists inter- and intra-organ representation learning of tumors and facilitates the resolution of these complex, anatomically related multi-organ cancer image reading tasks. UniT is trained end-to-end using a curated large-scale CT images of 10,042 patients including eight major types of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D tumor masks annotated by radiologists). On the test set of 631 patients, UniT has demonstrated strong performance under a set of clinically relevant evaluation metrics, substantially outperforming both multi-organ segmentation methods and an assembly of eight single-organ expert models in tumor detection, segmentation, and diagnosis. Such a unified multi-cancer image reading model (UniT) can significantly reduce the number of false positives produced by combined multi-system models. This moves one step closer towards a universal high-performance cancer screening tool.

Large Language Models (LLMs) are transforming artificial intelligence, evolving into task-oriented systems capable of autonomous planning and execution. One of the primary applications of LLMs is conversational AI systems, which must navigate multi-turn dialogues, integrate domain-specific APIs, and adhere to strict policy constraints. However, evaluating these agents remains a significant challenge, as traditional methods fail to capture the complexity and variability of real-world interactions. We introduce IntellAgent, a scalable, open-source multi-agent framework designed to evaluate conversational AI systems comprehensively. IntellAgent automates the creation of diverse, synthetic benchmarks by combining policy-driven graph modeling, realistic event generation, and interactive user-agent simulations. This innovative approach provides fine-grained diagnostics, addressing the limitations of static and manually curated benchmarks with coarse-grained metrics. IntellAgent represents a paradigm shift in evaluating conversational AI. By simulating realistic, multi-policy scenarios across varying levels of complexity, IntellAgent captures the nuanced interplay of agent capabilities and policy constraints. Unlike traditional methods, it employs a graph-based policy model to represent relationships, likelihoods, and complexities of policy interactions, enabling highly detailed diagnostics. IntellAgent also identifies critical performance gaps, offering actionable insights for targeted optimization. Its modular, open-source design supports seamless integration of new domains, policies, and APIs, fostering reproducibility and community collaboration. Our findings demonstrate that IntellAgent serves as an effective framework for advancing conversational AI by addressing challenges in bridging research and deployment. The framework is available at https://github.com/plurai-ai/intellagent

In medical applications, deep learning methods are built to automate diagnostic tasks. However, a clinically relevant question that practitioners usually face, is how to predict the future trajectory of a disease (prognosis). Current methods for such a problem often require domain knowledge, and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many forecasting problem from multimodal data. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner, we model a prognosis prediction problem with two transformer-based components that share information between each other. The first block in this model aims to analyze the imaging data, and the second block leverages the internal representations of the first one as inputs, also fusing them with auxiliary patient data. We show the effectiveness of our method in predicting the development of structural knee osteoarthritis changes over time. Our results show that the proposed method outperforms the state-of-the-art baselines in terms of various performance metrics. In addition, we empirically show that the existence of the multi-agent transformers with depths of 2 is sufficient to achieve good performances. Our code is publicly available at https://github.com/MIPT-Oulu/CLIMAT.

There has been a rapidly growing interest in Automatic Symptom Detection (ASD) and Automatic Diagnosis (AD) systems in the machine learning research literature, aiming to assist doctors in telemedicine services. These systems are designed to interact with patients, collect evidence about their symptoms and relevant antecedents, and possibly make predictions about the underlying diseases. Doctors would review the interactions, including the evidence and the predictions, collect if necessary additional information from patients, before deciding on next steps. Despite recent progress in this area, an important piece of doctors' interactions with patients is missing in the design of these systems, namely the differential diagnosis. Its absence is largely due to the lack of datasets that include such information for models to train on. In this work, we present a large-scale synthetic dataset of roughly 1.3 million patients that includes a differential diagnosis, along with the ground truth pathology, symptoms and antecedents for each patient. Unlike existing datasets which only contain binary symptoms and antecedents, this dataset also contains categorical and multi-choice symptoms and antecedents useful for efficient data collection. Moreover, some symptoms are organized in a hierarchy, making it possible to design systems able to interact with patients in a logical way. As a proof-of-concept, we extend two existing AD and ASD systems to incorporate the differential diagnosis, and provide empirical evidence that using differentials as training signals is essential for the efficiency of such systems or for helping doctors better understand the reasoning of those systems.

Automated diagnosis prediction from medical images is a valuable resource to support clinical decision-making. However, such systems usually need to be trained on large amounts of annotated data, which often is scarce in the medical domain. Zero-shot methods address this challenge by allowing a flexible adaption to new settings with different clinical findings without relying on labeled data. Further, to integrate automated diagnosis in the clinical workflow, methods should be transparent and explainable, increasing medical professionals' trust and facilitating correctness verification. In this work, we introduce Xplainer, a novel framework for explainable zero-shot diagnosis in the clinical setting. Xplainer adapts the classification-by-description approach of contrastive vision-language models to the multi-label medical diagnosis task. Specifically, instead of directly predicting a diagnosis, we prompt the model to classify the existence of descriptive observations, which a radiologist would look for on an X-Ray scan, and use the descriptor probabilities to estimate the likelihood of a diagnosis. Our model is explainable by design, as the final diagnosis prediction is directly based on the prediction of the underlying descriptors. We evaluate Xplainer on two chest X-ray datasets, CheXpert and ChestX-ray14, and demonstrate its effectiveness in improving the performance and explainability of zero-shot diagnosis. Our results suggest that Xplainer provides a more detailed understanding of the decision-making process and can be a valuable tool for clinical diagnosis.

We present our vision for developing an automated tool capable of translating visual properties observed in Machine Learning (ML) visualisations into Python assertions. The tool aims to streamline the process of manually verifying these visualisations in the ML development cycle, which is critical as real-world data and assumptions often change post-deployment. In a prior study, we mined 54,070 Jupyter notebooks from Github and created a catalogue of 269 semantically related visualisation-assertion (VA) pairs. Building on this catalogue, we propose to build a taxonomy that organises the VA pairs based on ML verification tasks. The input feature space comprises of a rich source of information mined from the Jupyter notebooks -- visualisations, Python source code, and associated markdown text. The effectiveness of various AI models, including traditional NLP4Code models and modern Large Language Models, will be compared using established machine translation metrics and evaluated through a qualitative study with human participants. The paper also plans to address the challenge of extending the existing VA pair dataset with additional pairs from Kaggle and to compare the tool's effectiveness with commercial generative AI models like ChatGPT. This research not only contributes to the field of ML system validation but also explores novel ways to leverage AI for automating and enhancing software engineering practices in ML.

Machine learning, the foundation of modern artificial intelligence, has driven innovations that have fundamentally transformed the world. Yet, behind advancements lies a complex and often tedious process requiring labor and compute intensive iteration and experimentation. Engineers and scientists developing machine learning models spend much of their time on trial-and-error tasks instead of conceptualizing innovative solutions or research hypotheses. To address this challenge, we introduce AI-Driven Exploration (AIDE), a machine learning engineering agent powered by large language models (LLMs). AIDE frames machine learning engineering as a code optimization problem, and formulates trial-and-error as a tree search in the space of potential solutions. By strategically reusing and refining promising solutions, AIDE effectively trades computational resources for enhanced performance, achieving state-of-the-art results on multiple machine learning engineering benchmarks, including our Kaggle evaluations, OpenAI MLE-Bench and METRs RE-Bench.

A promising application of AI to healthcare is the retrieval of information from electronic health records (EHRs), e.g. to aid clinicians in finding relevant information for a consultation or to recruit suitable patients for a study. This requires search capabilities far beyond simple string matching, including the retrieval of concepts (diagnoses, symptoms, medications, etc.) related to the one in question. The suitability of AI methods for such applications is tested by predicting the relatedness of concepts with known relatedness scores. However, all existing biomedical concept relatedness datasets are notoriously small and consist of hand-picked concept pairs. We open-source a novel concept relatedness benchmark overcoming these issues: it is six times larger than existing datasets and concept pairs are chosen based on co-occurrence in EHRs, ensuring their relevance for the application of interest. We present an in-depth analysis of our new dataset and compare it to existing ones, highlighting that it is not only larger but also complements existing datasets in terms of the types of concepts included. Initial experiments with state-of-the-art embedding methods show that our dataset is a challenging new benchmark for testing concept relatedness models.

AI-driven medical history-taking is an important component in symptom checking, automated patient intake, triage, and other AI virtual care applications. As history-taking is extremely varied, machine learning models require a significant amount of data to train. To overcome this challenge, existing systems are developed using indirect data or expert knowledge. This leads to a training-inference gap as models are trained on different kinds of data than what they observe at inference time. In this work, we present a two-stage re-ranking approach that helps close the training-inference gap by re-ranking the first-stage question candidates using a dialogue-contextualized model. For this, we propose a new model, global re-ranker, which cross-encodes the dialogue with all questions simultaneously, and compare it with several existing neural baselines. We test both transformer and S4-based language model backbones. We find that relative to the expert system, the best performance is achieved by our proposed global re-ranker with a transformer backbone, resulting in a 30% higher normalized discount cumulative gain (nDCG) and a 77% higher mean average precision (mAP).

Large Language Models (LLMs), such as ChatGPT, are becoming increasingly sophisticated, demonstrating capabilities that closely resemble those of humans. These AI models are playing an essential role in assisting humans with a wide array of tasks in daily life. A significant application of AI is its use as a chat agent, responding to human inquiries across various domains. Current LLMs have shown proficiency in answering general questions. However, basic question-answering dialogue often falls short in complex diagnostic scenarios, such as legal or medical consultations. These scenarios typically necessitate Task-Oriented Dialogue (TOD), wherein an AI chat agent needs to proactively pose questions and guide users towards specific task completion. Previous fine-tuning models have underperformed in TOD, and current LLMs do not inherently possess this capability. In this paper, we introduce DiagGPT (Dialogue in Diagnosis GPT), an innovative method that extends LLMs to TOD scenarios. Our experiments reveal that DiagGPT exhibits outstanding performance in conducting TOD with users, demonstrating its potential for practical applications.

Automatic medical report generation (MRG) is of great research value as it has the potential to relieve radiologists from the heavy burden of report writing. Despite recent advancements, accurate MRG remains challenging due to the need for precise clinical understanding and the identification of clinical findings. Moreover, the imbalanced distribution of diseases makes the challenge even more pronounced, as rare diseases are underrepresented in training data, making their diagnostic performance unreliable. To address these challenges, we propose diagnosis-driven prompts for medical report generation (PromptMRG), a novel framework that aims to improve the diagnostic accuracy of MRG with the guidance of diagnosis-aware prompts. Specifically, PromptMRG is based on encoder-decoder architecture with an extra disease classification branch. When generating reports, the diagnostic results from the classification branch are converted into token prompts to explicitly guide the generation process. To further improve the diagnostic accuracy, we design cross-modal feature enhancement, which retrieves similar reports from the database to assist the diagnosis of a query image by leveraging the knowledge from a pre-trained CLIP. Moreover, the disease imbalanced issue is addressed by applying an adaptive logit-adjusted loss to the classification branch based on the individual learning status of each disease, which overcomes the barrier of text decoder's inability to manipulate disease distributions. Experiments on two MRG benchmarks show the effectiveness of the proposed method, where it obtains state-of-the-art clinical efficacy performance on both datasets.

Current medical artificial intelligence systems are often limited to narrow applications, hindering their widespread adoption in clinical practice. To address this limitation, we propose MedVersa, a generalist learner that enables flexible learning and tasking for medical image interpretation. By leveraging a large language model as a learnable orchestrator, MedVersa can learn from both visual and linguistic supervision, support multimodal inputs, and perform real-time task specification. This versatility allows MedVersa to adapt to various clinical scenarios and perform multifaceted medical image analysis. We introduce MedInterp, the largest multimodal dataset to date for medical image interpretation, consisting of over 13 million annotated instances spanning 11 tasks across 3 modalities, to support the development of MedVersa. Our experiments demonstrate that MedVersa achieves state-of-the-art performance in 9 tasks, sometimes outperforming specialist counterparts by over 10%. MedVersa is the first to showcase the viability of multimodal generative medical AI in implementing multimodal outputs, inputs, and dynamic task specification, highlighting its potential as a multifunctional system for comprehensive medical image analysis. This generalist approach to medical image interpretation paves the way for more adaptable and efficient AI-assisted clinical decision-making.

Echocardiography is the most widely used cardiac imaging modality, capturing ultrasound video data to assess cardiac structure and function. Artificial intelligence (AI) in echocardiography has the potential to streamline manual tasks and improve reproducibility and precision. However, most echocardiography AI models are single-view, single-task systems that do not synthesize complementary information from multiple views captured during a full exam, and thus lead to limited performance and scope of applications. To address this problem, we introduce EchoPrime, a multi-view, view-informed, video-based vision-language foundation model trained on over 12 million video-report pairs. EchoPrime uses contrastive learning to train a unified embedding model for all standard views in a comprehensive echocardiogram study with representation of both rare and common diseases and diagnoses. EchoPrime then utilizes view-classification and a view-informed anatomic attention model to weight video-specific interpretations that accurately maps the relationship between echocardiographic views and anatomical structures. With retrieval-augmented interpretation, EchoPrime integrates information from all echocardiogram videos in a comprehensive study and performs holistic comprehensive clinical echocardiography interpretation. In datasets from two independent healthcare systems, EchoPrime achieves state-of-the art performance on 23 diverse benchmarks of cardiac form and function, surpassing the performance of both task-specific approaches and prior foundation models. Following rigorous clinical evaluation, EchoPrime can assist physicians in the automated preliminary assessment of comprehensive echocardiography.

Explaining Artificial Intelligence (AI) decisions is a major challenge nowadays in AI, in particular when applied to sensitive scenarios like medicine and law. However, the need to explain the rationale behind decisions is a main issue also for human-based deliberation as it is important to justify why a certain decision has been taken. Resident medical doctors for instance are required not only to provide a (possibly correct) diagnosis, but also to explain how they reached a certain conclusion. Developing new tools to aid residents to train their explanation skills is therefore a central objective of AI in education. In this paper, we follow this direction, and we present, to the best of our knowledge, the first multilingual dataset for Medical Question Answering where correct and incorrect diagnoses for a clinical case are enriched with a natural language explanation written by doctors. These explanations have been manually annotated with argument components (i.e., premise, claim) and argument relations (i.e., attack, support), resulting in the Multilingual CasiMedicos-Arg dataset which consists of 558 clinical cases in four languages (English, Spanish, French, Italian) with explanations, where we annotated 5021 claims, 2313 premises, 2431 support relations, and 1106 attack relations. We conclude by showing how competitive baselines perform over this challenging dataset for the argument mining task.

The rapid advancement of large-scale vision-language models has showcased remarkable capabilities across various tasks. However, the lack of extensive and high-quality image-text data in medicine has greatly hindered the development of large-scale medical vision-language models. In this work, we present a diagnosis-guided bootstrapping strategy that exploits both image and label information to construct vision-language datasets. Based on the constructed dataset, we developed MedDr, a generalist foundation model for healthcare capable of handling diverse medical data modalities, including radiology, pathology, dermatology, retinography, and endoscopy. Moreover, during inference, we propose a simple but effective retrieval-augmented medical diagnosis strategy, which enhances the model's generalization ability. Extensive experiments on visual question answering, medical report generation, and medical image diagnosis demonstrate the superiority of our method.

Clinical diagnosis prediction models, when provided with a patient's medical history, aim to detect potential diseases early, facilitating timely intervention and improving prognostic outcomes. However, the inherent scarcity of patient data and large disease candidate space often pose challenges in developing satisfactory models for this intricate task. The exploration of leveraging Large Language Models (LLMs) for encapsulating clinical decision processes has been limited. We introduce MERA, a clinical diagnosis prediction model that bridges pertaining natural language knowledge with medical practice. We apply hierarchical contrastive learning on a disease candidate ranking list to alleviate the large decision space issue. With concept memorization through fine-tuning, we bridge the natural language clinical knowledge with medical codes. Experimental results on MIMIC-III and IV datasets show that MERA achieves the state-of-the-art diagnosis prediction performance and dramatically elevates the diagnosis prediction capabilities of generative LMs.

This paper presents our team's participation in the MEDIQA-ClinicalNLP2024 shared task B. We present a novel approach to diagnosing clinical dermatology cases by integrating large multimodal models, specifically leveraging the capabilities of GPT-4V under a retriever and a re-ranker framework. Our investigation reveals that GPT-4V, when used as a retrieval agent, can accurately retrieve the correct skin condition 85% of the time using dermatological images and brief patient histories. Additionally, we empirically show that Naive Chain-of-Thought (CoT) works well for retrieval while Medical Guidelines Grounded CoT is required for accurate dermatological diagnosis. Further, we introduce a Multi-Agent Conversation (MAC) framework and show its superior performance and potential over the best CoT strategy. The experiments suggest that using naive CoT for retrieval and multi-agent conversation for critique-based diagnosis, GPT-4V can lead to an early and accurate diagnosis of dermatological conditions. The implications of this work extend to improving diagnostic workflows, supporting dermatological education, and enhancing patient care by providing a scalable, accessible, and accurate diagnostic tool.

Artificial intelligence has advanced in Medical Visual Question Answering (Med-VQA), but prevalent research tends to focus on the accuracy of the answers, often overlooking the reasoning paths and interpretability, which are crucial in clinical settings. Besides, current Med-VQA algorithms, typically reliant on singular models, lack the robustness needed for real-world medical diagnostics which usually require collaborative expert evaluation. To address these shortcomings, this paper presents MedCoT, a novel hierarchical expert verification reasoning chain method designed to enhance interpretability and accuracy in biomedical imaging inquiries. MedCoT is predicated on two principles: The necessity for explicit reasoning paths in Med-VQA and the requirement for multi-expert review to formulate accurate conclusions. The methodology involves an Initial Specialist proposing diagnostic rationales, followed by a Follow-up Specialist who validates these rationales, and finally, a consensus is reached through a vote among a sparse Mixture of Experts within the locally deployed Diagnostic Specialist, which then provides the definitive diagnosis. Experimental evaluations on four standard Med-VQA datasets demonstrate that MedCoT surpasses existing state-of-the-art approaches, providing significant improvements in performance and interpretability.

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgment that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce the cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, DR.BENCH, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models. Experiments with state-of-the-art pre-trained generative language models using large general domain models and models that were continually trained on a medical corpus demonstrate opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community.

The remarkable capabilities and intricate nature of Artificial Intelligence (AI) have dramatically escalated the imperative for specialized AI accelerators. Nonetheless, designing these accelerators for various AI workloads remains both labor- and time-intensive. While existing design exploration and automation tools can partially alleviate the need for extensive human involvement, they still demand substantial hardware expertise, posing a barrier to non-experts and stifling AI accelerator development. Motivated by the astonishing potential of large language models (LLMs) for generating high-quality content in response to human language instructions, we embark on this work to examine the possibility of harnessing LLMs to automate AI accelerator design. Through this endeavor, we develop GPT4AIGChip, a framework intended to democratize AI accelerator design by leveraging human natural languages instead of domain-specific languages. Specifically, we first perform an in-depth investigation into LLMs' limitations and capabilities for AI accelerator design, thus aiding our understanding of our current position and garnering insights into LLM-powered automated AI accelerator design. Furthermore, drawing inspiration from the above insights, we develop a framework called GPT4AIGChip, which features an automated demo-augmented prompt-generation pipeline utilizing in-context learning to guide LLMs towards creating high-quality AI accelerator design. To our knowledge, this work is the first to demonstrate an effective pipeline for LLM-powered automated AI accelerator generation. Accordingly, we anticipate that our insights and framework can serve as a catalyst for innovations in next-generation LLM-powered design automation tools.

Panoramic X-rays are frequently used in dentistry for treatment planning, but their interpretation can be both time-consuming and prone to error. Artificial intelligence (AI) has the potential to aid in the analysis of these X-rays, thereby improving the accuracy of dental diagnoses and treatment plans. Nevertheless, designing automated algorithms for this purpose poses significant challenges, mainly due to the scarcity of annotated data and variations in anatomical structure. To address these issues, the Dental Enumeration and Diagnosis on Panoramic X-rays Challenge (DENTEX) has been organized in association with the International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) in 2023. This challenge aims to promote the development of algorithms for multi-label detection of abnormal teeth, using three types of hierarchically annotated data: partially annotated quadrant data, partially annotated quadrant-enumeration data, and fully annotated quadrant-enumeration-diagnosis data, inclusive of four different diagnoses. In this paper, we present the results of evaluating participant algorithms on the fully annotated data, additionally investigating performance variation for quadrant, enumeration, and diagnosis labels in the detection of abnormal teeth. The provision of this annotated dataset, alongside the results of this challenge, may lay the groundwork for the creation of AI-powered tools that can offer more precise and efficient diagnosis and treatment planning in the field of dentistry. The evaluation code and datasets can be accessed at https://github.com/ibrahimethemhamamci/DENTEX

Tool-augmented LLMs are a promising approach to create AI agents that can have realistic conversations, follow procedures, and call appropriate functions. However, evaluating them is challenging due to the diversity of possible conversations, and existing datasets focus only on single interactions and function-calling. We present a test generation pipeline to evaluate LLMs as conversational AI agents. Our framework uses LLMs to generate diverse tests grounded on user-defined procedures. For that, we use intermediate graphs to limit the LLM test generator's tendency to hallucinate content that is not grounded on input procedures, and enforces high coverage of the possible conversations. Additionally, we put forward ALMITA, a manually curated dataset for evaluating AI agents in customer support, and use it to evaluate existing LLMs. Our results show that while tool-augmented LLMs perform well in single interactions, they often struggle to handle complete conversations. While our focus is on customer support, our method is general and capable of AI agents for different domains.

Interventions on model-internal states are fundamental operations in many areas of AI, including model editing, steering, robustness, and interpretability. To facilitate such research, we introduce pyvene, an open-source Python library that supports customizable interventions on a range of different PyTorch modules. pyvene supports complex intervention schemes with an intuitive configuration format, and its interventions can be static or include trainable parameters. We show how pyvene provides a unified and extensible framework for performing interventions on neural models and sharing the intervened upon models with others. We illustrate the power of the library via interpretability analyses using causal abstraction and knowledge localization. We publish our library through Python Package Index (PyPI) and provide code, documentation, and tutorials at https://github.com/stanfordnlp/pyvene.

Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical licensing exam. However, LLMs currently have difficulty processing images, making it challenging to interpret information from medical images, which are rich in information that supports clinical decisions. On the other hand, computer-aided diagnosis (CAD) networks for medical images have seen significant success in the medical field by using advanced deep-learning algorithms to support clinical decision-making. This paper presents a method for integrating LLMs into medical-image CAD networks. The proposed framework uses LLMs to enhance the output of multiple CAD networks, such as diagnosis networks, lesion segmentation networks, and report generation networks, by summarizing and reorganizing the information presented in natural language text format. The goal is to merge the strengths of LLMs' medical domain knowledge and logical reasoning with the vision understanding capability of existing medical-image CAD models to create a more user-friendly and understandable system for patients compared to conventional CAD systems. In the future, LLM's medical knowledge can be also used to improve the performance of vision-based medical-image CAD models.

Major cloud providers have employed advanced AI-based solutions like large language models to aid humans in identifying the root causes of cloud incidents. Despite the growing prevalence of AI-driven assistants in the root cause analysis process, their effectiveness in assisting on-call engineers is constrained by low accuracy due to the intrinsic difficulty of the task, a propensity for LLM-based approaches to hallucinate, and difficulties in distinguishing these well-disguised hallucinations. To address this challenge, we propose to perform confidence estimation for the predictions to help on-call engineers make decisions on whether to adopt the model prediction. Considering the black-box nature of many LLM-based root cause predictors, fine-tuning or temperature-scaling-based approaches are inapplicable. We therefore design an innovative confidence estimation framework based on prompting retrieval-augmented large language models (LLMs) that demand a minimal amount of information from the root cause predictor. This approach consists of two scoring phases: the LLM-based confidence estimator first evaluates its confidence in making judgments in the face of the current incident that reflects its ``grounded-ness" level in reference data, then rates the root cause prediction based on historical references. An optimization step combines these two scores for a final confidence assignment. We show that our method is able to produce calibrated confidence estimates for predicted root causes, validate the usefulness of retrieved historical data and the prompting strategy as well as the generalizability across different root cause prediction models. Our study takes an important move towards reliably and effectively embedding LLMs into cloud incident management systems.

Scientific discovery is a complex cognitive process that has driven human knowledge and technological progress for centuries. While artificial intelligence (AI) has made significant advances in automating aspects of scientific reasoning, simulation, and experimentation, we still lack integrated AI systems capable of performing autonomous long-term scientific research and discovery. This paper examines the current state of AI for scientific discovery, highlighting recent progress in large language models and other AI techniques applied to scientific tasks. We then outline key challenges and promising research directions toward developing more comprehensive AI systems for scientific discovery, including the need for science-focused AI agents, improved benchmarks and evaluation metrics, multimodal scientific representations, and unified frameworks combining reasoning, theorem proving, and data-driven modeling. Addressing these challenges could lead to transformative AI tools to accelerate progress across disciplines towards scientific discovery.

Over 85 million computed tomography (CT) scans are performed annually in the US, of which approximately one quarter focus on the abdomen. Given the current radiologist shortage, there is a large impetus to use artificial intelligence to alleviate the burden of interpreting these complex imaging studies. Prior state-of-the-art approaches for automated medical image interpretation leverage vision language models (VLMs). However, current medical VLMs are generally limited to 2D images and short reports, and do not leverage electronic health record (EHR) data for supervision. We introduce Merlin - a 3D VLM that we train using paired CT scans (6+ million images from 15,331 CTs), EHR diagnosis codes (1.8+ million codes), and radiology reports (6+ million tokens). We evaluate Merlin on 6 task types and 752 individual tasks. The non-adapted (off-the-shelf) tasks include zero-shot findings classification (31 findings), phenotype classification (692 phenotypes), and zero-shot cross-modal retrieval (image to findings and image to impressions), while model adapted tasks include 5-year disease prediction (6 diseases), radiology report generation, and 3D semantic segmentation (20 organs). We perform internal validation on a test set of 5,137 CTs, and external validation on 7,000 clinical CTs and on two public CT datasets (VerSe, TotalSegmentator). Beyond these clinically-relevant evaluations, we assess the efficacy of various network architectures and training strategies to depict that Merlin has favorable performance to existing task-specific baselines. We derive data scaling laws to empirically assess training data needs for requisite downstream task performance. Furthermore, unlike conventional VLMs that require hundreds of GPUs for training, we perform all training on a single GPU.

With the rapid development of artificial intelligence, large language models (LLMs) have shown promising capabilities in mimicking human-level language comprehension and reasoning. This has sparked significant interest in applying LLMs to enhance various aspects of healthcare, ranging from medical education to clinical decision support. However, medicine involves multifaceted data modalities and nuanced reasoning skills, presenting challenges for integrating LLMs. This paper provides a comprehensive review on the applications and implications of LLMs in medicine. It begins by examining the fundamental applications of general-purpose and specialized LLMs, demonstrating their utilities in knowledge retrieval, research support, clinical workflow automation, and diagnostic assistance. Recognizing the inherent multimodality of medicine, the review then focuses on multimodal LLMs, investigating their ability to process diverse data types like medical imaging and EHRs to augment diagnostic accuracy. To address LLMs' limitations regarding personalization and complex clinical reasoning, the paper explores the emerging development of LLM-powered autonomous agents for healthcare. Furthermore, it summarizes the evaluation methodologies for assessing LLMs' reliability and safety in medical contexts. Overall, this review offers an extensive analysis on the transformative potential of LLMs in modern medicine. It also highlights the pivotal need for continuous optimizations and ethical oversight before these models can be effectively integrated into clinical practice. Visit https://github.com/mingze-yuan/Awesome-LLM-Healthcare for an accompanying GitHub repository containing latest papers.

Histopathology plays a central role in clinical medicine and biomedical research. While artificial intelligence shows promising results on many pathological tasks, generalization and dealing with rare diseases, where training data is scarce, remains a challenge. Distilling knowledge from unlabeled data into a foundation model before learning from, potentially limited, labeled data provides a viable path to address these challenges. In this work, we extend the state of the art of foundation models for digital pathology whole slide images by semi-automated data curation and incorporating pathologist domain knowledge. Specifically, we combine computational and pathologist domain knowledge (1) to curate a diverse dataset of 103k slides corresponding to 750 million image patches covering data from different fixation, staining, and scanning protocols as well as data from different indications and labs across the EU and US, (2) for grouping semantically similar slides and tissue patches, and (3) to augment the input images during training. We evaluate the resulting model on a set of public and internal benchmarks and show that although our foundation model is trained with an order of magnitude less slides, it performs on par or better than competing models. We expect that scaling our approach to more data and larger models will further increase its performance and capacity to deal with increasingly complex real world tasks in diagnostics and biomedical research.

As deep learning models gain attraction in medical data, ensuring transparent and trustworthy decision-making is essential. In skin cancer diagnosis, while advancements in lesion detection and classification have improved accuracy, the black-box nature of these methods poses challenges in understanding their decision processes, leading to trust issues among physicians. This study leverages the CLIP (Contrastive Language-Image Pretraining) model, trained on different skin lesion datasets, to capture meaningful relationships between visual features and diagnostic criteria terms. To further enhance transparency, we propose a method called MedGrad E-CLIP, which builds on gradient-based E-CLIP by incorporating a weighted entropy mechanism designed for complex medical imaging like skin lesions. This approach highlights critical image regions linked to specific diagnostic descriptions. The developed integrated pipeline not only classifies skin lesions by matching corresponding descriptions but also adds an essential layer of explainability developed especially for medical data. By visually explaining how different features in an image relates to diagnostic criteria, this approach demonstrates the potential of advanced vision-language models in medical image analysis, ultimately improving transparency, robustness, and trust in AI-driven diagnostic systems.

Trustworthiness is essential for the precise and interpretable application of artificial intelligence (AI) in medical imaging. Traditionally, precision and interpretability have been addressed as separate tasks, namely medical image analysis and explainable AI, each developing its own models independently. In this study, for the first time, we investigate the development of a unified medical vision-language pre-training model that can achieve both accurate analysis and interpretable understanding of medical images across various modalities. To build the model, we construct MedConcept-23M, a large-scale dataset comprising 23 million medical image-text pairs extracted from 6.2 million scientific articles, enriched with concepts from the Unified Medical Language System (UMLS). Based on MedConcept-23M, we introduce ConceptCLIP, a medical AI model utilizing concept-enhanced contrastive language-image pre-training. The pre-training of ConceptCLIP involves two primary components: image-text alignment learning (IT-Align) and patch-concept alignment learning (PC-Align). This dual alignment strategy enhances the model's capability to associate specific image regions with relevant concepts, thereby improving both the precision of analysis and the interpretability of the AI system. We conducted extensive experiments on 5 diverse types of medical image analysis tasks, spanning 51 subtasks across 10 image modalities, with the broadest range of downstream tasks. The results demonstrate the effectiveness of the proposed vision-language pre-training model. Further explainability analysis across 6 modalities reveals that ConceptCLIP achieves superior performance, underscoring its robust ability to advance explainable AI in medical imaging. These findings highlight ConceptCLIP's capability in promoting trustworthy AI in the field of medicine.

Large language models (LLMs), particularly those with reasoning capabilities, have rapidly advanced in recent years, demonstrating significant potential across a wide range of applications. However, their deployment in healthcare, especially in disease reasoning tasks, is hindered by the challenge of acquiring expert-level cognitive data. In this paper, we introduce Citrus, a medical language model that bridges the gap between clinical expertise and AI reasoning by emulating the cognitive processes of medical experts. The model is trained on a large corpus of simulated expert disease reasoning data, synthesized using a novel approach that accurately captures the decision-making pathways of clinicians. This approach enables Citrus to better simulate the complex reasoning processes involved in diagnosing and treating medical conditions.To further address the lack of publicly available datasets for medical reasoning tasks, we release the last-stage training data, including a custom-built medical diagnostic dialogue dataset. This open-source contribution aims to support further research and development in the field. Evaluations using authoritative benchmarks such as MedQA, covering tasks in medical reasoning and language understanding, show that Citrus achieves superior performance compared to other models of similar size. These results highlight Citrus potential to significantly enhance medical decision support systems, providing a more accurate and efficient tool for clinical decision-making.

Despite significant advancements in general artificial intelligence, such as GPT-4, their effectiveness in the medical domain (general medical AI, GMAI) remains constrained due to the absence of specialized medical knowledge. To address this challenge, we present GMAI-VL-5.5M, a comprehensive multimodal medical dataset created by converting hundreds of specialized medical datasets into meticulously constructed image-text pairs. This dataset features comprehensive task coverage, diverse modalities, and high-quality image-text data. Building upon this multimodal dataset, we propose GMAI-VL, a general medical vision-language model with a progressively three-stage training strategy. This approach significantly enhances the model's ability by integrating visual and textual information, thereby improving its ability to process multimodal data and support accurate diagnosis and clinical decision-making. Experimental evaluations demonstrate that GMAI-VL achieves state-of-the-art results across a wide range of multimodal medical tasks, such as visual question answering and medical image diagnosis. Our contributions include the development of the GMAI-VL-5.5M dataset, the introduction of the GMAI-VL model, and the establishment of new benchmarks in multiple medical domains. Code and dataset will be released at https://github.com/uni-medical/GMAI-VL.

The rapid development of generative AI (GenAI) models in computer vision necessitates effective evaluation methods to ensure their quality and fairness. Existing tools primarily focus on dataset quality assurance and model explainability, leaving a significant gap in GenAI output evaluation during model development. Current practices often depend on developers' subjective visual assessments, which may lack scalability and generalizability. This paper bridges this gap by conducting a formative study with GenAI model developers in an industrial setting. Our findings led to the development of GenLens, a visual analytic interface designed for the systematic evaluation of GenAI model outputs during the early stages of model development. GenLens offers a quantifiable approach for overviewing and annotating failure cases, customizing issue tags and classifications, and aggregating annotations from multiple users to enhance collaboration. A user study with model developers reveals that GenLens effectively enhances their workflow, evidenced by high satisfaction rates and a strong intent to integrate it into their practices. This research underscores the importance of robust early-stage evaluation tools in GenAI development, contributing to the advancement of fair and high-quality GenAI models.

With over 85 million CT scans performed annually in the United States, creating tumor-related reports is a challenging and time-consuming task for radiologists. To address this need, we present RadGPT, an Anatomy-Aware Vision-Language AI Agent for generating detailed reports from CT scans. RadGPT first segments tumors, including benign cysts and malignant tumors, and their surrounding anatomical structures, then transforms this information into both structured reports and narrative reports. These reports provide tumor size, shape, location, attenuation, volume, and interactions with surrounding blood vessels and organs. Extensive evaluation on unseen hospitals shows that RadGPT can produce accurate reports, with high sensitivity/specificity for small tumor (<2 cm) detection: 80/73% for liver tumors, 92/78% for kidney tumors, and 77/77% for pancreatic tumors. For large tumors, sensitivity ranges from 89% to 97%. The results significantly surpass the state-of-the-art in abdominal CT report generation. RadGPT generated reports for 17 public datasets. Through radiologist review and refinement, we have ensured the reports' accuracy, and created the first publicly available image-text 3D medical dataset, comprising over 1.8 million text tokens and 2.7 million images from 9,262 CT scans, including 2,947 tumor scans/reports of 8,562 tumor instances. Our reports can: (1) localize tumors in eight liver sub-segments and three pancreatic sub-segments annotated per-voxel; (2) determine pancreatic tumor stage (T1-T4) in 260 reports; and (3) present individual analyses of multiple tumors--rare in human-made reports. Importantly, 948 of the reports are for early-stage tumors.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

Artificial intelligence (AI) enables machines to learn from human experience, adjust to new inputs, and perform human-like tasks. AI is progressing rapidly and is transforming the way businesses operate, from process automation to cognitive augmentation of tasks and intelligent process/data analytics. However, the main challenge for human users would be to understand and appropriately trust the result of AI algorithms and methods. In this paper, to address this challenge, we study and analyze the recent work done in Explainable Artificial Intelligence (XAI) methods and tools. We introduce a novel XAI process, which facilitates producing explainable models while maintaining a high level of learning performance. We present an interactive evidence-based approach to assist human users in comprehending and trusting the results and output created by AI-enabled algorithms. We adopt a typical scenario in the Banking domain for analyzing customer transactions. We develop a digital dashboard to facilitate interacting with the algorithm results and discuss how the proposed XAI method can significantly improve the confidence of data scientists in understanding the result of AI-enabled algorithms.

Automatic disease diagnosis has become increasingly valuable in clinical practice. The advent of large language models (LLMs) has catalyzed a paradigm shift in artificial intelligence, with growing evidence supporting the efficacy of LLMs in diagnostic tasks. Despite the increasing attention in this field, a holistic view is still lacking. Many critical aspects remain unclear, such as the diseases and clinical data to which LLMs have been applied, the LLM techniques employed, and the evaluation methods used. In this article, we perform a comprehensive review of LLM-based methods for disease diagnosis. Our review examines the existing literature across various dimensions, including disease types and associated clinical specialties, clinical data, LLM techniques, and evaluation methods. Additionally, we offer recommendations for applying and evaluating LLMs for diagnostic tasks. Furthermore, we assess the limitations of current research and discuss future directions. To our knowledge, this is the first comprehensive review for LLM-based disease diagnosis.

The widespread consumer-grade 3D printers and learning resources online enable novices to self-train in remote settings. While troubleshooting plays an essential part of 3D printing, the process remains challenging for many remote novices even with the help of well-developed online sources, such as online troubleshooting archives and online community help. We conducted a formative study with 76 active 3D printing users to learn how remote novices leverage online resources in troubleshooting and their challenges. We found that remote novices cannot fully utilize online resources. For example, the online archives statically provide general information, making it hard to search and relate their unique cases with existing descriptions. Online communities can potentially ease their struggles by providing more targeted suggestions, but a helper who can provide custom help is rather scarce, making it hard to obtain timely assistance. We propose 3DPFIX, an interactive 3D troubleshooting system powered by the pipeline to facilitate Human-AI Collaboration, designed to improve novices' 3D printing experiences and thus help them easily accumulate their domain knowledge. We built 3DPFIX that supports automated diagnosis and solution-seeking. 3DPFIX was built upon shared dialogues about failure cases from Q&A discourses accumulated in online communities. We leverage social annotations (i.e., comments) to build an annotated failure image dataset for AI classifiers and extract a solution pool. Our summative study revealed that using 3DPFIX helped participants spend significantly less effort in diagnosing failures and finding a more accurate solution than relying on their common practice. We also found that 3DPFIX users learn about 3D printing domain-specific knowledge. We discuss the implications of leveraging community-driven data in developing future Human-AI Collaboration designs.

The field of medical diagnosis has undergone a significant transformation with the advent of large language models (LLMs), yet the challenges of interpretability within these models remain largely unaddressed. This study introduces Chain-of-Diagnosis (CoD) to enhance the interpretability of LLM-based medical diagnostics. CoD transforms the diagnostic process into a diagnostic chain that mirrors a physician's thought process, providing a transparent reasoning pathway. Additionally, CoD outputs the disease confidence distribution to ensure transparency in decision-making. This interpretability makes model diagnostics controllable and aids in identifying critical symptoms for inquiry through the entropy reduction of confidences. With CoD, we developed DiagnosisGPT, capable of diagnosing 9604 diseases. Experimental results demonstrate that DiagnosisGPT outperforms other LLMs on diagnostic benchmarks. Moreover, DiagnosisGPT provides interpretability while ensuring controllability in diagnostic rigor.

When building artificial intelligence systems that can reason and answer questions about visual data, we need diagnostic tests to analyze our progress and discover shortcomings. Existing benchmarks for visual question answering can help, but have strong biases that models can exploit to correctly answer questions without reasoning. They also conflate multiple sources of error, making it hard to pinpoint model weaknesses. We present a diagnostic dataset that tests a range of visual reasoning abilities. It contains minimal biases and has detailed annotations describing the kind of reasoning each question requires. We use this dataset to analyze a variety of modern visual reasoning systems, providing novel insights into their abilities and limitations.

The field of explainable AI (XAI) has quickly become a thriving and prolific community. However, a silent, recurrent and acknowledged issue in this area is the lack of consensus regarding its terminology. In particular, each new contribution seems to rely on its own (and often intuitive) version of terms like "explanation" and "interpretation". Such disarray encumbers the consolidation of advances in the field towards the fulfillment of scientific and regulatory demands e.g., when comparing methods or establishing their compliance with respect to biases and fairness constraints. We propose a theoretical framework that not only provides concrete definitions for these terms, but it also outlines all steps necessary to produce explanations and interpretations. The framework also allows for existing contributions to be re-contextualized such that their scope can be measured, thus making them comparable to other methods. We show that this framework is compliant with desiderata on explanations, on interpretability and on evaluation metrics. We present a use-case showing how the framework can be used to compare LIME, SHAP and MDNet, establishing their advantages and shortcomings. Finally, we discuss relevant trends in XAI as well as recommendations for future work, all from the standpoint of our framework.

AI holds promise for transforming scientific processes, including hypothesis generation. Prior work on hypothesis generation can be broadly categorized into theory-driven and data-driven approaches. While both have proven effective in generating novel and plausible hypotheses, it remains an open question whether they can complement each other. To address this, we develop the first method that combines literature-based insights with data to perform LLM-powered hypothesis generation. We apply our method on five different datasets and demonstrate that integrating literature and data outperforms other baselines (8.97\% over few-shot, 15.75\% over literature-based alone, and 3.37\% over data-driven alone). Additionally, we conduct the first human evaluation to assess the utility of LLM-generated hypotheses in assisting human decision-making on two challenging tasks: deception detection and AI generated content detection. Our results show that human accuracy improves significantly by 7.44\% and 14.19\% on these tasks, respectively. These findings suggest that integrating literature-based and data-driven approaches provides a comprehensive and nuanced framework for hypothesis generation and could open new avenues for scientific inquiry.

With the increasing availability of structured and unstructured data and the swift progress of analytical techniques, Artificial Intelligence (AI) is bringing a revolution to the healthcare industry. With the increasingly indispensable role of AI in healthcare, there are growing concerns over the lack of transparency and explainability in addition to potential bias encountered by predictions of the model. This is where Explainable Artificial Intelligence (XAI) comes into the picture. XAI increases the trust placed in an AI system by medical practitioners as well as AI researchers, and thus, eventually, leads to an increasingly widespread deployment of AI in healthcare. In this paper, we present different interpretability techniques. The aim is to enlighten practitioners on the understandability and interpretability of explainable AI systems using a variety of techniques available which can be very advantageous in the health-care domain. Medical diagnosis model is responsible for human life and we need to be confident enough to treat a patient as instructed by a black-box model. Our paper contains examples based on the heart disease dataset and elucidates on how the explainability techniques should be preferred to create trustworthiness while using AI systems in healthcare.

Despite a surge collection of XAI methods, users still struggle to obtain required AI explanations. Previous research suggests chatbots as dynamic solutions, but the effective design of conversational XAI agents for practical human needs remains under-explored. This paper focuses on Conversational XAI for AI-assisted scientific writing tasks. Drawing from human linguistic theories and formative studies, we identify four design rationales: "multifaceted", "controllability", "mix-initiative", "context-aware drill-down". We incorporate them into an interactive prototype, ConvXAI, which facilitates heterogeneous AI explanations for scientific writing through dialogue. In two studies with 21 users, ConvXAI outperforms a GUI-based baseline on improving human-perceived understanding and writing improvement. The paper further discusses the practical human usage patterns in interacting with ConvXAI for scientific co-writing.

Humans possess an extraordinary ability to create and utilize tools, allowing them to overcome physical limitations and explore new frontiers. With the advent of foundation models, AI systems have the potential to be equally adept in tool use as humans. This paradigm, i.e., tool learning with foundation models, combines the strengths of specialized tools and foundation models to achieve enhanced accuracy, efficiency, and automation in problem-solving. Despite its immense potential, there is still a lack of a comprehensive understanding of key challenges, opportunities, and future endeavors in this field. To this end, we present a systematic investigation of tool learning in this paper. We first introduce the background of tool learning, including its cognitive origins, the paradigm shift of foundation models, and the complementary roles of tools and models. Then we recapitulate existing tool learning research into tool-augmented and tool-oriented learning. We formulate a general tool learning framework: starting from understanding the user instruction, models should learn to decompose a complex task into several subtasks, dynamically adjust their plan through reasoning, and effectively conquer each sub-task by selecting appropriate tools. We also discuss how to train models for improved tool-use capabilities and facilitate the generalization in tool learning. Considering the lack of a systematic tool learning evaluation in prior works, we experiment with 17 representative tools and show the potential of current foundation models in skillfully utilizing tools. Finally, we discuss several open problems that require further investigation for tool learning. Overall, we hope this paper could inspire future research in integrating tools with foundation models.

We present a new dataset for machine comprehension in the medical domain. Our dataset uses clinical case reports with around 100,000 gap-filling queries about these cases. We apply several baselines and state-of-the-art neural readers to the dataset, and observe a considerable gap in performance (20% F1) between the best human and machine readers. We analyze the skills required for successful answering and show how reader performance varies depending on the applicable skills. We find that inferences using domain knowledge and object tracking are the most frequently required skills, and that recognizing omitted information and spatio-temporal reasoning are the most difficult for the machines.

Providing high quality explanations for AI predictions based on machine learning is a challenging and complex task. To work well it requires, among other factors: selecting a proper level of generality/specificity of the explanation; considering assumptions about the familiarity of the explanation beneficiary with the AI task under consideration; referring to specific elements that have contributed to the decision; making use of additional knowledge (e.g. expert evidence) which might not be part of the prediction process; and providing evidence supporting negative hypothesis. Finally, the system needs to formulate the explanation in a clearly interpretable, and possibly convincing, way. Given these considerations, ANTIDOTE fosters an integrated vision of explainable AI, where low-level characteristics of the deep learning process are combined with higher level schemes proper of the human argumentation capacity. ANTIDOTE will exploit cross-disciplinary competences in deep learning and argumentation to support a broader and innovative view of explainable AI, where the need for high-quality explanations for clinical cases deliberation is critical. As a first result of the project, we publish the Antidote CasiMedicos dataset to facilitate research on explainable AI in general, and argumentation in the medical domain in particular.

Predictive process monitoring is a process mining task aimed at forecasting information about a running process trace, such as the most correct next activity to be executed. In medical domains, predictive process monitoring can provide valuable decision support in atypical and nontrivial situations. Decision support and quality assessment in medicine cannot ignore domain knowledge, in order to be grounded on all the available information (which is not limited to data) and to be really acceptable by end users. In this paper, we propose a predictive process monitoring approach relying on the use of a {\em transformer}, a deep learning architecture based on the attention mechanism. A major contribution of our work lies in the incorporation of ontological domain-specific knowledge, carried out through a graph positional encoding technique. The paper presents and discusses the encouraging experimental result we are collecting in the domain of stroke management.

The widespread use of chest X-rays (CXRs), coupled with a shortage of radiologists, has driven growing interest in automated CXR analysis and AI-assisted reporting. While existing vision-language models (VLMs) show promise in specific tasks such as report generation or abnormality detection, they often lack support for interactive diagnostic capabilities. In this work we present RadVLM, a compact, multitask conversational foundation model designed for CXR interpretation. To this end, we curate a large-scale instruction dataset comprising over 1 million image-instruction pairs containing both single-turn tasks -- such as report generation, abnormality classification, and visual grounding -- and multi-turn, multi-task conversational interactions. After fine-tuning RadVLM on this instruction dataset, we evaluate it across different tasks along with re-implemented baseline VLMs. Our results show that RadVLM achieves state-of-the-art performance in conversational capabilities and visual grounding while remaining competitive in other radiology tasks. Ablation studies further highlight the benefit of joint training across multiple tasks, particularly for scenarios with limited annotated data. Together, these findings highlight the potential of RadVLM as a clinically relevant AI assistant, providing structured CXR interpretation and conversational capabilities to support more effective and accessible diagnostic workflows.

Artificial intelligence-assisted imaging analysis has made substantial strides in tumor diagnosis and management. Here we present PASTA, a pan-tumor CT foundation model that achieves state-of-the-art performance on 45 of 46 representative oncology tasks -- including lesion segmentation, tumor detection in plain CT, tumor staging, survival prediction, structured report generation, and cross-modality transfer learning, significantly outperforming the second-best models on 35 tasks. This remarkable advancement is driven by our development of PASTA-Gen, an innovative synthetic tumor generation framework that produces a comprehensive dataset of 30,000 CT scans with pixel-level annotated lesions and paired structured reports, encompassing malignancies across ten organs and five benign lesion types. By leveraging this rich, high-quality synthetic data, we overcome a longstanding bottleneck in the development of CT foundation models -- specifically, the scarcity of publicly available, high-quality annotated datasets due to privacy constraints and the substantial labor required for scaling precise data annotation. Encouragingly, PASTA demonstrates exceptional data efficiency with promising practical value, markedly improving performance on various tasks with only a small amount of real-world data. The open release of both the synthetic dataset and PASTA foundation model effectively addresses the challenge of data scarcity, thereby advancing oncological research and clinical translation.

The PI-CAI (Prostate Imaging: Cancer AI) challenge led to expert-level diagnostic algorithms for clinically significant prostate cancer detection. The algorithms receive biparametric MRI scans as input, which consist of T2-weighted and diffusion-weighted scans. These scans can be misaligned due to multiple factors in the scanning process. Image registration can alleviate this issue by predicting the deformation between the sequences. We investigate the effect of image registration on the diagnostic performance of AI-based prostate cancer diagnosis. First, the image registration algorithm, developed in MeVisLab, is analyzed using a dataset with paired lesion annotations. Second, the effect on diagnosis is evaluated by comparing case-level cancer diagnosis performance between using the original dataset, rigidly aligned diffusion-weighted scans, or deformably aligned diffusion-weighted scans. Rigid registration showed no improvement. Deformable registration demonstrated a substantial improvement in lesion overlap (+10% median Dice score) and a positive yet non-significant improvement in diagnostic performance (+0.3% AUROC, p=0.18). Our investigation shows that a substantial improvement in lesion alignment does not directly lead to a significant improvement in diagnostic performance. Qualitative analysis indicated that jointly developing image registration methods and diagnostic AI algorithms could enhance diagnostic accuracy and patient outcomes.

In this work, we present MedImageInsight, an open-source medical imaging embedding model. MedImageInsight is trained on medical images with associated text and labels across a diverse collection of domains, including X-Ray, CT, MRI, dermoscopy, OCT, fundus photography, ultrasound, histopathology, and mammography. Rigorous evaluations demonstrate MedImageInsight's ability to achieve state-of-the-art (SOTA) or human expert level performance across classification, image-image search, and fine-tuning tasks. Specifically, on public datasets, MedImageInsight achieves SOTA in CT 3D medical image retrieval, as well as SOTA in disease classification and search for chest X-ray, dermatology, and OCT imaging. Furthermore, MedImageInsight achieves human expert performance in bone age estimation (on both public and partner data), as well as AUC above 0.9 in most other domains. When paired with a text decoder, MedImageInsight achieves near SOTA level single image report findings generation with less than 10\% the parameters of other models. Compared to fine-tuning GPT-4o with only MIMIC-CXR data for the same task, MedImageInsight outperforms in clinical metrics, but underperforms on lexical metrics where GPT-4o sets a new SOTA. Importantly for regulatory purposes, MedImageInsight can generate ROC curves, adjust sensitivity and specificity based on clinical need, and provide evidence-based decision support through image-image search (which can also enable retrieval augmented generation). In an independent clinical evaluation of image-image search in chest X-ray, MedImageInsight outperformed every other publicly available foundation model evaluated by large margins (over 6 points AUC), and significantly outperformed other models in terms of AI fairness (across age and gender). We hope releasing MedImageInsight will help enhance collective progress in medical imaging AI research and development.

The absence of transparency and explainability hinders the clinical adoption of Machine learning (ML) algorithms. Although various methods of explainable artificial intelligence (XAI) have been suggested, there is a lack of literature that delves into their practicality and assesses them based on criteria that could foster trust in clinical environments. To address this gap this study evaluates two popular XAI methods used for explaining predictive models in the healthcare context in terms of whether they (i) generate domain-appropriate representation, i.e. coherent with respect to the application task, (ii) impact clinical workflow and (iii) are consistent. To that end, explanations generated at the cohort and patient levels were analysed. The paper reports the first benchmarking of the XAI methods applied to risk prediction models obtained by evaluating the concordance between generated explanations and the trigger of a future clinical deterioration episode recorded by the data collection system. We carried out an analysis using two Electronic Medical Records (EMR) datasets sourced from Australian major hospitals. The findings underscore the limitations of state-of-the-art XAI methods in the clinical context and their potential benefits. We discuss these limitations and contribute to the theoretical development of trustworthy XAI solutions where clinical decision support guides the choice of intervention by suggesting the pattern or drivers for clinical deterioration in the future.

Medicine is inherently multimodal, with rich data modalities spanning text, imaging, genomics, and more. Generalist biomedical artificial intelligence (AI) systems that flexibly encode, integrate, and interpret this data at scale can potentially enable impactful applications ranging from scientific discovery to care delivery. To enable the development of these models, we first curate MultiMedBench, a new multimodal biomedical benchmark. MultiMedBench encompasses 14 diverse tasks such as medical question answering, mammography and dermatology image interpretation, radiology report generation and summarization, and genomic variant calling. We then introduce Med-PaLM Multimodal (Med-PaLM M), our proof of concept for a generalist biomedical AI system. Med-PaLM M is a large multimodal generative model that flexibly encodes and interprets biomedical data including clinical language, imaging, and genomics with the same set of model weights. Med-PaLM M reaches performance competitive with or exceeding the state of the art on all MultiMedBench tasks, often surpassing specialist models by a wide margin. We also report examples of zero-shot generalization to novel medical concepts and tasks, positive transfer learning across tasks, and emergent zero-shot medical reasoning. To further probe the capabilities and limitations of Med-PaLM M, we conduct a radiologist evaluation of model-generated (and human) chest X-ray reports and observe encouraging performance across model scales. In a side-by-side ranking on 246 retrospective chest X-rays, clinicians express a pairwise preference for Med-PaLM M reports over those produced by radiologists in up to 40.50% of cases, suggesting potential clinical utility. While considerable work is needed to validate these models in real-world use cases, our results represent a milestone towards the development of generalist biomedical AI systems.

Recently, there is an increasing interest in using artificial intelligence (AI) to automate aspects of the research process, or even autonomously conduct the full research cycle from idea generation, over data analysis, to composing and evaluation of scientific manuscripts. Examples of working AI scientist systems have been demonstrated for computer science tasks and running molecular biology labs. While some approaches aim for full autonomy of the scientific AI, others rather aim for leveraging human-AI teaming. Here, we address how to adapt such approaches for boosting Brain-Computer Interface (BCI) development, as well as brain research resp. neuroscience at large. We argue that at this time, a strong emphasis on human-AI teaming, in contrast to fully autonomous AI BCI researcher will be the most promising way forward. We introduce the collaborative workspaces concept for human-AI teaming based on a set of Janusian design principles, looking both ways, to the human as well as to the AI side. Based on these principles, we present ChatBCI, a Python-based toolbox for enabling human-AI collaboration based on interaction with Large Language Models (LLMs), designed for BCI research and development projects. We show how ChatBCI was successfully used in a concrete BCI project on advancing motor imagery decoding from EEG signals. Our approach can be straightforwardly extended to broad neurotechnological and neuroscientific topics, and may by design facilitate human expert knowledge transfer to scientific AI systems in general.

To generate evidence regarding the safety and efficacy of artificial intelligence (AI) enabled medical devices, AI models need to be evaluated on a diverse population of patient cases, some of which may not be readily available. We propose an evaluation approach for testing medical imaging AI models that relies on in silico imaging pipelines in which stochastic digital models of human anatomy (in object space) with and without pathology are imaged using a digital replica imaging acquisition system to generate realistic synthetic image datasets. Here, we release M-SYNTH, a dataset of cohorts with four breast fibroglandular density distributions imaged at different exposure levels using Monte Carlo x-ray simulations with the publicly available Virtual Imaging Clinical Trial for Regulatory Evaluation (VICTRE) toolkit. We utilize the synthetic dataset to analyze AI model performance and find that model performance decreases with increasing breast density and increases with higher mass density, as expected. As exposure levels decrease, AI model performance drops with the highest performance achieved at exposure levels lower than the nominal recommended dose for the breast type.

We introduce a novel framework for incorporating human expertise into algorithmic predictions. Our approach leverages human judgment to distinguish inputs which are algorithmically indistinguishable, or "look the same" to predictive algorithms. We argue that this framing clarifies the problem of human-AI collaboration in prediction tasks, as experts often form judgments by drawing on information which is not encoded in an algorithm's training data. Algorithmic indistinguishability yields a natural test for assessing whether experts incorporate this kind of "side information", and further provides a simple but principled method for selectively incorporating human feedback into algorithmic predictions. We show that this method provably improves the performance of any feasible algorithmic predictor and precisely quantify this improvement. We find empirically that although algorithms often outperform their human counterparts on average, human judgment can improve algorithmic predictions on specific instances (which can be identified ex-ante). In an X-ray classification task, we find that this subset constitutes nearly 30% of the patient population. Our approach provides a natural way of uncovering this heterogeneity and thus enabling effective human-AI collaboration.

Recent advancements in machine learning and natural language processing have led to the rapid development of artificial intelligence (AI) as a valuable tool in the healthcare industry. Using large language models (LLMs) as conversational agents or chatbots has the potential to assist doctors in diagnosing patients, detecting early symptoms of diseases, and providing health advice to patients. This paper focuses on the role of chatbots in healthcare and explores the use of avatars to make AI interactions more appealing to patients. A framework of a general-purpose AI avatar application is demonstrated by using a three-category prompt dictionary and prompt improvement mechanism. A two-phase approach is suggested to fine-tune a general-purpose AI language model and create different AI avatars to discuss medical issues with users. Prompt engineering enhances the chatbot's conversational abilities and personality traits, fostering a more human-like interaction with patients. Ultimately, the injection of personality into the chatbot could potentially increase patient engagement. Future directions for research include investigating ways to improve chatbots' understanding of context and ensuring the accuracy of their outputs through fine-tuning with specialized medical data sets.

Cancer is a complex disease, the understanding and treatment of which are being aided through increases in the volume of collected data and in the scale of deployed computing power. Consequently, there is a growing need for the development of data-driven and, in particular, deep learning methods for various tasks such as cancer diagnosis, detection, prognosis, and prediction. Despite recent successes, however, designing high-performing deep learning models for nonimage and nontext cancer data is a time-consuming, trial-and-error, manual task that requires both cancer domain and deep learning expertise. To that end, we develop a reinforcement-learning-based neural architecture search to automate deep-learning-based predictive model development for a class of representative cancer data. We develop custom building blocks that allow domain experts to incorporate the cancer-data-specific characteristics. We show that our approach discovers deep neural network architectures that have significantly fewer trainable parameters, shorter training time, and accuracy similar to or higher than those of manually designed architectures. We study and demonstrate the scalability of our approach on up to 1,024 Intel Knights Landing nodes of the Theta supercomputer at the Argonne Leadership Computing Facility.

Artificial intelligence is transforming education through data-driven, personalized learning solutions. This paper introduces AI Tutor, an innovative web application that provides personalized tutoring in any subject using state-of-the-art Large Language Model (LLM). AI Tutor ingests course materials to construct an adaptive knowledge base tailored to the course. When students pose questions, it retrieves the most relevant information and generates detailed, conversational responses citing supporting evidence. The system is powered by advanced large language models and Retrieval-Augmented Generation (RAG) techniques for accurate, natural question answering. We present a fully-functional web interface and video demonstration that showcase AI Tutor's versatility across diverse subjects and its ability to produce pedagogically cogent responses. While an initial prototype, this work represents a pioneering step toward AI-enabled tutoring systems that can democratize access to high-quality, customized educational support.

Background: General-purpose large language models that utilize both text and images have not been evaluated on a diverse array of challenging medical cases. Methods: Using 934 cases from the NEJM Image Challenge published between 2005 and 2023, we evaluated the accuracy of the recently released Generative Pre-trained Transformer 4 with Vision model (GPT-4V) compared to human respondents overall and stratified by question difficulty, image type, and skin tone. We further conducted a physician evaluation of GPT-4V on 69 NEJM clinicopathological conferences (CPCs). Analyses were conducted for models utilizing text alone, images alone, and both text and images. Results: GPT-4V achieved an overall accuracy of 61% (95% CI, 58 to 64%) compared to 49% (95% CI, 49 to 50%) for humans. GPT-4V outperformed humans at all levels of difficulty and disagreement, skin tones, and image types; the exception was radiographic images, where performance was equivalent between GPT-4V and human respondents. Longer, more informative captions were associated with improved performance for GPT-4V but similar performance for human respondents. GPT-4V included the correct diagnosis in its differential for 80% (95% CI, 68 to 88%) of CPCs when using text alone, compared to 58% (95% CI, 45 to 70%) of CPCs when using both images and text. Conclusions: GPT-4V outperformed human respondents on challenging medical cases and was able to synthesize information from both images and text, but performance deteriorated when images were added to highly informative text. Overall, our results suggest that multimodal AI models may be useful in medical diagnostic reasoning but that their accuracy may depend heavily on context.

With the rapid development of generative models, discerning AI-generated content has evoked increasing attention from both industry and academia. In this paper, we conduct a sanity check on "whether the task of AI-generated image detection has been solved". To start with, we present Chameleon dataset, consisting AIgenerated images that are genuinely challenging for human perception. To quantify the generalization of existing methods, we evaluate 9 off-the-shelf AI-generated image detectors on Chameleon dataset. Upon analysis, almost all models classify AI-generated images as real ones. Later, we propose AIDE (AI-generated Image DEtector with Hybrid Features), which leverages multiple experts to simultaneously extract visual artifacts and noise patterns. Specifically, to capture the high-level semantics, we utilize CLIP to compute the visual embedding. This effectively enables the model to discern AI-generated images based on semantics or contextual information; Secondly, we select the highest frequency patches and the lowest frequency patches in the image, and compute the low-level patchwise features, aiming to detect AI-generated images by low-level artifacts, for example, noise pattern, anti-aliasing, etc. While evaluating on existing benchmarks, for example, AIGCDetectBenchmark and GenImage, AIDE achieves +3.5% and +4.6% improvements to state-of-the-art methods, and on our proposed challenging Chameleon benchmarks, it also achieves the promising results, despite this problem for detecting AI-generated images is far from being solved. The dataset, codes, and pre-train models will be published at https://github.com/shilinyan99/AIDE.

The applications of generative AI have become extremely impressive, and the interplay between users and AI is even more so. Current human-AI interaction literature has taken a broad look at how humans interact with generative AI, but it lacks specificity regarding the user interface designs and patterns used to create these applications. Therefore, we present a survey that comprehensively presents taxonomies of how a human interacts with AI and the user interaction patterns designed to meet the needs of a variety of relevant use cases. We focus primarily on user-guided interactions, surveying interactions that are initiated by the user and do not include any implicit signals given by the user. With this survey, we aim to create a compendium of different user-interaction patterns that can be used as a reference for designers and developers alike. In doing so, we also strive to lower the entry barrier for those attempting to learn more about the design of generative AI applications.

The advancement in generative AI could be boosted with more accessible mathematics. Beyond human-AI chat, large language models (LLMs) are emerging in programming, algorithm discovery, and theorem proving, yet their genomics application is limited. This project introduces Math Agents and mathematical embedding as fresh entries to the "Moore's Law of Mathematics", using a GPT-based workflow to convert equations from literature into LaTeX and Python formats. While many digital equation representations exist, there's a lack of automated large-scale evaluation tools. LLMs are pivotal as linguistic user interfaces, providing natural language access for human-AI chat and formal languages for large-scale AI-assisted computational infrastructure. Given the infinite formal possibility spaces, Math Agents, which interact with math, could potentially shift us from "big data" to "big math". Math, unlike the more flexible natural language, has properties subject to proof, enabling its use beyond traditional applications like high-validation math-certified icons for AI alignment aims. This project aims to use Math Agents and mathematical embeddings to address the ageing issue in information systems biology by applying multiscalar physics mathematics to disease models and genomic data. Generative AI with episodic memory could help analyse causal relations in longitudinal health records, using SIR Precision Health models. Genomic data is suggested for addressing the unsolved Alzheimer's disease problem.

Forensic pathology is critical in determining the cause and manner of death through post-mortem examinations, both macroscopic and microscopic. The field, however, grapples with issues such as outcome variability, laborious processes, and a scarcity of trained professionals. This paper presents SongCi, an innovative visual-language model (VLM) designed specifically for forensic pathology. SongCi utilizes advanced prototypical cross-modal self-supervised contrastive learning to enhance the accuracy, efficiency, and generalizability of forensic analyses. It was pre-trained and evaluated on a comprehensive multi-center dataset, which includes over 16 million high-resolution image patches, 2,228 vision-language pairs of post-mortem whole slide images (WSIs), and corresponding gross key findings, along with 471 distinct diagnostic outcomes. Our findings indicate that SongCi surpasses existing multi-modal AI models in many forensic pathology tasks, performs comparably to experienced forensic pathologists and significantly better than less experienced ones, and provides detailed multi-modal explainability, offering critical assistance in forensic investigations. To the best of our knowledge, SongCi is the first VLM specifically developed for forensic pathological analysis and the first large-vocabulary computational pathology (CPath) model that directly processes gigapixel WSIs in forensic science.

Augmenting large language models (LLMs) with external tools has emerged as a promising approach to extend their utility, empowering them to solve practical tasks. Existing work typically empowers LLMs as tool users with a manually designed workflow, where the LLM plans a series of tools in a step-by-step manner, and sequentially executes each tool to obtain intermediate results until deriving the final answer. However, they suffer from two challenges in realistic scenarios: (1) The handcrafted control flow is often ad-hoc and constraints the LLM to local planning; (2) The LLM is instructed to use only manually demonstrated tools or well-trained Python functions, which limits its generalization to new tools. In this work, we first propose Automatic Tool Chain (ATC), a framework that enables the LLM to act as a multi-tool user, which directly utilizes a chain of tools through programming. To scale up the scope of the tools, we next propose a black-box probing method. This further empowers the LLM as a tool learner that can actively discover and document tool usages, teaching themselves to properly master new tools. For a comprehensive evaluation, we build a challenging benchmark named ToolFlow, which diverges from previous benchmarks by its long-term planning scenarios and complex toolset. Experiments on both existing datasets and ToolFlow illustrate the superiority of our framework. Analysis on different settings also validates the effectiveness and the utility of our black-box probing algorithm.

Automated interpretation of electrocardiograms (ECG) has garnered significant attention with the advancements in machine learning methodologies. Despite the growing interest, most current studies focus solely on classification or regression tasks, which overlook a crucial aspect of clinical cardio-disease diagnosis: the diagnostic report generated by experienced human clinicians. In this paper, we introduce a novel approach to ECG interpretation, leveraging recent breakthroughs in Large Language Models (LLMs) and Vision-Transformer (ViT) models. Rather than treating ECG diagnosis as a classification or regression task, we propose an alternative method of automatically identifying the most similar clinical cases based on the input ECG data. Also, since interpreting ECG as images is more affordable and accessible, we process ECG as encoded images and adopt a vision-language learning paradigm to jointly learn vision-language alignment between encoded ECG images and ECG diagnosis reports. Encoding ECG into images can result in an efficient ECG retrieval system, which will be highly practical and useful in clinical applications. More importantly, our findings could serve as a crucial resource for providing diagnostic services in underdeveloped regions.

Developing the required technology to assist medical experts in their everyday activities is currently a hot topic in the Artificial Intelligence research field. Thus, a number of large language models (LLMs) and automated benchmarks have recently been proposed with the aim of facilitating information extraction in Evidence-Based Medicine (EBM) using natural language as a tool for mediating in human-AI interaction. The most representative benchmarks are limited to either multiple-choice or long-form answers and are available only in English. In order to address these shortcomings, in this paper we present a new dataset which, unlike previous work: (i) includes not only explanatory arguments for the correct answer, but also arguments to reason why the incorrect answers are not correct; (ii) the explanations are written originally by medical doctors to answer questions from the Spanish Residency Medical Exams. Furthermore, this new benchmark allows us to setup a novel extractive task which consists of identifying the explanation of the correct answer written by medical doctors. An additional benefit of our setting is that we can leverage the extractive QA paradigm to automatically evaluate performance of LLMs without resorting to costly manual evaluation by medical experts. Comprehensive experimentation with language models for Spanish shows that sometimes multilingual models fare better than monolingual ones, even outperforming models which have been adapted to the medical domain. Furthermore, results across the monolingual models are mixed, with supposedly smaller and inferior models performing competitively. In any case, the obtained results show that our novel dataset and approach can be an effective technique to help medical practitioners in identifying relevant evidence-based explanations for medical questions.

Recently, large language model (LLM) based artificial intelligence (AI) systems have demonstrated remarkable capabilities in natural language understanding and generation. However, these models face a significant challenge when it comes to sensitive applications, such as reasoning over medical knowledge and answering medical questions in a physician-like manner. Prior studies attempted to overcome this challenge by increasing the model size (>100B) to learn more general medical knowledge, while there is still room for improvement in LLMs with smaller-scale model sizes (<100B). In this work, we start from a pre-trained general LLM model (AntGLM-10B) and fine-tune it from a medical beginner towards a medical expert (called AntGLM-Med-10B), which leverages a 3-stage optimization procedure, i.e., general medical knowledge injection, medical domain instruction tuning, and specific medical task adaptation. Our contributions are threefold: (1) We specifically investigate how to adapt a pre-trained general LLM in medical domain, especially for a specific medical task. (2) We collect and construct large-scale medical datasets for each stage of the optimization process. These datasets encompass various data types and tasks, such as question-answering, medical reasoning, multi-choice questions, and medical conversations. (3) Specifically for multi-choice questions in the medical domain, we propose a novel Verification-of-Choice approach for prompting engineering, which significantly enhances the reasoning ability of LLMs. Remarkably, by combining the above approaches, our AntGLM-Med-10B model can outperform the most of LLMs on PubMedQA, including both general and medical LLMs, even when these LLMs have larger model size.

Considering the increased workload in pathology laboratories today, automated tools such as artificial intelligence models can help pathologists with their tasks and ease the workload. In this paper, we are proposing a segmentation model (DRU-Net) that can provide a delineation of human non-small cell lung carcinomas and an augmentation method that can improve classification results. The proposed model is a fused combination of truncated pre-trained DenseNet201 and ResNet101V2 as a patch-wise classifier followed by a lightweight U-Net as a refinement model. We have used two datasets (Norwegian Lung Cancer Biobank and Haukeland University Hospital lung cancer cohort) to create our proposed model. The DRU-Net model achieves an average of 0.91 Dice similarity coefficient. The proposed spatial augmentation method (multi-lens distortion) improved the network performance by 3%. Our findings show that choosing image patches that specifically include regions of interest leads to better results for the patch-wise classifier compared to other sampling methods. The qualitative analysis showed that the DRU-Net model is generally successful in detecting the tumor. On the test set, some of the cases showed areas of false positive and false negative segmentation in the periphery, particularly in tumors with inflammatory and reactive changes.

The integration of Computer-Assisted Diagnosis (CAD) with Large Language Models (LLMs) holds great potential in clinical applications, specifically in the roles of virtual family doctors and clinic assistants. However, current works in this field are plagued by limitations, specifically a restricted scope of applicable image domains and the provision of unreliable medical advice. This restricts their overall processing capabilities. Furthermore, the mismatch in writing style between LLMs and radiologists undermines their practical usefulness. To tackle these challenges, we introduce ChatCAD+, which is designed to be universal and reliable. It is capable of handling medical images from diverse domains and leveraging up-to-date information from reputable medical websites to provide reliable medical advice. Additionally, it incorporates a template retrieval system that improves report generation performance via exemplar reports. This approach ensures greater consistency with the expertise of human professionals. The source code is available at https://github.com/zhaozh10/ChatCAD.

Recent neural language models have taken a significant step forward in producing remarkably controllable, fluent, and grammatical text. Although studies have found that AI-generated text is not distinguishable from human-written text for crowd-sourcing workers, there still exist errors in AI-generated text which are even subtler and harder to spot. We primarily focus on the scenario in which scientific AI writing assistant is deeply involved. First, we construct a feature description framework to distinguish between AI-generated text and human-written text from syntax, semantics, and pragmatics based on the human evaluation. Then we utilize the features, i.e., writing style, coherence, consistency, and argument logistics, from the proposed framework to analyze two types of content. Finally, we adopt several publicly available methods to investigate the gap of between AI-generated scientific text and human-written scientific text by AI-generated scientific text detection models. The results suggest that while AI has the potential to generate scientific content that is as accurate as human-written content, there is still a gap in terms of depth and overall quality. The AI-generated scientific content is more likely to contain errors in factual issues. We find that there exists a "writing style" gap between AI-generated scientific text and human-written scientific text. Based on the analysis result, we summarize a series of model-agnostic and distribution-agnostic features for detection tasks in other domains. Findings in this paper contribute to guiding the optimization of AI models to produce high-quality content and addressing related ethical and security concerns.

Passively collected behavioral health data from ubiquitous sensors holds significant promise to provide mental health professionals insights from patient's daily lives; however, developing analysis tools to use this data in clinical practice requires addressing challenges of generalization across devices and weak or ambiguous correlations between the measured signals and an individual's mental health. To address these challenges, we take a novel approach that leverages large language models (LLMs) to synthesize clinically useful insights from multi-sensor data. We develop chain of thought prompting methods that use LLMs to generate reasoning about how trends in data such as step count and sleep relate to conditions like depression and anxiety. We first demonstrate binary depression classification with LLMs achieving accuracies of 61.1% which exceed the state of the art. While it is not robust for clinical use, this leads us to our key finding: even more impactful and valued than classification is a new human-AI collaboration approach in which clinician experts interactively query these tools and combine their domain expertise and context about the patient with AI generated reasoning to support clinical decision-making. We find models like GPT-4 correctly reference numerical data 75% of the time, and clinician participants express strong interest in using this approach to interpret self-tracking data.

Electrocardiograms (ECGs) are non-invasive diagnostic tools crucial for detecting cardiac arrhythmic diseases in clinical practice. While ECG Self-supervised Learning (eSSL) methods show promise in representation learning from unannotated ECG data, they often overlook the clinical knowledge that can be found in reports. This oversight and the requirement for annotated samples for downstream tasks limit eSSL's versatility. In this work, we address these issues with the Multimodal ECG Representation Learning (MERL}) framework. Through multimodal learning on ECG records and associated reports, MERL is capable of performing zero-shot ECG classification with text prompts, eliminating the need for training data in downstream tasks. At test time, we propose the Clinical Knowledge Enhanced Prompt Engineering (CKEPE) approach, which uses Large Language Models (LLMs) to exploit external expert-verified clinical knowledge databases, generating more descriptive prompts and reducing hallucinations in LLM-generated content to boost zero-shot classification. Based on MERL, we perform the first benchmark across six public ECG datasets, showing the superior performance of MERL compared against eSSL methods. Notably, MERL achieves an average AUC score of 75.2% in zero-shot classification (without training data), 3.2% higher than linear probed eSSL methods with 10\% annotated training data, averaged across all six datasets. Code and models are available at https://github.com/cheliu-computation/MERL

Artificial intelligence has significantly advanced skin cancer diagnosis by enabling rapid and accurate detection of malignant lesions. In this domain, most publicly available image datasets consist of single, isolated skin lesions positioned at the center of the image. While these lesion-centric datasets have been fundamental for developing diagnostic algorithms, they lack the context of the surrounding skin, which is critical for improving lesion detection. The iToBoS dataset was created to address this challenge. It includes 16,954 images of skin regions from 100 participants, captured using 3D total body photography. Each image roughly corresponds to a 7 times 9 cm section of skin with all suspicious lesions annotated using bounding boxes. Additionally, the dataset provides metadata such as anatomical location, age group, and sun damage score for each image. This dataset aims to facilitate training and benchmarking of algorithms, with the goal of enabling early detection of skin cancer and deployment of this technology in non-clinical environments.

Recent advancements in Large Language Models (LLMs) have drawn increasing attention since the learned embeddings pretrained on large-scale datasets have shown powerful ability in various downstream applications. However, whether the learned knowledge by LLMs can be transferred to clinical cardiology remains unknown. In this work, we aim to bridge this gap by transferring the knowledge of LLMs to clinical Electrocardiography (ECG). We propose an approach for cardiovascular disease diagnosis and automatic ECG diagnosis report generation. We also introduce an additional loss function by Optimal Transport (OT) to align the distribution between ECG and language embedding. The learned embeddings are evaluated on two downstream tasks: (1) automatic ECG diagnosis report generation, and (2) zero-shot cardiovascular disease detection. Our approach is able to generate high-quality cardiac diagnosis reports and also achieves competitive zero-shot classification performance even compared with supervised baselines, which proves the feasibility of transferring knowledge from LLMs to the cardiac domain.

Heart disease remains a significant threat to human health. As a non-invasive diagnostic tool, the electrocardiogram (ECG) is one of the most widely used methods for cardiac screening. However, the scarcity of high-quality ECG data, driven by privacy concerns and limited medical resources, creates a pressing need for effective ECG signal generation. Existing approaches for generating ECG signals typically rely on small training datasets, lack comprehensive evaluation frameworks, and overlook potential applications beyond data augmentation. To address these challenges, we propose DiffuSETS, a novel framework capable of generating ECG signals with high semantic alignment and fidelity. DiffuSETS accepts various modalities of clinical text reports and patient-specific information as inputs, enabling the creation of clinically meaningful ECG signals. Additionally, to address the lack of standardized evaluation in ECG generation, we introduce a comprehensive benchmarking methodology to assess the effectiveness of generative models in this domain. Our model achieve excellent results in tests, proving its superiority in the task of ECG generation. Furthermore, we showcase its potential to mitigate data scarcity while exploring novel applications in cardiology education and medical knowledge discovery, highlighting the broader impact of our work.

In this study, we present an innovative fusion of language models and query analysis techniques to unlock cognition in artificial intelligence. Our system seamlessly integrates a Chess engine with a language model, enabling it to predict moves and provide strategic explanations. Leveraging a vector database to achieve retrievable answer generation, our OpenSI AI system elucidates its decision-making process, bridging the gap between raw computation and human-like understanding. Our choice of Chess as the demonstration environment underscores the versatility of our approach. Beyond Chess, our system holds promise for diverse applications, from medical diagnostics to financial forecasting.

Rapid development of artificial intelligence has drastically accelerated the development of scientific discovery. Trained with large-scale observation data, deep neural networks extract the underlying patterns in an end-to-end manner and assist human researchers with highly-precised predictions in unseen scenarios. The recent rise of Large Language Models (LLMs) and the empowered autonomous agents enable scientists to gain help through interaction in different stages of their research, including but not limited to literature review, research ideation, idea implementation, and academic writing. However, AI researchers instantiated by foundation model empowered agents with full-process autonomy are still in their infancy. In this paper, we study AI-Generated Science (AIGS), where agents independently and autonomously complete the entire research process and discover scientific laws. By revisiting the definition of scientific research, we argue that falsification is the essence of both human research process and the design of an AIGS system. Through the lens of falsification, prior systems attempting towards AI-Generated Science either lack the part in their design, or rely heavily on existing verification engines that narrow the use in specialized domains. In this work, we propose Baby-AIGS as a baby-step demonstration of a full-process AIGS system, which is a multi-agent system with agents in roles representing key research process. By introducing FalsificationAgent, which identify and then verify possible scientific discoveries, we empower the system with explicit falsification. Experiments on three tasks preliminarily show that Baby-AIGS could produce meaningful scientific discoveries, though not on par with experienced human researchers. Finally, we discuss on the limitations of current Baby-AIGS, actionable insights, and related ethical issues in detail.

As large language models (LLMs) advance, their inability to autonomously execute tasks by directly interacting with external tools remains a critical limitation. Traditional methods rely on inputting tool descriptions as context, which is constrained by context length and requires separate, often inefficient, retrieval mechanisms. We introduce ToolGen, a paradigm shift that integrates tool knowledge directly into the LLM's parameters by representing each tool as a unique token. This enables the LLM to generate tool calls and arguments as part of its next token prediction capabilities, seamlessly blending tool invocation with language generation. Our framework allows the LLM to access and utilize a vast amount of tools with no additional retrieval step, significantly enhancing both performance and scalability. Experimental results with over 47,000 tools show that ToolGen not only achieves superior results in both tool retrieval and autonomous task completion but also sets the stage for a new era of AI agents that can adapt to tools across diverse domains. By fundamentally transforming tool retrieval into a generative process, ToolGen paves the way for more versatile, efficient, and autonomous AI systems. ToolGen enables end-to-end tool learning and opens opportunities for integration with other advanced techniques such as chain-of-thought and reinforcement learning, thereby expanding the practical capabilities of LLMs.

There are two main barriers to using large language models (LLMs) in clinical reasoning. Firstly, while LLMs exhibit significant promise in Natural Language Processing (NLP) tasks, their performance in complex reasoning and planning falls short of expectations. Secondly, LLMs use uninterpretable methods to make clinical decisions that are fundamentally different from the clinician's cognitive processes. This leads to user distrust. In this paper, we present a multi-agent framework called ArgMed-Agents, which aims to enable LLM-based agents to make explainable clinical decision reasoning through interaction. ArgMed-Agents performs self-argumentation iterations via Argumentation Scheme for Clinical Discussion (a reasoning mechanism for modeling cognitive processes in clinical reasoning), and then constructs the argumentation process as a directed graph representing conflicting relationships. Ultimately, use symbolic solver to identify a series of rational and coherent arguments to support decision. We construct a formal model of ArgMed-Agents and present conjectures for theoretical guarantees. ArgMed-Agents enables LLMs to mimic the process of clinical argumentative reasoning by generating explanations of reasoning in a self-directed manner. The setup experiments show that ArgMed-Agents not only improves accuracy in complex clinical decision reasoning problems compared to other prompt methods, but more importantly, it provides users with decision explanations that increase their confidence.

Legal practice has witnessed a sharp rise in products incorporating artificial intelligence (AI). Such tools are designed to assist with a wide range of core legal tasks, from search and summarization of caselaw to document drafting. But the large language models used in these tools are prone to "hallucinate," or make up false information, making their use risky in high-stakes domains. Recently, certain legal research providers have touted methods such as retrieval-augmented generation (RAG) as "eliminating" (Casetext, 2023) or "avoid[ing]" hallucinations (Thomson Reuters, 2023), or guaranteeing "hallucination-free" legal citations (LexisNexis, 2023). Because of the closed nature of these systems, systematically assessing these claims is challenging. In this article, we design and report on the first preregistered empirical evaluation of AI-driven legal research tools. We demonstrate that the providers' claims are overstated. While hallucinations are reduced relative to general-purpose chatbots (GPT-4), we find that the AI research tools made by LexisNexis (Lexis+ AI) and Thomson Reuters (Westlaw AI-Assisted Research and Ask Practical Law AI) each hallucinate between 17% and 33% of the time. We also document substantial differences between systems in responsiveness and accuracy. Our article makes four key contributions. It is the first to assess and report the performance of RAG-based proprietary legal AI tools. Second, it introduces a comprehensive, preregistered dataset for identifying and understanding vulnerabilities in these systems. Third, it proposes a clear typology for differentiating between hallucinations and accurate legal responses. Last, it provides evidence to inform the responsibilities of legal professionals in supervising and verifying AI outputs, which remains a central open question for the responsible integration of AI into law.

We present Azimuth, an open-source and easy-to-use tool to perform error analysis for text classification. Compared to other stages of the ML development cycle, such as model training and hyper-parameter tuning, the process and tooling for the error analysis stage are less mature. However, this stage is critical for the development of reliable and trustworthy AI systems. To make error analysis more systematic, we propose an approach comprising dataset analysis and model quality assessment, which Azimuth facilitates. We aim to help AI practitioners discover and address areas where the model does not generalize by leveraging and integrating a range of ML techniques, such as saliency maps, similarity, uncertainty, and behavioral analyses, all in one tool. Our code and documentation are available at github.com/servicenow/azimuth.

Researchers have long recognized the socio-technical gaps in personal tracking research, where machines can never fully model the complexity of human behavior, making it only able to produce basic rule-based outputs or "black-box" results that lack clear explanations. Real-world deployments rely on experts for this complex translation from sparse data to meaningful insights. In this study, we consider this translation process from data to insights by experts as "sensemaking" and explore how HCI researchers can support it through Vital Insight, an evidence-based 'sensemaking' system that combines direct representation and indirect inference through visualization and Large Language Models. We evaluate Vital Insight in user testing sessions with 14 experts in multi-modal tracking, synthesize design implications, and develop an expert sensemaking model where they iteratively move between direct data representations and AI-supported inferences to explore, retrieve, question, and validate insights.

Understanding the irregular electrical activity of atrial fibrillation (AFib) has been a key challenge in electrocardiography. For serious cases of AFib, catheter ablations are performed to collect intracardiac electrograms (EGMs). EGMs offer intricately detailed and localized electrical activity of the heart and are an ideal modality for interpretable cardiac studies. Recent advancements in artificial intelligence (AI) has allowed some works to utilize deep learning frameworks to interpret EGMs during AFib. Additionally, language models (LMs) have shown exceptional performance in being able to generalize to unseen domains, especially in healthcare. In this study, we are the first to leverage pretrained LMs for finetuning of EGM interpolation and AFib classification via masked language modeling. We formulate the EGM as a textual sequence and present competitive performances on AFib classification compared against other representations. Lastly, we provide a comprehensive interpretability study to provide a multi-perspective intuition of the model's behavior, which could greatly benefit the clinical use.

Diagnosing and managing a patient is a complex, sequential decision making process that requires physicians to obtain information -- such as which tests to perform -- and to act upon it. Recent advances in artificial intelligence (AI) and large language models (LLMs) promise to profoundly impact clinical care. However, current evaluation schemes overrely on static medical question-answering benchmarks, falling short on interactive decision-making that is required in real-life clinical work. Here, we present AgentClinic: a multimodal benchmark to evaluate LLMs in their ability to operate as agents in simulated clinical environments. In our benchmark, the doctor agent must uncover the patient's diagnosis through dialogue and active data collection. We present two open medical agent benchmarks: a multimodal image and dialogue environment, AgentClinic-NEJM, and a dialogue-only environment, AgentClinic-MedQA. We embed cognitive and implicit biases both in patient and doctor agents to emulate realistic interactions between biased agents. We find that introducing bias leads to large reductions in diagnostic accuracy of the doctor agents, as well as reduced compliance, confidence, and follow-up consultation willingness in patient agents. Evaluating a suite of state-of-the-art LLMs, we find that several models that excel in benchmarks like MedQA are performing poorly in AgentClinic-MedQA. We find that the LLM used in the patient agent is an important factor for performance in the AgentClinic benchmark. We show that both having limited interactions as well as too many interaction reduces diagnostic accuracy in doctor agents. The code and data for this work is publicly available at https://AgentClinic.github.io.

Scientific reasoning poses an excessive challenge for even the most advanced Large Language Models (LLMs). To make this task more practical and solvable for LLMs, we introduce a new task setting named tool-augmented scientific reasoning. This setting supplements LLMs with scalable toolsets, and shifts the focus from pursuing an omniscient problem solver to a proficient tool-user. To facilitate the research of such setting, we construct a tool-augmented training corpus named MathFunc which encompasses over 30,000 samples and roughly 6,000 tools. Building on MathFunc, we develop SciAgent to retrieve, understand and, if necessary, use tools for scientific problem solving. Additionally, we craft a benchmark, SciToolBench, spanning five scientific domains to evaluate LLMs' abilities with tool assistance. Extensive experiments on SciToolBench confirm the effectiveness of SciAgent. Notably, SciAgent-Mistral-7B surpasses other LLMs with the same size by more than 13% in absolute accuracy. Furthermore, SciAgent-DeepMath-7B shows much superior performance than ChatGPT.

Radiotherapy (RT) planning is complex, subjective, and time-intensive. Advances in artificial intelligence (AI) promise to improve its precision, efficiency, and consistency, but progress is often limited by the scarcity of large, standardized datasets. To address this, we introduce the Automated Iterative RT Planning (AIRTP) system, a scalable solution for generating high-quality treatment plans. This scalable solution is designed to generate substantial volumes of consistently high-quality treatment plans, overcoming a key obstacle in the advancement of AI-driven RT planning. Our AIRTP pipeline adheres to clinical guidelines and automates essential steps, including organ-at-risk (OAR) contouring, helper structure creation, beam setup, optimization, and plan quality improvement, using AI integrated with RT planning software like Eclipse of Varian. Furthermore, a novel approach for determining optimization parameters to reproduce 3D dose distributions, i.e. a method to convert dose predictions to deliverable treatment plans constrained by machine limitations. A comparative analysis of plan quality reveals that our automated pipeline produces treatment plans of quality comparable to those generated manually, which traditionally require several hours of labor per plan. Committed to public research, the first data release of our AIRTP pipeline includes nine cohorts covering head-and-neck and lung cancer sites to support an AAPM 2025 challenge. This data set features more than 10 times the number of plans compared to the largest existing well-curated public data set to our best knowledge. Repo:{https://github.com/RiqiangGao/GDP-HMM_AAPMChallenge}

Run-time steering strategies like Medprompt are valuable for guiding large language models (LLMs) to top performance on challenging tasks. Medprompt demonstrates that a general LLM can be focused to deliver state-of-the-art performance on specialized domains like medicine by using a prompt to elicit a run-time strategy involving chain of thought reasoning and ensembling. OpenAI's o1-preview model represents a new paradigm, where a model is designed to do run-time reasoning before generating final responses. We seek to understand the behavior of o1-preview on a diverse set of medical challenge problem benchmarks. Following on the Medprompt study with GPT-4, we systematically evaluate the o1-preview model across various medical benchmarks. Notably, even without prompting techniques, o1-preview largely outperforms the GPT-4 series with Medprompt. We further systematically study the efficacy of classic prompt engineering strategies, as represented by Medprompt, within the new paradigm of reasoning models. We found that few-shot prompting hinders o1's performance, suggesting that in-context learning may no longer be an effective steering approach for reasoning-native models. While ensembling remains viable, it is resource-intensive and requires careful cost-performance optimization. Our cost and accuracy analysis across run-time strategies reveals a Pareto frontier, with GPT-4o representing a more affordable option and o1-preview achieving state-of-the-art performance at higher cost. Although o1-preview offers top performance, GPT-4o with steering strategies like Medprompt retains value in specific contexts. Moreover, we note that the o1-preview model has reached near-saturation on many existing medical benchmarks, underscoring the need for new, challenging benchmarks. We close with reflections on general directions for inference-time computation with LLMs.

Chest X-rays play a pivotal role in diagnosing respiratory diseases such as pneumonia, tuberculosis, and COVID-19, which are prevalent and present unique diagnostic challenges due to overlapping visual features and variability in image quality. Severe class imbalance and the complexity of medical images hinder automated analysis. This study leverages deep learning techniques, including transfer learning on pre-trained models (AlexNet, ResNet, and InceptionNet), to enhance disease detection and classification. By fine-tuning these models and incorporating focal loss to address class imbalance, significant performance improvements were achieved. Grad-CAM visualizations further enhance model interpretability, providing insights into clinically relevant regions influencing predictions. The InceptionV3 model, for instance, achieved a 28% improvement in AUC and a 15% increase in F1-Score. These findings highlight the potential of deep learning to improve diagnostic workflows and support clinical decision-making.

Cervical disc herniation (CDH) is a prevalent musculoskeletal disorder that significantly impacts health and requires labor-intensive analysis from experts. Despite advancements in automated detection of medical imaging, two significant challenges hinder the real-world application of these methods. First, the computational complexity and resource demands present a significant gap for real-time application. Second, noise in MRI reduces the effectiveness of existing methods by distorting feature extraction. To address these challenges, we propose three key contributions: Firstly, we introduced MedDet, which leverages the multi-teacher single-student knowledge distillation for model compression and efficiency, meanwhile integrating generative adversarial training to enhance performance. Additionally, we customize the second-order nmODE to improve the model's resistance to noise in MRI. Lastly, we conducted comprehensive experiments on the CDH-1848 dataset, achieving up to a 5% improvement in mAP compared to previous methods. Our approach also delivers over 5 times faster inference speed, with approximately 67.8% reduction in parameters and 36.9% reduction in FLOPs compared to the teacher model. These advancements significantly enhance the performance and efficiency of automated CDH detection, demonstrating promising potential for future application in clinical practice. See project website https://steve-zeyu-zhang.github.io/MedDet

This review paper explores recent advances in deep learning approaches for non-invasive cognitive impairment detection. We examine various non-invasive indicators of cognitive decline, including speech and language, facial, and motoric mobility. The paper provides an overview of relevant datasets, feature-extracting techniques, and deep-learning architectures applied to this domain. We have analyzed the performance of different methods across modalities and observed that speech and language-based methods generally achieved the highest detection performance. Studies combining acoustic and linguistic features tended to outperform those using a single modality. Facial analysis methods showed promise for visual modalities but were less extensively studied. Most papers focused on binary classification (impaired vs. non-impaired), with fewer addressing multi-class or regression tasks. Transfer learning and pre-trained language models emerged as popular and effective techniques, especially for linguistic analysis. Despite significant progress, several challenges remain, including data standardization and accessibility, model explainability, longitudinal analysis limitations, and clinical adaptation. Lastly, we propose future research directions, such as investigating language-agnostic speech analysis methods, developing multi-modal diagnostic systems, and addressing ethical considerations in AI-assisted healthcare. By synthesizing current trends and identifying key obstacles, this review aims to guide further development of deep learning-based cognitive impairment detection systems to improve early diagnosis and ultimately patient outcomes.

Deep learning models have shown promise in histopathology image analysis, but their opaque decision-making process poses challenges in high-risk medical scenarios. Here we introduce HIPPO, an explainable AI method that interrogates attention-based multiple instance learning (ABMIL) models in computational pathology by generating counterfactual examples through tissue patch modifications in whole slide images. Applying HIPPO to ABMIL models trained to detect breast cancer metastasis reveals that they may overlook small tumors and can be misled by non-tumor tissue, while attention mapsx2014widely used for interpretationx2014often highlight regions that do not directly influence predictions. By interpreting ABMIL models trained on a prognostic prediction task, HIPPO identified tissue areas with stronger prognostic effects than high-attention regions, which sometimes showed counterintuitive influences on risk scores. These findings demonstrate HIPPO's capacity for comprehensive model evaluation, bias detection, and quantitative hypothesis testing. HIPPO greatly expands the capabilities of explainable AI tools to assess the trustworthy and reliable development, deployment, and regulation of weakly-supervised models in computational pathology.

Large language models (LLMs) are powerful AI tools that can generate and comprehend natural language text and other complex information. However, the field lacks a mathematical framework to systematically describe, compare and improve LLMs. We propose Hex a framework that clarifies key terms and concepts in LLM research, such as hallucinations, alignment, self-verification and chain-of-thought reasoning. The Hex framework offers a precise and consistent way to characterize LLMs, identify their strengths and weaknesses, and integrate new findings. Using Hex, we differentiate chain-of-thought reasoning from chain-of-thought prompting and establish the conditions under which they are equivalent. This distinction clarifies the basic assumptions behind chain-of-thought prompting and its implications for methods that use it, such as self-verification and prompt programming. Our goal is to provide a formal framework for LLMs that can help both researchers and practitioners explore new possibilities for generative AI. We do not claim to have a definitive solution, but rather a tool for opening up new research avenues. We argue that our formal definitions and results are crucial for advancing the discussion on how to build generative AI systems that are safe, reliable, fair and robust, especially in domains like healthcare and software engineering.

Following the impressive development of LLMs, vision-language alignment in LLMs is actively being researched to enable multimodal reasoning and visual IO. This direction of research is particularly relevant to medical imaging because medical image analysis and generation consist of reasoning based on a combination of visual features and prior knowledge. Many recent works have focused on training adapter networks that serve as an information bridge between image processing networks and LLMs; but presumably, in order to achieve maximum reasoning potential of LLMs on visual information as well, visual and language features should be allowed to interact more freely. This is especially important in the medical domain because understanding and generating medical images such as chest X-rays (CXR) require not only accurate visual and language-based reasoning but also a more intimate mapping between the two modalities. Thus, taking inspiration from previous work on the transformer and VQ-GAN combination for bidirectional image and text generation, we build upon this approach and develop a method for instruction-tuning an LLM pre-trained only on text to gain vision-language capabilities for medical images. Specifically, we leverage a pretrained LLM's existing question-answering and instruction-following abilities to teach it to understand visual inputs by instructing it to answer questions about image inputs and, symmetrically, output both text and image responses appropriate to a given query by tuning the LLM with diverse tasks that encompass image-based text-generation and text-based image-generation. We show that our model, LLM-CXR, trained in this approach shows better image-text alignment in both CXR understanding and generation tasks while being smaller in size compared to previously developed models that perform a narrower range of tasks. The code is at https://github.com/hyn2028/llm-cxr.

Tool-augmented large language models (LLMs) are rapidly being integrated into real-world applications. Due to the lack of benchmarks, the community still needs to fully understand the hallucination issues within these models. To address this challenge, we introduce a comprehensive diagnostic benchmark, ToolBH. Specifically, we assess the LLM's hallucinations through two perspectives: depth and breadth. In terms of depth, we propose a multi-level diagnostic process, including (1) solvability detection, (2) solution planning, and (3) missing-tool analysis. For breadth, we consider three scenarios based on the characteristics of the toolset: missing necessary tools, potential tools, and limited functionality tools. Furthermore, we developed seven tasks and collected 700 evaluation samples through multiple rounds of manual annotation. The results show the significant challenges presented by the ToolBH benchmark. The current advanced models Gemini-1.5-Pro and GPT-4o only achieve a total score of 45.3 and 37.0, respectively, on a scale of 100. In this benchmark, larger model parameters do not guarantee better performance; the training data and response strategies also play a crucial role in tool-enhanced LLM scenarios. Our diagnostic analysis indicates that the primary reason for model errors lies in assessing task solvability. Additionally, open-weight models suffer from performance drops with verbose replies, whereas proprietary models excel with longer reasoning.

Medical imaging plays a crucial role in diagnosis, with radiology reports serving as vital documentation. Automating report generation has emerged as a critical need to alleviate the workload of radiologists. While machine learning has facilitated report generation for 2D medical imaging, extending this to 3D has been unexplored due to computational complexity and data scarcity. We introduce the first method to generate radiology reports for 3D medical imaging, specifically targeting chest CT volumes. Given the absence of comparable methods, we establish a baseline using an advanced 3D vision encoder in medical imaging to demonstrate our method's effectiveness, which leverages a novel auto-regressive causal transformer. Furthermore, recognizing the benefits of leveraging information from previous visits, we augment CT2Rep with a cross-attention-based multi-modal fusion module and hierarchical memory, enabling the incorporation of longitudinal multimodal data. Access our code at https://github.com/ibrahimethemhamamci/CT2Rep

Inductive reasoning is a core problem-solving capacity: humans can identify underlying principles from a few examples, which can then be robustly generalized to novel scenarios. Recent work has evaluated large language models (LLMs) on inductive reasoning tasks by directly prompting them yielding "in context learning." This can work well for straightforward inductive tasks, but performs very poorly on more complex tasks such as the Abstraction and Reasoning Corpus (ARC). In this work, we propose to improve the inductive reasoning ability of LLMs by generating explicit hypotheses at multiple levels of abstraction: we prompt the LLM to propose multiple abstract hypotheses about the problem, in natural language, then implement the natural language hypotheses as concrete Python programs. These programs can be directly verified by running on the observed examples and generalized to novel inputs. Because of the prohibitive cost of generation with state-of-the-art LLMs, we consider a middle step to filter the set of hypotheses that will be implemented into programs: we either ask the LLM to summarize into a smaller set of hypotheses, or ask human annotators to select a subset of the hypotheses. We verify our pipeline's effectiveness on the ARC visual inductive reasoning benchmark, its variant 1D-ARC, and string transformation dataset SyGuS. On a random 40-problem subset of ARC, our automated pipeline using LLM summaries achieves 27.5% accuracy, significantly outperforming the direct prompting baseline (accuracy of 12.5%). With the minimal human input of selecting from LLM-generated candidates, the performance is boosted to 37.5%. (And we argue this is a lower bound on the performance of our approach without filtering.) Our ablation studies show that abstract hypothesis generation and concrete program representations are both beneficial for LLMs to perform inductive reasoning tasks.

Large Language Models (LLMs) have shown impressive performance on existing medical question-answering benchmarks. This high performance makes it increasingly difficult to meaningfully evaluate and differentiate advanced methods. We present MedAgentsBench, a benchmark that focuses on challenging medical questions requiring multi-step clinical reasoning, diagnosis formulation, and treatment planning-scenarios where current models still struggle despite their strong performance on standard tests. Drawing from seven established medical datasets, our benchmark addresses three key limitations in existing evaluations: (1) the prevalence of straightforward questions where even base models achieve high performance, (2) inconsistent sampling and evaluation protocols across studies, and (3) lack of systematic analysis of the interplay between performance, cost, and inference time. Through experiments with various base models and reasoning methods, we demonstrate that the latest thinking models, DeepSeek R1 and OpenAI o3, exhibit exceptional performance in complex medical reasoning tasks. Additionally, advanced search-based agent methods offer promising performance-to-cost ratios compared to traditional approaches. Our analysis reveals substantial performance gaps between model families on complex questions and identifies optimal model selections for different computational constraints. Our benchmark and evaluation framework are publicly available at https://github.com/gersteinlab/medagents-benchmark.

Large language models (LLMs) represent a transformative class of AI tools capable of revolutionizing various aspects of healthcare by generating human-like responses across diverse contexts and adapting to novel tasks following human instructions. Their potential application spans a broad range of medical tasks, such as clinical documentation, matching patients to clinical trials, and answering medical questions. In this primer paper, we propose an actionable guideline to help healthcare professionals more efficiently utilize LLMs in their work, along with a set of best practices. This approach consists of several main phases, including formulating the task, choosing LLMs, prompt engineering, fine-tuning, and deployment. We start with the discussion of critical considerations in identifying healthcare tasks that align with the core capabilities of LLMs and selecting models based on the selected task and data, performance requirements, and model interface. We then review the strategies, such as prompt engineering and fine-tuning, to adapt standard LLMs to specialized medical tasks. Deployment considerations, including regulatory compliance, ethical guidelines, and continuous monitoring for fairness and bias, are also discussed. By providing a structured step-by-step methodology, this tutorial aims to equip healthcare professionals with the tools necessary to effectively integrate LLMs into clinical practice, ensuring that these powerful technologies are applied in a safe, reliable, and impactful manner.

Reasoning is a critical frontier for advancing medical image analysis, where transparency and trustworthiness play a central role in both clinician trust and regulatory approval. Although Medical Visual Language Models (VLMs) show promise for radiological tasks, most existing VLMs merely produce final answers without revealing the underlying reasoning. To address this gap, we introduce MedVLM-R1, a medical VLM that explicitly generates natural language reasoning to enhance transparency and trustworthiness. Instead of relying on supervised fine-tuning (SFT), which often suffers from overfitting to training distributions and fails to foster genuine reasoning, MedVLM-R1 employs a reinforcement learning framework that incentivizes the model to discover human-interpretable reasoning paths without using any reasoning references. Despite limited training data (600 visual question answering samples) and model parameters (2B), MedVLM-R1 boosts accuracy from 55.11% to 78.22% across MRI, CT, and X-ray benchmarks, outperforming larger models trained on over a million samples. It also demonstrates robust domain generalization under out-of-distribution tasks. By unifying medical image analysis with explicit reasoning, MedVLM-R1 marks a pivotal step toward trustworthy and interpretable AI in clinical practice.

Generative Artificial Intelligence (GenAI) systems are being increasingly deployed across all parts of industry and research settings. Developers and end users interact with these systems through the use of prompting or prompt engineering. While prompting is a widespread and highly researched concept, there exists conflicting terminology and a poor ontological understanding of what constitutes a prompt due to the area's nascency. This paper establishes a structured understanding of prompts, by assembling a taxonomy of prompting techniques and analyzing their use. We present a comprehensive vocabulary of 33 vocabulary terms, a taxonomy of 58 text-only prompting techniques, and 40 techniques for other modalities. We further present a meta-analysis of the entire literature on natural language prefix-prompting.

Automatic radiology report generation is booming due to its huge application potential for the healthcare industry. However, existing computer vision and natural language processing approaches to tackle this problem are limited in two aspects. First, when extracting image features, most of them neglect multi-view reasoning in vision and model single-view structure of medical images, such as space-view or channel-view. However, clinicians rely on multi-view imaging information for comprehensive judgment in daily clinical diagnosis. Second, when generating reports, they overlook context reasoning with multi-modal information and focus on pure textual optimization utilizing retrieval-based methods. We aim to address these two issues by proposing a model that better simulates clinicians' perspectives and generates more accurate reports. Given the above limitation in feature extraction, we propose a Globally-intensive Attention (GIA) module in the medical image encoder to simulate and integrate multi-view vision perception. GIA aims to learn three types of vision perception: depth view, space view, and pixel view. On the other hand, to address the above problem in report generation, we explore how to involve multi-modal signals to generate precisely matched reports, i.e., how to integrate previously predicted words with region-aware visual content in next word prediction. Specifically, we design a Visual Knowledge-guided Decoder (VKGD), which can adaptively consider how much the model needs to rely on visual information and previously predicted text to assist next word prediction. Hence, our final Intensive Vision-guided Network (IVGN) framework includes a GIA-guided Visual Encoder and the VKGD. Experiments on two commonly-used datasets IU X-Ray and MIMIC-CXR demonstrate the superior ability of our method compared with other state-of-the-art approaches.

The field of machine learning (ML) has gained widespread adoption, leading to a significant demand for adapting ML to specific scenarios, which is yet expensive and non-trivial. The predominant approaches towards the automation of solving ML tasks (e.g., AutoML) are often time consuming and hard to understand for human developers. In contrast, though human engineers have the incredible ability to understand tasks and reason about solutions, their experience and knowledge are often sparse and difficult to utilize by quantitative approaches. In this paper, we aim to bridge the gap between machine intelligence and human knowledge by introducing a novel framework MLCopilot, which leverages the state-of-the-art LLMs to develop ML solutions for novel tasks. We showcase the possibility of extending the capability of LLMs to comprehend structured inputs and perform thorough reasoning for solving novel ML tasks. And we find that, after some dedicated design, the LLM can (i) observe from the existing experiences of ML tasks and (ii) reason effectively to deliver promising results for new tasks. The solution generated can be used directly to achieve high levels of competitiveness.

Medical image classification in radiology faces significant challenges, particularly in generalizing to unseen pathologies. In contrast, CLIP offers a promising solution by leveraging multimodal learning to improve zero-shot classification performance. However, in the medical domain, lesions can be small and might not be well represented in the embedding space. Therefore, in this paper, we explore the potential of visual prompt engineering to enhance the capabilities of Vision Language Models (VLMs) in radiology. Leveraging BiomedCLIP, trained on extensive biomedical image-text pairs, we investigate the impact of embedding visual markers directly within radiological images to guide the model's attention to critical regions. Our evaluation on the JSRT dataset, focusing on lung nodule malignancy classification, demonstrates that incorporating visual prompts x2013 such as arrows, circles, and contours x2013 significantly improves classification metrics including AUROC, AUPRC, F1 score, and accuracy. Moreover, the study provides attention maps, showcasing enhanced model interpretability and focus on clinically relevant areas. These findings underscore the efficacy of visual prompt engineering as a straightforward yet powerful approach to advance VLM performance in medical image analysis.

Generating Natural Language Explanations (NLEs) for model predictions on medical images, particularly those depicting thoracic pathologies, remains a critical and challenging task. Existing methodologies often struggle due to general models' insufficient domain-specific medical knowledge and privacy concerns associated with retrieval-based augmentation techniques. To address these issues, we propose a novel Vision-Language framework augmented with a Knowledge Graph (KG)-based datastore, which enhances the model's understanding by incorporating additional domain-specific medical knowledge essential for generating accurate and informative NLEs. Our framework employs a KG-based retrieval mechanism that not only improves the precision of the generated explanations but also preserves data privacy by avoiding direct data retrieval. The KG datastore is designed as a plug-and-play module, allowing for seamless integration with various model architectures. We introduce and evaluate three distinct frameworks within this paradigm: KG-LLaVA, which integrates the pre-trained LLaVA model with KG-RAG; Med-XPT, a custom framework combining MedCLIP, a transformer-based projector, and GPT-2; and Bio-LLaVA, which adapts LLaVA by incorporating the Bio-ViT-L vision model. These frameworks are validated on the MIMIC-NLE dataset, where they achieve state-of-the-art results, underscoring the effectiveness of KG augmentation in generating high-quality NLEs for thoracic pathologies.

Artificial intelligence (AI) has demonstrated significant potential in ECG analysis and cardiovascular disease assessment. Recently, foundation models have played a remarkable role in advancing medical AI. The development of an ECG foundation model holds the promise of elevating AI-ECG research to new heights. However, building such a model faces several challenges, including insufficient database sample sizes and inadequate generalization across multiple domains. Additionally, there is a notable performance gap between single-lead and multi-lead ECG analyses. We introduced an ECG Foundation Model (ECGFounder), a general-purpose model that leverages real-world ECG annotations from cardiology experts to broaden the diagnostic capabilities of ECG analysis. ECGFounder was trained on over 10 million ECGs with 150 label categories from the Harvard-Emory ECG Database, enabling comprehensive cardiovascular disease diagnosis through ECG analysis. The model is designed to be both an effective out-of-the-box solution, and a to be fine-tunable for downstream tasks, maximizing usability. Importantly, we extended its application to lower rank ECGs, and arbitrary single-lead ECGs in particular. ECGFounder is applicable to supporting various downstream tasks in mobile monitoring scenarios. Experimental results demonstrate that ECGFounder achieves expert-level performance on internal validation sets, with AUROC exceeding 0.95 for eighty diagnoses. It also shows strong classification performance and generalization across various diagnoses on external validation sets. When fine-tuned, ECGFounder outperforms baseline models in demographic analysis, clinical event detection, and cross-modality cardiac rhythm diagnosis. The trained model and data will be publicly released upon publication through the bdsp.io. Our code is available at https://github.com/bdsp-core/ECGFounder

The outbreak of COVID-19 has shocked the entire world with its fairly rapid spread and has challenged different sectors. One of the most effective ways to limit its spread is the early and accurate diagnosing infected patients. Medical imaging, such as X-ray and Computed Tomography (CT), combined with the potential of Artificial Intelligence (AI), plays an essential role in supporting medical personnel in the diagnosis process. Thus, in this article five different deep learning models (ResNet18, ResNet34, InceptionV3, InceptionResNetV2 and DenseNet161) and their ensemble, using majority voting have been used to classify COVID-19, pneumoni{\ae} and healthy subjects using chest X-ray images. Multilabel classification was performed to predict multiple pathologies for each patient, if present. Firstly, the interpretability of each of the networks was thoroughly studied using local interpretability methods - occlusion, saliency, input X gradient, guided backpropagation, integrated gradients, and DeepLIFT, and using a global technique - neuron activation profiles. The mean Micro-F1 score of the models for COVID-19 classifications ranges from 0.66 to 0.875, and is 0.89 for the ensemble of the network models. The qualitative results showed that the ResNets were the most interpretable models. This research demonstrates the importance of using interpretability methods to compare different models before making a decision regarding the best performing model.

Users of social platforms often perceive these sites as supportive spaces to post about their mental health issues. Those conversations contain important traces about individuals' health risks. Recently, researchers have exploited this online information to construct mental health detection models, which aim to identify users at risk on platforms like Twitter, Reddit or Facebook. Most of these models are centred on achieving good classification results, ignoring the explainability and interpretability of the decisions. Recent research has pointed out the importance of using clinical markers, such as the use of symptoms, to improve trust in the computational models by health professionals. In this paper, we propose using transformer-based architectures to detect and explain the appearance of depressive symptom markers in the users' writings. We present two approaches: i) train a model to classify, and another one to explain the classifier's decision separately and ii) unify the two tasks simultaneously using a single model. Additionally, for this latter manner, we also investigated the performance of recent conversational LLMs when using in-context learning. Our natural language explanations enable clinicians to interpret the models' decisions based on validated symptoms, enhancing trust in the automated process. We evaluate our approach using recent symptom-based datasets, employing both offline and expert-in-the-loop metrics to assess the quality of the explanations generated by our models. The experimental results show that it is possible to achieve good classification results while generating interpretable symptom-based explanations.

The objective of Radiology Report Generation (RRG) is to automatically generate coherent textual analyses of diseases based on radiological images, thereby alleviating the workload of radiologists. Current AI-based methods for RRG primarily focus on modifications to the encoder-decoder model architecture. To advance these approaches, this paper introduces an Organ-Regional Information Driven (ORID) framework which can effectively integrate multi-modal information and reduce the influence of noise from unrelated organs. Specifically, based on the LLaVA-Med, we first construct an RRG-related instruction dataset to improve organ-regional diagnosis description ability and get the LLaVA-Med-RRG. After that, we propose an organ-based cross-modal fusion module to effectively combine the information from the organ-regional diagnosis description and radiology image. To further reduce the influence of noise from unrelated organs on the radiology report generation, we introduce an organ importance coefficient analysis module, which leverages Graph Neural Network (GNN) to examine the interconnections of the cross-modal information of each organ region. Extensive experiments an1d comparisons with state-of-the-art methods across various evaluation metrics demonstrate the superior performance of our proposed method.

Deep neural networks are often applied to medical images to automate the problem of medical diagnosis. However, a more clinically relevant question that practitioners usually face is how to predict the future trajectory of a disease. Current methods for prognosis or disease trajectory forecasting often require domain knowledge and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many prediction problem. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner -- we predict prognosis with two transformer-based components that share information with each other. The first transformer in this framework aims to analyze the imaging data, and the second one leverages its internal states as inputs, also fusing them with auxiliary clinical data. The temporal nature of the problem is modeled within the transformer states, allowing us to treat the forecasting problem as a multi-task classification, for which we propose a novel loss. We show the effectiveness of our approach in predicting the development of structural knee osteoarthritis changes and forecasting Alzheimer's disease clinical status directly from raw multi-modal data. The proposed method outperforms multiple state-of-the-art baselines with respect to performance and calibration, both of which are needed for real-world applications. An open-source implementation of our method is made publicly available at https://github.com/Oulu-IMEDS/CLIMATv2.

Research is a fundamental process driving the advancement of human civilization, yet it demands substantial time and effort from researchers. In recent years, the rapid development of artificial intelligence (AI) technologies has inspired researchers to explore how AI can accelerate and enhance research. To monitor relevant advancements, this paper presents a systematic review of the progress in this domain. Specifically, we organize the relevant studies into three main categories: hypothesis formulation, hypothesis validation, and manuscript publication. Hypothesis formulation involves knowledge synthesis and hypothesis generation. Hypothesis validation includes the verification of scientific claims, theorem proving, and experiment validation. Manuscript publication encompasses manuscript writing and the peer review process. Furthermore, we identify and discuss the current challenges faced in these areas, as well as potential future directions for research. Finally, we also offer a comprehensive overview of existing benchmarks and tools across various domains that support the integration of AI into the research process. We hope this paper serves as an introduction for beginners and fosters future research. Resources have been made publicly available at https://github.com/zkzhou126/AI-for-Research.

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

Medical images and radiology reports are crucial for diagnosing medical conditions, highlighting the importance of quantitative analysis for clinical decision-making. However, the diversity and cross-source heterogeneity of these data challenge the generalizability of current data-mining methods. Multimodal large language models (MLLMs) have recently transformed many domains, significantly affecting the medical field. Notably, Gemini-Vision-series (Gemini) and GPT-4-series (GPT-4) models have epitomized a paradigm shift in Artificial General Intelligence (AGI) for computer vision, showcasing their potential in the biomedical domain. In this study, we evaluated the performance of the Gemini, GPT-4, and 4 popular large models for an exhaustive evaluation across 14 medical imaging datasets, including 5 medical imaging categories (dermatology, radiology, dentistry, ophthalmology, and endoscopy), and 3 radiology report datasets. The investigated tasks encompass disease classification, lesion segmentation, anatomical localization, disease diagnosis, report generation, and lesion detection. Our experimental results demonstrated that Gemini-series models excelled in report generation and lesion detection but faces challenges in disease classification and anatomical localization. Conversely, GPT-series models exhibited proficiency in lesion segmentation and anatomical localization but encountered difficulties in disease diagnosis and lesion detection. Additionally, both the Gemini series and GPT series contain models that have demonstrated commendable generation efficiency. While both models hold promise in reducing physician workload, alleviating pressure on limited healthcare resources, and fostering collaboration between clinical practitioners and artificial intelligence technologies, substantial enhancements and comprehensive validations remain imperative before clinical deployment.

The integration of Large Language Models (LLMs) into healthcare promises to transform medical diagnostics, research, and patient care. Yet, the progression of medical LLMs faces obstacles such as complex training requirements, rigorous evaluation demands, and the dominance of proprietary models that restrict academic exploration. Transparent, comprehensive access to LLM resources is essential for advancing the field, fostering reproducibility, and encouraging innovation in healthcare AI. We present Hippocrates, an open-source LLM framework specifically developed for the medical domain. In stark contrast to previous efforts, it offers unrestricted access to its training datasets, codebase, checkpoints, and evaluation protocols. This open approach is designed to stimulate collaborative research, allowing the community to build upon, refine, and rigorously evaluate medical LLMs within a transparent ecosystem. Also, we introduce Hippo, a family of 7B models tailored for the medical domain, fine-tuned from Mistral and LLaMA2 through continual pre-training, instruction tuning, and reinforcement learning from human and AI feedback. Our models outperform existing open medical LLMs models by a large-margin, even surpassing models with 70B parameters. Through Hippocrates, we aspire to unlock the full potential of LLMs not just to advance medical knowledge and patient care but also to democratize the benefits of AI research in healthcare, making them available across the globe.

Disease risk prediction has attracted increasing attention in the field of modern healthcare, especially with the latest advances in artificial intelligence (AI). Electronic health records (EHRs), which contain heterogeneous patient information, are widely used in disease risk prediction tasks. One challenge of applying AI models for risk prediction lies in generating interpretable evidence to support the prediction results while retaining the prediction ability. In order to address this problem, we propose the method of jointly embedding words and labels whereby attention modules learn the weights of words from medical notes according to their relevance to the names of risk prediction labels. This approach boosts interpretability by employing an attention mechanism and including the names of prediction tasks in the model. However, its application is only limited to the handling of textual inputs such as medical notes. In this paper, we propose a label dependent attention model LDAM to 1) improve the interpretability by exploiting Clinical-BERT (a biomedical language model pre-trained on a large clinical corpus) to encode biomedically meaningful features and labels jointly; 2) extend the idea of joint embedding to the processing of time-series data, and develop a multi-modal learning framework for integrating heterogeneous information from medical notes and time-series health status indicators. To demonstrate our method, we apply LDAM to the MIMIC-III dataset to predict different disease risks. We evaluate our method both quantitatively and qualitatively. Specifically, the predictive power of LDAM will be shown, and case studies will be carried out to illustrate its interpretability.

Artificial Intelligence (AI) is a broad field that is upturning mental health care in many ways, from addressing anxiety, depression, and stress to increasing access, personalization of treatment, and real-time monitoring that enhances patient outcomes. The current paper discusses the evolution, present application, and future challenges in the field of AI for mental health and well-being. From the early chatbot models, such as ELIZA, to modern machine learning systems, the integration of AI in mental health has grown rapidly to augment traditional treatment and open innovative solutions. AI-driven tools provide continuous support, offering personalized interventions and addressing issues such as treatment access and patient stigma. AI also enables early diagnosis through the analysis of complex datasets, including speech patterns and social media behavior, to detect early signs of conditions like depression and Post-Traumatic Stress Disorder (PTSD). Ethical challenges persist, however, most notably around privacy, data security, and algorithmic bias. With AI at the core of mental health care, there is a dire need to develop strong ethical frameworks that ensure patient rights are protected, access is equitable, and transparency is maintained in AI applications. Going forward, the role of AI in mental health will continue to evolve, and continued research and policy development will be needed to meet the diverse needs of patients while mitigating associated risks.

Recent advances in generative AI have brought incredible breakthroughs in several areas, including medical imaging. These generative models have tremendous potential not only to help safely share medical data via synthetic datasets but also to perform an array of diverse applications, such as anomaly detection, image-to-image translation, denoising, and MRI reconstruction. However, due to the complexity of these models, their implementation and reproducibility can be difficult. This complexity can hinder progress, act as a use barrier, and dissuade the comparison of new methods with existing works. In this study, we present MONAI Generative Models, a freely available open-source platform that allows researchers and developers to easily train, evaluate, and deploy generative models and related applications. Our platform reproduces state-of-art studies in a standardised way involving different architectures (such as diffusion models, autoregressive transformers, and GANs), and provides pre-trained models for the community. We have implemented these models in a generalisable fashion, illustrating that their results can be extended to 2D or 3D scenarios, including medical images with different modalities (like CT, MRI, and X-Ray data) and from different anatomical areas. Finally, we adopt a modular and extensible approach, ensuring long-term maintainability and the extension of current applications for future features.

Recent advancements in artificial intelligence (AI) have precipitated significant breakthroughs in healthcare, particularly in refining diagnostic procedures. However, previous studies have often been constrained to limited functionalities. This study introduces MiniGPT-Med, a vision-language model derived from large-scale language models and tailored for medical applications. MiniGPT-Med demonstrates remarkable versatility across various imaging modalities, including X-rays, CT scans, and MRIs, enhancing its utility. The model is capable of performing tasks such as medical report generation, visual question answering (VQA), and disease identification within medical imagery. Its integrated processing of both image and textual clinical data markedly improves diagnostic accuracy. Our empirical assessments confirm MiniGPT-Med's superior performance in disease grounding, medical report generation, and VQA benchmarks, representing a significant step towards reducing the gap in assisting radiology practice. Furthermore, it achieves state-of-the-art performance on medical report generation, higher than the previous best model by 19\% accuracy. MiniGPT-Med promises to become a general interface for radiology diagnoses, enhancing diagnostic efficiency across a wide range of medical imaging applications.

Systematic literature review is essential for evidence-based medicine, requiring comprehensive analysis of clinical trial publications. However, the application of artificial intelligence (AI) models for medical literature mining has been limited by insufficient training and evaluation across broad therapeutic areas and diverse tasks. Here, we present LEADS, an AI foundation model for study search, screening, and data extraction from medical literature. The model is trained on 633,759 instruction data points in LEADSInstruct, curated from 21,335 systematic reviews, 453,625 clinical trial publications, and 27,015 clinical trial registries. We showed that LEADS demonstrates consistent improvements over four cutting-edge generic large language models (LLMs) on six tasks. Furthermore, LEADS enhances expert workflows by providing supportive references following expert requests, streamlining processes while maintaining high-quality results. A study with 16 clinicians and medical researchers from 14 different institutions revealed that experts collaborating with LEADS achieved a recall of 0.81 compared to 0.77 experts working alone in study selection, with a time savings of 22.6%. In data extraction tasks, experts using LEADS achieved an accuracy of 0.85 versus 0.80 without using LEADS, alongside a 26.9% time savings. These findings highlight the potential of specialized medical literature foundation models to outperform generic models, delivering significant quality and efficiency benefits when integrated into expert workflows for medical literature mining.

The field of Explainable Artificial Intelligence (XAI) aims to build explainable and interpretable machine learning (or deep learning) methods without sacrificing prediction performance. Convolutional Neural Networks (CNNs) have been successful in making predictions, especially in image classification. However, these famous deep learning models use tens of millions of parameters based on a large number of pre-trained filters which have been repurposed from previous data sets. We propose a novel Interaction-based Convolutional Neural Network (ICNN) that does not make assumptions about the relevance of local information. Instead, we use a model-free Influence Score (I-score) to directly extract the influential information from images to form important variable modules. We demonstrate that the proposed method produces state-of-the-art prediction performance of 99.8% on a real-world data set classifying COVID-19 Chest X-ray images without sacrificing the explanatory power of the model. This proposed design can efficiently screen COVID-19 patients before human diagnosis, and will be the benchmark for addressing future XAI problems in large-scale data sets.

Millions of users come to online peer counseling platforms to seek support on diverse topics ranging from relationship stress to anxiety. However, studies show that online peer support groups are not always as effective as expected largely due to users' negative experiences with unhelpful counselors. Peer counselors are key to the success of online peer counseling platforms, but most of them often do not have systematic ways to receive guidelines or supervision. In this work, we introduce CARE: an interactive AI-based tool to empower peer counselors through automatic suggestion generation. During the practical training stage, CARE helps diagnose which specific counseling strategies are most suitable in the given context and provides tailored example responses as suggestions. Counselors can choose to select, modify, or ignore any suggestion before replying to the support seeker. Building upon the Motivational Interviewing framework, CARE utilizes large-scale counseling conversation data together with advanced natural language generation techniques to achieve these functionalities. We demonstrate the efficacy of CARE by performing both quantitative evaluations and qualitative user studies through simulated chats and semi-structured interviews. We also find that CARE especially helps novice counselors respond better in challenging situations.

The exponential growth of astronomical literature poses significant challenges for researchers navigating and synthesizing general insights or even domain-specific knowledge. We present Pathfinder, a machine learning framework designed to enable literature review and knowledge discovery in astronomy, focusing on semantic searching with natural language instead of syntactic searches with keywords. Utilizing state-of-the-art large language models (LLMs) and a corpus of 350,000 peer-reviewed papers from the Astrophysics Data System (ADS), Pathfinder offers an innovative approach to scientific inquiry and literature exploration. Our framework couples advanced retrieval techniques with LLM-based synthesis to search astronomical literature by semantic context as a complement to currently existing methods that use keywords or citation graphs. It addresses complexities of jargon, named entities, and temporal aspects through time-based and citation-based weighting schemes. We demonstrate the tool's versatility through case studies, showcasing its application in various research scenarios. The system's performance is evaluated using custom benchmarks, including single-paper and multi-paper tasks. Beyond literature review, Pathfinder offers unique capabilities for reformatting answers in ways that are accessible to various audiences (e.g. in a different language or as simplified text), visualizing research landscapes, and tracking the impact of observatories and methodologies. This tool represents a significant advancement in applying AI to astronomical research, aiding researchers at all career stages in navigating modern astronomy literature.

Adversarial testing of large language models (LLMs) is crucial for their safe and responsible deployment. We introduce a novel approach for automated generation of adversarial evaluation datasets to test the safety of LLM generations on new downstream applications. We call it AI-assisted Red-Teaming (AART) - an automated alternative to current manual red-teaming efforts. AART offers a data generation and augmentation pipeline of reusable and customizable recipes that reduce human effort significantly and enable integration of adversarial testing earlier in new product development. AART generates evaluation datasets with high diversity of content characteristics critical for effective adversarial testing (e.g. sensitive and harmful concepts, specific to a wide range of cultural and geographic regions and application scenarios). The data generation is steered by AI-assisted recipes to define, scope and prioritize diversity within the application context. This feeds into a structured LLM-generation process that scales up evaluation priorities. Compared to some state-of-the-art tools, AART shows promising results in terms of concept coverage and data quality.

Driven by the recent advances in deep learning methods and, in particular, by the development of modern self-supervised learning algorithms, increased interest and efforts have been devoted to build foundation models (FMs) for medical images. In this work, we present our scalable training pipeline for large pathology imaging data, and a comprehensive analysis of various hyperparameter choices and training techniques for building pathology FMs. We release and make publicly available the first batch of our pathology FMs (https://github.com/kaiko-ai/towards_large_pathology_fms) trained on open-access TCGA whole slide images, a commonly used collection of pathology images. The experimental evaluation shows that our models reach state-of-the-art performance on various patch-level downstream tasks, ranging from breast cancer subtyping to colorectal nuclear segmentation. Finally, to unify the evaluation approaches used in the field and to simplify future comparisons of different FMs, we present an open-source framework (https://github.com/kaiko-ai/eva) designed for the consistent evaluation of pathology FMs across various downstream tasks.

Machine learning is a general-purpose technology holding promises for many interdisciplinary research problems. However, significant barriers exist in crossing disciplinary boundaries when most machine learning tools are developed in different areas separately. We present Pykale - a Python library for knowledge-aware machine learning on graphs, images, texts, and videos to enable and accelerate interdisciplinary research. We formulate new green machine learning guidelines based on standard software engineering practices and propose a novel pipeline-based application programming interface (API). PyKale focuses on leveraging knowledge from multiple sources for accurate and interpretable prediction, thus supporting multimodal learning and transfer learning (particularly domain adaptation) with latest deep learning and dimensionality reduction models. We build PyKale on PyTorch and leverage the rich PyTorch ecosystem. Our pipeline-based API design enforces standardization and minimalism, embracing green machine learning concepts via reducing repetitions and redundancy, reusing existing resources, and recycling learning models across areas. We demonstrate its interdisciplinary nature via examples in bioinformatics, knowledge graph, image/video recognition, and medical imaging.

The evolution of Artificial Intelligence (AI) has been significantly accelerated by advancements in Large Language Models (LLMs) and Large Multimodal Models (LMMs), gradually showcasing potential cognitive reasoning abilities in problem-solving and scientific discovery (i.e., AI4Science) once exclusive to human intellect. To comprehensively evaluate current models' performance in cognitive reasoning abilities, we introduce OlympicArena, which includes 11,163 bilingual problems across both text-only and interleaved text-image modalities. These challenges encompass a wide range of disciplines spanning seven fields and 62 international Olympic competitions, rigorously examined for data leakage. We argue that the challenges in Olympic competition problems are ideal for evaluating AI's cognitive reasoning due to their complexity and interdisciplinary nature, which are essential for tackling complex scientific challenges and facilitating discoveries. Beyond evaluating performance across various disciplines using answer-only criteria, we conduct detailed experiments and analyses from multiple perspectives. We delve into the models' cognitive reasoning abilities, their performance across different modalities, and their outcomes in process-level evaluations, which are vital for tasks requiring complex reasoning with lengthy solutions. Our extensive evaluations reveal that even advanced models like GPT-4o only achieve a 39.97% overall accuracy, illustrating current AI limitations in complex reasoning and multimodal integration. Through the OlympicArena, we aim to advance AI towards superintelligence, equipping it to address more complex challenges in science and beyond. We also provide a comprehensive set of resources to support AI research, including a benchmark dataset, an open-source annotation platform, a detailed evaluation tool, and a leaderboard with automatic submission features.

Depression poses significant challenges to patients and healthcare organizations, necessitating efficient assessment methods. Existing paradigms typically focus on a patient-doctor way that overlooks multi-role interactions, such as family involvement in the evaluation and caregiving process. Moreover, current automatic depression detection (ADD) methods usually model depression detection as a classification or regression task, lacking interpretability for the decision-making process. To address these issues, we developed InterMind, a doctor-patient-family interactive depression assessment system empowered by large language models (LLMs). Our system enables patients and families to contribute descriptions, generates assistive diagnostic reports for doctors, and provides actionable insights, improving diagnostic precision and efficiency. To enhance LLMs' performance in psychological counseling and diagnostic interpretability, we integrate retrieval-augmented generation (RAG) and chain-of-thoughts (CoT) techniques for data augmentation, which mitigates the hallucination issue of LLMs in specific scenarios after instruction fine-tuning. Quantitative experiments and professional assessments by clinicians validate the effectiveness of our system.

In this paper, we study how well humans can detect text generated by commercial LLMs (GPT-4o, Claude, o1). We hire annotators to read 300 non-fiction English articles, label them as either human-written or AI-generated, and provide paragraph-length explanations for their decisions. Our experiments show that annotators who frequently use LLMs for writing tasks excel at detecting AI-generated text, even without any specialized training or feedback. In fact, the majority vote among five such "expert" annotators misclassifies only 1 of 300 articles, significantly outperforming most commercial and open-source detectors we evaluated even in the presence of evasion tactics like paraphrasing and humanization. Qualitative analysis of the experts' free-form explanations shows that while they rely heavily on specific lexical clues ('AI vocabulary'), they also pick up on more complex phenomena within the text (e.g., formality, originality, clarity) that are challenging to assess for automatic detectors. We release our annotated dataset and code to spur future research into both human and automated detection of AI-generated text.

Current techniques for detecting AI-generated text are largely confined to manual feature crafting and supervised binary classification paradigms. These methodologies typically lead to performance bottlenecks and unsatisfactory generalizability. Consequently, these methods are often inapplicable for out-of-distribution (OOD) data and newly emerged large language models (LLMs). In this paper, we revisit the task of AI-generated text detection. We argue that the key to accomplishing this task lies in distinguishing writing styles of different authors, rather than simply classifying the text into human-written or AI-generated text. To this end, we propose DeTeCtive, a multi-task auxiliary, multi-level contrastive learning framework. DeTeCtive is designed to facilitate the learning of distinct writing styles, combined with a dense information retrieval pipeline for AI-generated text detection. Our method is compatible with a range of text encoders. Extensive experiments demonstrate that our method enhances the ability of various text encoders in detecting AI-generated text across multiple benchmarks and achieves state-of-the-art results. Notably, in OOD zero-shot evaluation, our method outperforms existing approaches by a large margin. Moreover, we find our method boasts a Training-Free Incremental Adaptation (TFIA) capability towards OOD data, further enhancing its efficacy in OOD detection scenarios. We will open-source our code and models in hopes that our work will spark new thoughts in the field of AI-generated text detection, ensuring safe application of LLMs and enhancing compliance. Our code is available at https://github.com/heyongxin233/DeTeCtive.

While interpretability research has shed light on some internal algorithms utilized by transformer-based LLMs, reasoning in natural language, with its deep contextuality and ambiguity, defies easy categorization. As a result, formulating clear and motivating questions for circuit analysis that rely on well-defined in-domain and out-of-domain examples required for causal interventions is challenging. Although significant work has investigated circuits for specific tasks, such as indirect object identification (IOI), deciphering natural language reasoning through circuits remains difficult due to its inherent complexity. In this work, we take initial steps to characterize causal reasoning in LLMs by analyzing clear-cut cause-and-effect sentences like "I opened an umbrella because it started raining," where causal interventions may be possible through carefully crafted scenarios using GPT-2 small. Our findings indicate that causal syntax is localized within the first 2-3 layers, while certain heads in later layers exhibit heightened sensitivity to nonsensical variations of causal sentences. This suggests that models may infer reasoning by (1) detecting syntactic cues and (2) isolating distinct heads in the final layers that focus on semantic relationships.

Developing accurate machine learning models for oncology requires large-scale, high-quality multimodal datasets. However, creating such datasets remains challenging due to the complexity and heterogeneity of medical data. To address this challenge, we introduce HoneyBee, a scalable modular framework for building multimodal oncology datasets that leverages foundational models to generate representative embeddings. HoneyBee integrates various data modalities, including clinical records, imaging data, and patient outcomes. It employs data preprocessing techniques and transformer-based architectures to generate embeddings that capture the essential features and relationships within the raw medical data. The generated embeddings are stored in a structured format using Hugging Face datasets and PyTorch dataloaders for accessibility. Vector databases enable efficient querying and retrieval for machine learning applications. We demonstrate the effectiveness of HoneyBee through experiments assessing the quality and representativeness of the embeddings. The framework is designed to be extensible to other medical domains and aims to accelerate oncology research by providing high-quality, machine learning-ready datasets. HoneyBee is an ongoing open-source effort, and the code, datasets, and models are available at the project repository.

The breakthrough of OpenAI o1 highlights the potential of enhancing reasoning to improve LLM. Yet, most research in reasoning has focused on mathematical tasks, leaving domains like medicine underexplored. The medical domain, though distinct from mathematics, also demands robust reasoning to provide reliable answers, given the high standards of healthcare. However, verifying medical reasoning is challenging, unlike those in mathematics. To address this, we propose verifiable medical problems with a medical verifier to check the correctness of model outputs. This verifiable nature enables advancements in medical reasoning through a two-stage approach: (1) using the verifier to guide the search for a complex reasoning trajectory for fine-tuning LLMs, (2) applying reinforcement learning (RL) with verifier-based rewards to enhance complex reasoning further. Finally, we introduce HuatuoGPT-o1, a medical LLM capable of complex reasoning, which outperforms general and medical-specific baselines using only 40K verifiable problems. Experiments show complex reasoning improves medical problem-solving and benefits more from RL. We hope our approach inspires advancements in reasoning across medical and other specialized domains.

This paper proposes one of the first clinical applications of multimodal large language models (LLMs) as an assistant for radiologists to check errors in their reports. We created an evaluation dataset from two real-world radiology datasets (MIMIC-CXR and IU-Xray), with 1,000 subsampled reports each. A subset of original reports was modified to contain synthetic errors by introducing various type of mistakes. The evaluation contained two difficulty levels: SIMPLE for binary error-checking and COMPLEX for identifying error types. LLaVA (Large Language and Visual Assistant) variant models, including our instruction-tuned model, were used for the evaluation. Additionally, a domain expert evaluation was conducted on a small test set. At the SIMPLE level, the LLaVA v1.5 model outperformed other publicly available models. Instruction tuning significantly enhanced performance by 47.4% and 25.4% on MIMIC-CXR and IU-Xray data, respectively. The model also surpassed the domain experts accuracy in the MIMIC-CXR dataset by 1.67%. Notably, among the subsets (N=21) of the test set where a clinician did not achieve the correct conclusion, the LLaVA ensemble mode correctly identified 71.4% of these cases. This study marks a promising step toward utilizing multi-modal LLMs to enhance diagnostic accuracy in radiology. The ensemble model demonstrated comparable performance to clinicians, even capturing errors overlooked by humans. Nevertheless, future work is needed to improve the model ability to identify the types of inconsistency.

Traditional applications of natural language processing (NLP) in healthcare have predominantly focused on patient-centered services, enhancing patient interactions and care delivery, such as through medical dialogue systems. However, the potential of NLP to benefit inexperienced doctors, particularly in areas such as communicative medical coaching, remains largely unexplored. We introduce ``ChatCoach,'' an integrated human-AI cooperative framework. Within this framework, both a patient agent and a coaching agent collaboratively support medical learners in practicing their medical communication skills during consultations. Unlike traditional dialogue systems, ChatCoach provides a simulated environment where a human doctor can engage in medical dialogue with a patient agent. Simultaneously, a coaching agent provides real-time feedback to the doctor. To construct the ChatCoach system, we developed a dataset and integrated Large Language Models such as ChatGPT and Llama2, aiming to assess their effectiveness in communicative medical coaching tasks. Our comparative analysis demonstrates that instruction-tuned Llama2 significantly outperforms ChatGPT's prompting-based approaches.

Pathology diagnosis based on EEG signals and decoding brain activity holds immense importance in understanding neurological disorders. With the advancement of artificial intelligence methods and machine learning techniques, the potential for accurate data-driven diagnoses and effective treatments has grown significantly. However, applying machine learning algorithms to real-world datasets presents diverse challenges at multiple levels. The scarcity of labelled data, especially in low regime scenarios with limited availability of real patient cohorts due to high costs of recruitment, underscores the vital deployment of scaling and transfer learning techniques. In this study, we explore a real-world pathology classification task to highlight the effectiveness of data and model scaling and cross-dataset knowledge transfer. As such, we observe varying performance improvements through data scaling, indicating the need for careful evaluation and labelling. Additionally, we identify the challenges of possible negative transfer and emphasize the significance of some key components to overcome distribution shifts and potential spurious correlations and achieve positive transfer. We see improvement in the performance of the target model on the target (NMT) datasets by using the knowledge from the source dataset (TUAB) when a low amount of labelled data was available. Our findings indicate a small and generic model (e.g. ShallowNet) performs well on a single dataset, however, a larger model (e.g. TCN) performs better on transfer and learning from a larger and diverse dataset.

The drive toward automating cellular network operations has grown with the increasing complexity of these systems. Despite advancements, full autonomy currently remains out of reach due to reliance on human intervention for modeling network behaviors and defining policies to meet target requirements. Network Digital Twins (NDTs) have shown promise in enhancing network intelligence, but the successful implementation of this technology is constrained by use case-specific architectures, limiting its role in advancing network autonomy. A more capable network intelligence, or "telecommunications brain", is needed to enable seamless, autonomous management of cellular network. Large Language Models (LLMs) have emerged as potential enablers for this vision but face challenges in network modeling, especially in reasoning and handling diverse data types. To address these gaps, we introduce Hermes, a chain of LLM agents that uses "blueprints" for constructing NDT instances through structured and explainable logical steps. Hermes allows automatic, reliable, and accurate network modeling of diverse use cases and configurations, thus marking progress toward fully autonomous network operations.

The ability to automatically detect and track surgical instruments in endoscopic videos can enable transformational interventions. Assessing surgical performance and efficiency, identifying skilled tool use and choreography, and planning operational and logistical aspects of OR resources are just a few of the applications that could benefit. Unfortunately, obtaining the annotations needed to train machine learning models to identify and localize surgical tools is a difficult task. Annotating bounding boxes frame-by-frame is tedious and time-consuming, yet large amounts of data with a wide variety of surgical tools and surgeries must be captured for robust training. Moreover, ongoing annotator training is needed to stay up to date with surgical instrument innovation. In robotic-assisted surgery, however, potentially informative data like timestamps of instrument installation and removal can be programmatically harvested. The ability to rely on tool installation data alone would significantly reduce the workload to train robust tool-tracking models. With this motivation in mind we invited the surgical data science community to participate in the challenge, SurgToolLoc 2022. The goal was to leverage tool presence data as weak labels for machine learning models trained to detect tools and localize them in video frames with bounding boxes. We present the results of this challenge along with many of the team's efforts. We conclude by discussing these results in the broader context of machine learning and surgical data science. The training data used for this challenge consisting of 24,695 video clips with tool presence labels is also being released publicly and can be accessed at https://console.cloud.google.com/storage/browser/isi-surgtoolloc-2022.

The development of AI-driven generative audio mirrors broader AI trends, often prioritizing immediate accessibility at the expense of explainability. Consequently, integrating such tools into sustained artistic practice remains a significant challenge. In this paper, we explore several paths to improve explainability, drawing primarily from our research-creation practice in training and implementing generative audio models. As practical provisions for improved explainability, we highlight human agency over training materials, the viability of small-scale datasets, the facilitation of the iterative creative process, and the integration of interactive machine learning as a mapping tool. Importantly, these steps aim to enhance human agency over generative AI systems not only during model inference, but also when curating and preprocessing training data as well as during the training phase of models.

With the rapid advance of computer graphics and artificial intelligence technologies, the ways we interact with the world have undergone a transformative shift. Virtual Reality (VR) technology, aided by artificial intelligence (AI), has emerged as a dominant interaction media in multiple application areas, thanks to its advantage of providing users with immersive experiences. Among those applications, medicine is considered one of the most promising areas. In this paper, we present a comprehensive examination of the burgeoning field of AI-enhanced VR applications in medical care and services. By introducing a systematic taxonomy, we meticulously classify the pertinent techniques and applications into three well-defined categories based on different phases of medical diagnosis and treatment: Visualization Enhancement, VR-related Medical Data Processing, and VR-assisted Intervention. This categorization enables a structured exploration of the diverse roles that AI-powered VR plays in the medical domain, providing a framework for a more comprehensive understanding and evaluation of these technologies. To our best knowledge, this is the first systematic survey of AI-powered VR systems in medical settings, laying a foundation for future research in this interdisciplinary domain.

Artificial Intelligence (AI) advancement is heavily dependent on access to large-scale, high-quality training data. However, in specialized domains such as healthcare, data acquisition faces significant constraints due to privacy regulations, ethical considerations, and limited availability. While synthetic data generation offers a promising solution, conventional approaches typically require substantial real data for training generative models. The emergence of large-scale prompt-based models presents new opportunities for synthetic data generation without direct access to protected data. However, crafting effective prompts for domain-specific data generation remains challenging, and manual prompt engineering proves insufficient for achieving output with sufficient precision and authenticity. We review recent developments in automatic prompt optimization, following PRISMA guidelines. We analyze six peer-reviewed studies published between 2020 and 2024 that focus on automatic data-free prompt optimization methods. Our analysis reveals three approaches: feedback-driven, error-based, and control-theoretic. Although all approaches demonstrate promising capabilities in prompt refinement and adaptation, our findings suggest the need for an integrated framework that combines complementary optimization techniques to enhance synthetic data generation while minimizing manual intervention. We propose future research directions toward developing robust, iterative prompt optimization frameworks capable of improving the quality of synthetic data. This advancement can be particularly crucial for sensitive fields and in specialized domains where data access is restricted, potentially transforming how we approach synthetic data generation for AI development.

The usage of generative artificial intelligence (AI) tools based on large language models, including ChatGPT, Bard, and Claude, for text generation has many exciting applications with the potential for phenomenal productivity gains. One issue is authorship attribution when using AI tools. This is especially important in an academic setting where the inappropriate use of generative AI tools may hinder student learning or stifle research by creating a large amount of automatically generated derivative work. Existing plagiarism detection systems can trace the source of submitted text but are not yet equipped with methods to accurately detect AI-generated text. This paper introduces the idea of direct origin detection and evaluates whether generative AI systems can recognize their output and distinguish it from human-written texts. We argue why current transformer-based models may be able to self-detect their own generated text and perform a small empirical study using zero-shot learning to investigate if that is the case. Results reveal varying capabilities of AI systems to identify their generated text. Google's Bard model exhibits the largest capability of self-detection with an accuracy of 94\%, followed by OpenAI's ChatGPT with 83\%. On the other hand, Anthropic's Claude model seems to be not able to self-detect.

The rapid evolution of artificial intelligence, especially in large language models (LLMs), has significantly impacted various domains, including healthcare. In chest X-ray (CXR) analysis, previous studies have employed LLMs, but with limitations: either underutilizing the multi-tasking capabilities of LLMs or lacking clinical accuracy. This paper presents M4CXR, a multi-modal LLM designed to enhance CXR interpretation. The model is trained on a visual instruction-following dataset that integrates various task-specific datasets in a conversational format. As a result, the model supports multiple tasks such as medical report generation (MRG), visual grounding, and visual question answering (VQA). M4CXR achieves state-of-the-art clinical accuracy in MRG by employing a chain-of-thought prompting strategy, in which it identifies findings in CXR images and subsequently generates corresponding reports. The model is adaptable to various MRG scenarios depending on the available inputs, such as single-image, multi-image, and multi-study contexts. In addition to MRG, M4CXR performs visual grounding at a level comparable to specialized models and also demonstrates outstanding performance in VQA. Both quantitative and qualitative assessments reveal M4CXR's versatility in MRG, visual grounding, and VQA, while consistently maintaining clinical accuracy.

As opposed to evaluating computation and logic-based reasoning, current benchmarks for evaluating large language models (LLMs) in medicine are primarily focused on question-answering involving domain knowledge and descriptive reasoning. While such qualitative capabilities are vital to medical diagnosis, in real-world scenarios, doctors frequently use clinical calculators that follow quantitative equations and rule-based reasoning paradigms for evidence-based decision support. To this end, we propose MedCalc-Bench, a first-of-its-kind dataset focused on evaluating the medical calculation capability of LLMs. MedCalc-Bench contains an evaluation set of over 1000 manually reviewed instances from 55 different medical calculation tasks. Each instance in MedCalc-Bench consists of a patient note, a question requesting to compute a specific medical value, a ground truth answer, and a step-by-step explanation showing how the answer is obtained. While our evaluation results show the potential of LLMs in this area, none of them are effective enough for clinical settings. Common issues include extracting the incorrect entities, not using the correct equation or rules for a calculation task, or incorrectly performing the arithmetic for the computation. We hope our study highlights the quantitative knowledge and reasoning gaps in LLMs within medical settings, encouraging future improvements of LLMs for various clinical calculation tasks.

The gigapixel scale of whole slide images (WSIs) poses a challenge for histopathology multi-modal chatbots, requiring a global WSI analysis for diagnosis, compounding evidence from different WSI patches. Current visual instruction datasets, generated through large language models, focus on creating question/answer pairs for individual image patches, which may lack diagnostic capacity on their own in histopathology, further complicated by the absence of spatial grounding in histopathology image captions. To bridge this gap, we introduce Quilt-Instruct, a large-scale dataset of 107,131 histopathology-specific instruction question/answer pairs, that is collected by leveraging educational histopathology videos from YouTube, which provides spatial localization of captions by automatically extracting narrators' cursor movements. In addition, we provide contextual reasoning by extracting diagnosis and supporting facts from the entire video content to guide the extrapolative reasoning of GPT-4. Using Quilt-Instruct, we train Quilt-LLaVA, which can reason beyond the given single image patch, enabling diagnostic reasoning and the capability of spatial awareness. To evaluate Quilt-LLaVA, we propose a comprehensive evaluation dataset created from 985 images and 1283 human-generated question-answers. We also thoroughly evaluate Quilt-LLaVA using public histopathology datasets, where Quilt-LLaVA significantly outperforms SOTA by over 10% on relative GPT-4 score and 4% and 9% on open and closed set VQA. Our code, data, and model are publicly available at quilt-llava.github.io.

This study aims to explore the implementation of Natural Language Processing (NLP) and machine learning (ML) techniques to automate the coding of medical letters with visualised explainability and light-weighted local computer settings. Currently in clinical settings, coding is a manual process that involves assigning codes to each condition, procedure, and medication in a patient's paperwork (e.g., 56265001 heart disease using SNOMED CT code). There are preliminary research on automatic coding in this field using state-of-the-art ML models; however, due to the complexity and size of the models, the real-world deployment is not achieved. To further facilitate the possibility of automatic coding practice, we explore some solutions in a local computer setting; in addition, we explore the function of explainability for transparency of AI models. We used the publicly available MIMIC-III database and the HAN/HLAN network models for ICD code prediction purposes. We also experimented with the mapping between ICD and SNOMED CT knowledge bases. In our experiments, the models provided useful information for 97.98\% of codes. The result of this investigation can shed some light on implementing automatic clinical coding in practice, such as in hospital settings, on the local computers used by clinicians , project page https://github.com/Glenj01/Medical-Coding.

In this review, we explore the potential applications of Artificial General Intelligence (AGI) models in healthcare, focusing on foundational Large Language Models (LLMs), Large Vision Models, and Large Multimodal Models. We emphasize the importance of integrating clinical expertise, domain knowledge, and multimodal capabilities into AGI models. In addition, we lay out key roadmaps that guide the development and deployment of healthcare AGI models. Throughout the review, we provide critical perspectives on the potential challenges and pitfalls associated with deploying large-scale AGI models in the medical field. This comprehensive review aims to offer insights into the future implications of AGI in medical imaging, healthcare and beyond.

International Classification of Disease (ICD) coding procedure which refers to tagging medical notes with diagnosis codes has been shown to be effective and crucial to the billing system in medical sector. Currently, ICD codes are assigned to a clinical note manually which is likely to cause many errors. Moreover, training skilled coders also requires time and human resources. Therefore, automating the ICD code determination process is an important task. With the advancement of artificial intelligence theory and computational hardware, machine learning approach has emerged as a suitable solution to automate this process. In this project, we apply a transformer-based architecture to capture the interdependence among the tokens of a document and then use a code-wise attention mechanism to learn code-specific representations of the entire document. Finally, they are fed to separate dense layers for corresponding code prediction. Furthermore, to handle the imbalance in the code frequency of clinical datasets, we employ a label distribution aware margin (LDAM) loss function. The experimental results on the MIMIC-III dataset show that our proposed model outperforms other baselines by a significant margin. In particular, our best setting achieves a micro-AUC score of 0.923 compared to 0.868 of bidirectional recurrent neural networks. We also show that by using the code-wise attention mechanism, the model can provide more insights about its prediction, and thus it can support clinicians to make reliable decisions. Our code is available online (https://github.com/biplob1ly/TransICD)

We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy, it is biology at work. Biology in the physical world is too complex to manipulate and always expensive and risky to tamper with. In this perspective, we layout an engineering viable approach to address this challenge by constructing an AI-Driven Digital Organism (AIDO), a system of integrated multiscale foundation models, in a modular, connectable, and holistic fashion to reflect biological scales, connectedness, and complexities. An AIDO opens up a safe, affordable and high-throughput alternative platform for predicting, simulating and programming biology at all levels from molecules to cells to individuals. We envision that an AIDO is poised to trigger a new wave of better-guided wet-lab experimentation and better-informed first-principle reasoning, which can eventually help us better decode and improve life.

Predicting in-hospital mortality for intensive care unit (ICU) patients is key to final clinical outcomes. AI has shown advantaged accuracy but suffers from the lack of explainability. To address this issue, this paper proposes an eXplainable Multimodal Mortality Predictor (X-MMP) approaching an efficient, explainable AI solution for predicting in-hospital mortality via multimodal ICU data. We employ multimodal learning in our framework, which can receive heterogeneous inputs from clinical data and make decisions. Furthermore, we introduce an explainable method, namely Layer-Wise Propagation to Transformer, as a proper extension of the LRP method to Transformers, producing explanations over multimodal inputs and revealing the salient features attributed to prediction. Moreover, the contribution of each modality to clinical outcomes can be visualized, assisting clinicians in understanding the reasoning behind decision-making. We construct a multimodal dataset based on MIMIC-III and MIMIC-III Waveform Database Matched Subset. Comprehensive experiments on benchmark datasets demonstrate that our proposed framework can achieve reasonable interpretation with competitive prediction accuracy. In particular, our framework can be easily transferred to other clinical tasks, which facilitates the discovery of crucial factors in healthcare research.

Large Language Models (LLMs) have demonstrated significant progress in utilizing external APIs as tools for various tasks. However, their tool-using ability is limited by the availability of suitable APIs and the instability of implicit reasoning, particularly when simultaneously engaging in reasoning about plans and actual calculations. To address these limitations, we propose CREATOR, a novel framework that empowers LLMs to create their own tools through documentation and code realization. CREATOR disentangles the LLM's ability into two distinct phases: abstract tool creation and concrete decision execution, which results in improved LLM performance. We evaluate CREATOR on two established benchmarks: MATH, which consists of challenging math competition problems, and TabMWP, which includes diverse tabular contents for problem-solving. Remarkably, CREATOR significantly outperforms existing chain-of-thought (CoT), program-of-thought (PoT), and tool-using baselines on these two benchmarks. Additionally, we present a new dataset, Creation Challenge, comprising 2K diverse questions, to highlight the necessity and benefits of LLMs' tool creation ability in effectively addressing these problems. Furthermore, our research reveals that leveraging LLMs as tool creators facilitates knowledge transfer, and LLMs exhibit varying levels of tool creation abilities, enabling them to flexibly tackle diverse situations. Our study represents a promising avenue for maximizing the potential of LLMs and advancing toward truly intelligent and adaptable AI systems.

AI agents are systems capable of perceiving their environment, autonomously planning and executing tasks. Recent advancements in LLM have introduced a transformative paradigm for AI agents, enabling them to interact with external resources and tools through prompts. In such agents, the workflow integrates developer-written code, which manages framework construction and logic control, with LLM-generated natural language that enhances dynamic decision-making and interaction. However, discrepancies between developer-implemented logic and the dynamically generated content of LLMs in terms of behavior and expected outcomes can lead to defects, such as tool invocation failures and task execution errors. These issues introduce specific risks, leading to various defects in LLM-based AI Agents, such as service interruptions. Despite the importance of these issues, there is a lack of systematic work that focuses on analyzing LLM-based AI Agents to uncover defects in their code. In this paper, we present the first study focused on identifying and detecting defects in LLM Agents. We collected and analyzed 6,854 relevant posts from StackOverflow to define 8 types of agent defects. For each type, we provided detailed descriptions with an example. Then, we designed a static analysis tool, named Agentable, to detect the defects. Agentable leverages Code Property Graphs and LLMs to analyze Agent workflows by efficiently identifying specific code patterns and analyzing natural language descriptions. To evaluate Agentable, we constructed two datasets: AgentSet, consists of 84 real-world Agents, and AgentTest, which contains 78 Agents specifically designed to include various types of defects. Our results show that Agentable achieved an overall accuracy of 88.79% and a recall rate of 91.03%. Furthermore, our analysis reveals the 889 defects of the AgentSet, highlighting the prevalence of these defects.

Large language models (LLMs) have shown promising capabilities in using external tools to solve complex problems. However, existing approaches either involve fine-tuning on tool demonstrations, which do not generalize to new tools without additional training, or providing tool documentation in context, limiting the number of tools. Both approaches often generate syntactically invalid tool calls. In this paper, we propose ToolDec, a finite-state machine-guided decoding algorithm for tool-augmented LLMs. ToolDec eliminates tool-related errors for any tool-augmented LLMs by ensuring valid tool names and type-conforming arguments. Furthermore, ToolDec enables LLM to effectively select tools using only the information contained in their names, with no need for fine-tuning or in-context documentation. We evaluated multiple prior methods and their ToolDec-enhanced versions on a variety of tasks involving tools like math functions, knowledge graph relations, and complex real-world RESTful APIs. Our experiments show that ToolDec reduces syntactic errors to zero, consequently achieving significantly better performance and as much as a 2x speedup. We also show that ToolDec achieves superior generalization performance on unseen tools, performing up to 8x better than the baselines.

The emergence of large-scale multi-modal generative models has drastically advanced artificial intelligence, introducing unprecedented levels of performance and functionality. However, optimizing these models remains challenging due to historically isolated paths of model-centric and data-centric developments, leading to suboptimal outcomes and inefficient resource utilization. In response, we present a novel sandbox suite tailored for integrated data-model co-development. This sandbox provides a comprehensive experimental platform, enabling rapid iteration and insight-driven refinement of both data and models. Our proposed "Probe-Analyze-Refine" workflow, validated through applications on state-of-the-art LLaVA-like and DiT based models, yields significant performance boosts, such as topping the VBench leaderboard. We also uncover fruitful insights gleaned from exhaustive benchmarks, shedding light on the critical interplay between data quality, diversity, and model behavior. With the hope of fostering deeper understanding and future progress in multi-modal data and generative modeling, our codes, datasets, and models are maintained and accessible at https://github.com/modelscope/data-juicer/blob/main/docs/Sandbox.md.

AI-based design tools are proliferating in professional software to assist engineering and industrial designers in complex manufacturing and design tasks. These tools take on more agentic roles than traditional computer-aided design tools and are often portrayed as "co-creators." Yet, working effectively with such systems requires different skills than working with complex CAD tools alone. To date, we know little about how engineering designers learn to work with AI-based design tools. In this study, we observed trained designers as they learned to work with two AI-based tools on a realistic design task. We find that designers face many challenges in learning to effectively co-create with current systems, including challenges in understanding and adjusting AI outputs and in communicating their design goals. Based on our findings, we highlight several design opportunities to better support designer-AI co-creation.

The current literature on AI-advised decision making -- involving explainable AI systems advising human decision makers -- presents a series of inconclusive and confounding results. To synthesize these findings, we propose a simple theory that elucidates the frequent failure of AI explanations to engender appropriate reliance and complementary decision making performance. We argue explanations are only useful to the extent that they allow a human decision maker to verify the correctness of an AI's prediction, in contrast to other desiderata, e.g., interpretability or spelling out the AI's reasoning process. Prior studies find in many decision making contexts AI explanations do not facilitate such verification. Moreover, most tasks fundamentally do not allow easy verification, regardless of explanation method, limiting the potential benefit of any type of explanation. We also compare the objective of complementary performance with that of appropriate reliance, decomposing the latter into the notions of outcome-graded and strategy-graded reliance.

Recent advancements in artificial intelligence have sparked interest in scientific assistants that could support researchers across the full spectrum of scientific workflows, from literature review to experimental design and data analysis. A key capability for such systems is the ability to process and reason about scientific information in both visual and textual forms - from interpreting spectroscopic data to understanding laboratory setups. Here, we introduce MaCBench, a comprehensive benchmark for evaluating how vision-language models handle real-world chemistry and materials science tasks across three core aspects: data extraction, experimental understanding, and results interpretation. Through a systematic evaluation of leading models, we find that while these systems show promising capabilities in basic perception tasks - achieving near-perfect performance in equipment identification and standardized data extraction - they exhibit fundamental limitations in spatial reasoning, cross-modal information synthesis, and multi-step logical inference. Our insights have important implications beyond chemistry and materials science, suggesting that developing reliable multimodal AI scientific assistants may require advances in curating suitable training data and approaches to training those models.

In order to fully harness the potential of machine learning, it is crucial to establish a system that renders the field more accessible and less daunting for individuals who may not possess a comprehensive understanding of its intricacies. The paper describes the design of a system that integrates AutoML, XAI, and synthetic data generation to provide a great UX design for users. The system allows users to navigate and harness the power of machine learning while abstracting its complexities and providing high usability. The paper proposes two novel classifiers, Logistic Regression Forest and Support Vector Tree, for enhanced model performance, achieving 96\% accuracy on a diabetes dataset and 93\% on a survey dataset. The paper also introduces a model-dependent local interpreter called MEDLEY and evaluates its interpretation against LIME, Greedy, and Parzen. Additionally, the paper introduces LLM-based synthetic data generation, library-based data generation, and enhancing the original dataset with GAN. The findings on synthetic data suggest that enhancing the original dataset with GAN is the most reliable way to generate synthetic data, as evidenced by KS tests, standard deviation, and feature importance. The authors also found that GAN works best for quantitative datasets.

Recent research on Large Language Models (LLMs) has led to remarkable advancements in general NLP AI assistants. Some studies have further explored the use of LLMs for planning and invoking models or APIs to address more general multi-modal user queries. Despite this progress, complex visual-based tasks still remain challenging due to the diverse nature of visual tasks. This diversity is reflected in two aspects: 1) Reasoning paths. For many real-life applications, it is hard to accurately decompose a query simply by examining the query itself. Planning based on the specific visual content and the results of each step is usually required. 2) Flexible inputs and intermediate results. Input forms could be flexible for in-the-wild cases, and involves not only a single image or video but a mixture of videos and images, e.g., a user-view image with some reference videos. Besides, a complex reasoning process will also generate diverse multimodal intermediate results, e.g., video narrations, segmented video clips, etc. To address such general cases, we propose a multi-modal AI assistant, AssistGPT, with an interleaved code and language reasoning approach called Plan, Execute, Inspect, and Learn (PEIL) to integrate LLMs with various tools. Specifically, the Planner is capable of using natural language to plan which tool in Executor should do next based on the current reasoning progress. Inspector is an efficient memory manager to assist the Planner to feed proper visual information into a specific tool. Finally, since the entire reasoning process is complex and flexible, a Learner is designed to enable the model to autonomously explore and discover the optimal solution. We conducted experiments on A-OKVQA and NExT-QA benchmarks, achieving state-of-the-art results. Moreover, showcases demonstrate the ability of our system to handle questions far more complex than those found in the benchmarks.

The rapid advancement of large language models (LLMs) has significantly impacted various domains, including healthcare and biomedicine. However, the phenomenon of hallucination, where LLMs generate outputs that deviate from factual accuracy or context, poses a critical challenge, especially in high-stakes domains. This paper conducts a scoping study of existing techniques for mitigating hallucinations in knowledge-based task in general and especially for medical domains. Key methods covered in the paper include Retrieval-Augmented Generation (RAG)-based techniques, iterative feedback loops, supervised fine-tuning, and prompt engineering. These techniques, while promising in general contexts, require further adaptation and optimization for the medical domain due to its unique demands for up-to-date, specialized knowledge and strict adherence to medical guidelines. Addressing these challenges is crucial for developing trustworthy AI systems that enhance clinical decision-making and patient safety as well as accuracy of biomedical scientific research.

Extraction of relevant pathological terms from radiology reports is important for correct image label generation and disease population studies. In this letter, we compare the performance of some known application program interface (APIs) for the task of thoracic abnormality extraction from radiology reports. We explored several medical domain specific annotation tools like Medical Text Indexer(MTI) with Non-MEDLINE and Mesh On Demand(MOD) options and generic Natural Language Understanding (NLU) API provided by the IBM cloud. Our results show that although MTI and MOD are intended for extracting medical terms, their performance is worst compared to generic extraction API like IBM NLU. Finally, we trained a DNN-based Named Entity Recognition (NER) model to extract the key concept words from radiology reports. Our model outperforms the medical specific and generic API performance by a large margin. Our results demonstrate the inadequacy of generic APIs for pathology extraction task and establish the importance of domain specific model training for improved results. We hope that these results motivate the research community to release larger de-identified radiology reports corpus for building high accuracy machine learning models for the important task of pathology extraction.

This paper introduces MedTrinity-25M, a comprehensive, large-scale multimodal dataset for medicine, covering over 25 million images across 10 modalities, with multigranular annotations for more than 65 diseases. These enriched annotations encompass both global textual information, such as disease/lesion type, modality, region-specific descriptions, and inter-regional relationships, as well as detailed local annotations for regions of interest (ROIs), including bounding boxes, segmentation masks. Unlike existing approach which is limited by the availability of image-text pairs, we have developed the first automated pipeline that scales up multimodal data by generating multigranular visual and texual annotations (in the form of image-ROI-description triplets) without the need for any paired text descriptions. Specifically, data from over 90 different sources have been collected, preprocessed, and grounded using domain-specific expert models to identify ROIs related to abnormal regions. We then build a comprehensive knowledge base and prompt multimodal large language models to perform retrieval-augmented generation with the identified ROIs as guidance, resulting in multigranular texual descriptions. Compared to existing datasets, MedTrinity-25M provides the most enriched annotations, supporting a comprehensive range of multimodal tasks such as captioning and report generation, as well as vision-centric tasks like classification and segmentation. Pretraining on MedTrinity-25M, our model achieves state-of-the-art performance on VQA-RAD and PathVQA, surpassing both multimodal large language models and other representative SoTA approaches. This dataset can also be utilized to support large-scale pre-training of multimodal medical AI models, contributing to the development of future foundation models in the medical domain.

Humans prove theorems by relying on substantial high-level reasoning and problem-specific insights. Proof assistants offer a formalism that resembles human mathematical reasoning, representing theorems in higher-order logic and proofs as high-level tactics. However, human experts have to construct proofs manually by entering tactics into the proof assistant. In this paper, we study the problem of using machine learning to automate the interaction with proof assistants. We construct CoqGym, a large-scale dataset and learning environment containing 71K human-written proofs from 123 projects developed with the Coq proof assistant. We develop ASTactic, a deep learning-based model that generates tactics as programs in the form of abstract syntax trees (ASTs). Experiments show that ASTactic trained on CoqGym can generate effective tactics and can be used to prove new theorems not previously provable by automated methods. Code is available at https://github.com/princeton-vl/CoqGym.

Tool use has turned large language models (LLMs) into powerful agents that can perform complex multi-step tasks by dynamically utilising external software components. However, these tools must be implemented in advance by human developers, hindering the applicability of LLM agents in domains which demand large numbers of highly specialised tools, like in life sciences and medicine. Motivated by the growing trend of scientific studies accompanied by public code repositories, we propose ToolMaker, a novel agentic framework that autonomously transforms papers with code into LLM-compatible tools. Given a short task description and a repository URL, ToolMaker autonomously installs required dependencies and generates code to perform the task, using a closed-loop self-correction mechanism to iteratively diagnose and rectify errors. To evaluate our approach, we introduce a benchmark comprising 15 diverse and complex computational tasks spanning both medical and non-medical domains with over 100 unit tests to objectively assess tool correctness and robustness. ToolMaker correctly implements 80% of the tasks, substantially outperforming current state-of-the-art software engineering agents. ToolMaker therefore is a step towards fully autonomous agent-based scientific workflows.

The utilization of large language models (LLMs) in the Healthcare domain has generated both excitement and concern due to their ability to effectively respond to freetext queries with certain professional knowledge. This survey outlines the capabilities of the currently developed LLMs for Healthcare and explicates their development process, with the aim of providing an overview of the development roadmap from traditional Pretrained Language Models (PLMs) to LLMs. Specifically, we first explore the potential of LLMs to enhance the efficiency and effectiveness of various Healthcare applications highlighting both the strengths and limitations. Secondly, we conduct a comparison between the previous PLMs and the latest LLMs, as well as comparing various LLMs with each other. Then we summarize related Healthcare training data, training methods, optimization strategies, and usage. Finally, the unique concerns associated with deploying LLMs in Healthcare settings are investigated, particularly regarding fairness, accountability, transparency and ethics. Our survey provide a comprehensive investigation from perspectives of both computer science and Healthcare specialty. Besides the discussion about Healthcare concerns, we supports the computer science community by compiling a collection of open source resources, such as accessible datasets, the latest methodologies, code implementations, and evaluation benchmarks in the Github. Summarily, we contend that a significant paradigm shift is underway, transitioning from PLMs to LLMs. This shift encompasses a move from discriminative AI approaches to generative AI approaches, as well as a shift from model-centered methodologies to datacentered methodologies.

Large language models (LLMs) can perform complex reasoning in few- and zero-shot settings by generating intermediate chain of thought (CoT) reasoning steps. Further, each reasoning step can rely on external tools to support computation beyond the core LLM capabilities (e.g. search/running code). Prior work on CoT prompting and tool use typically requires hand-crafting task-specific demonstrations and carefully scripted interleaving of model generations with tool use. We introduce Automatic Reasoning and Tool-use (ART), a framework that uses frozen LLMs to automatically generate intermediate reasoning steps as a program. Given a new task to solve, ART selects demonstrations of multi-step reasoning and tool use from a task library. At test time, ART seamlessly pauses generation whenever external tools are called, and integrates their output before resuming generation. ART achieves a substantial improvement over few-shot prompting and automatic CoT on unseen tasks in the BigBench and MMLU benchmarks, and matches performance of hand-crafted CoT prompts on a majority of these tasks. ART is also extensible, and makes it easy for humans to improve performance by correcting errors in task-specific programs or incorporating new tools, which we demonstrate by drastically improving performance on select tasks with minimal human intervention.

With the rise of prolific ChatGPT, the risk and consequences of AI-generated text has increased alarmingly. To address the inevitable question of ownership attribution for AI-generated artifacts, the US Copyright Office released a statement stating that 'If a work's traditional elements of authorship were produced by a machine, the work lacks human authorship and the Office will not register it'. Furthermore, both the US and the EU governments have recently drafted their initial proposals regarding the regulatory framework for AI. Given this cynosural spotlight on generative AI, AI-generated text detection (AGTD) has emerged as a topic that has already received immediate attention in research, with some initial methods having been proposed, soon followed by emergence of techniques to bypass detection. This paper introduces the Counter Turing Test (CT^2), a benchmark consisting of techniques aiming to offer a comprehensive evaluation of the robustness of existing AGTD techniques. Our empirical findings unequivocally highlight the fragility of the proposed AGTD methods under scrutiny. Amidst the extensive deliberations on policy-making for regulating AI development, it is of utmost importance to assess the detectability of content generated by LLMs. Thus, to establish a quantifiable spectrum facilitating the evaluation and ranking of LLMs according to their detectability levels, we propose the AI Detectability Index (ADI). We conduct a thorough examination of 15 contemporary LLMs, empirically demonstrating that larger LLMs tend to have a higher ADI, indicating they are less detectable compared to smaller LLMs. We firmly believe that ADI holds significant value as a tool for the wider NLP community, with the potential to serve as a rubric in AI-related policy-making.

This paper introduces a novel, entity-aware metric, termed as Radiological Report (Text) Evaluation (RaTEScore), to assess the quality of medical reports generated by AI models. RaTEScore emphasizes crucial medical entities such as diagnostic outcomes and anatomical details, and is robust against complex medical synonyms and sensitive to negation expressions. Technically, we developed a comprehensive medical NER dataset, RaTE-NER, and trained an NER model specifically for this purpose. This model enables the decomposition of complex radiological reports into constituent medical entities. The metric itself is derived by comparing the similarity of entity embeddings, obtained from a language model, based on their types and relevance to clinical significance. Our evaluations demonstrate that RaTEScore aligns more closely with human preference than existing metrics, validated both on established public benchmarks and our newly proposed RaTE-Eval benchmark.

Large Multimodal Models (LMMs) have shown remarkable progress in the field of medical Visual Question Answering (Med-VQA), achieving high accuracy on existing benchmarks. However, their reliability under robust evaluation is questionable. This study reveals that state-of-the-art models, when subjected to simple probing evaluation, perform worse than random guessing on medical diagnosis questions. To address this critical evaluation problem, we introduce the Probing Evaluation for Medical Diagnosis (ProbMed) dataset to rigorously assess LMM performance in medical imaging through probing evaluation and procedural diagnosis. Particularly, probing evaluation features pairing original questions with negation questions with hallucinated attributes, while procedural diagnosis requires reasoning across various diagnostic dimensions for each image, including modality recognition, organ identification, clinical findings, abnormalities, and positional grounding. Our evaluation reveals that top-performing models like GPT-4V and Gemini Pro perform worse than random guessing on specialized diagnostic questions, indicating significant limitations in handling fine-grained medical inquiries. Besides, models like LLaVA-Med struggle even with more general questions, and results from CheXagent demonstrate the transferability of expertise across different modalities of the same organ, showing that specialized domain knowledge is still crucial for improving performance. This study underscores the urgent need for more robust evaluation to ensure the reliability of LMMs in critical fields like medical diagnosis, and current LMMs are still far from applicable to those fields.

We propose CAD-Assistant, a general-purpose CAD agent for AI-assisted design. Our approach is based on a powerful Vision and Large Language Model (VLLM) as a planner and a tool-augmentation paradigm using CAD-specific modules. CAD-Assistant addresses multimodal user queries by generating actions that are iteratively executed on a Python interpreter equipped with the FreeCAD software, accessed via its Python API. Our framework is able to assess the impact of generated CAD commands on geometry and adapts subsequent actions based on the evolving state of the CAD design. We consider a wide range of CAD-specific tools including Python libraries, modules of the FreeCAD Python API, helpful routines, rendering functions and other specialized modules. We evaluate our method on multiple CAD benchmarks and qualitatively demonstrate the potential of tool-augmented VLLMs as generic CAD task solvers across diverse CAD workflows.

In this work, we provide a comprehensive survey of AI music generation tools, including both research projects and commercialized applications. To conduct our analysis, we classified music generation approaches into three categories: parameter-based, text-based, and visual-based classes. Our survey highlights the diverse possibilities and functional features of these tools, which cater to a wide range of users, from regular listeners to professional musicians. We observed that each tool has its own set of advantages and limitations. As a result, we have compiled a comprehensive list of these factors that should be considered during the tool selection process. Moreover, our survey offers critical insights into the underlying mechanisms and challenges of AI music generation.

The electrocardiogram (ECG) remains a fundamental tool in cardiac diagnostics, yet its interpretation traditionally reliant on the expertise of cardiologists. The emergence of deep learning has heralded a revolutionary era in medical data analysis, particularly in the domain of ECG diagnostics. However, inter-patient variability prohibit the generalibility of ECG-AI model trained on a population dataset, hence degrade the performance of ECG-AI on specific patient or patient group. Many studies have address this challenge using different deep learning technologies. This comprehensive review systematically synthesizes research from a wide range of studies to provide an in-depth examination of cutting-edge deep-learning techniques in personalized ECG diagnosis. The review outlines a rigorous methodology for the selection of pertinent scholarly articles and offers a comprehensive overview of deep learning approaches applied to personalized ECG diagnostics. Moreover, the challenges these methods encounter are investigated, along with future research directions, culminating in insights into how the integration of deep learning can transform personalized ECG diagnosis and enhance cardiac care. By emphasizing both the strengths and limitations of current methodologies, this review underscores the immense potential of deep learning to refine and redefine ECG analysis in clinical practice, paving the way for more accurate, efficient, and personalized cardiac diagnostics.

We introduce tulip agent, an architecture for autonomous LLM-based agents with Create, Read, Update, and Delete access to a tool library containing a potentially large number of tools. In contrast to state-of-the-art implementations, tulip agent does not encode the descriptions of all available tools in the system prompt, which counts against the model's context window, or embed the entire prompt for retrieving suitable tools. Instead, the tulip agent can recursively search for suitable tools in its extensible tool library, implemented exemplarily as a vector store. The tulip agent architecture significantly reduces inference costs, allows using even large tool libraries, and enables the agent to adapt and extend its set of tools. We evaluate the architecture with several ablation studies in a mathematics context and demonstrate its generalizability with an application to robotics. A reference implementation and the benchmark are available at github.com/HRI-EU/tulip_agent.

One of the grand challenges of artificial general intelligence is developing agents capable of conducting scientific research and discovering new knowledge. While frontier models have already been used as aids to human scientists, e.g. for brainstorming ideas, writing code, or prediction tasks, they still conduct only a small part of the scientific process. This paper presents the first comprehensive framework for fully automatic scientific discovery, enabling frontier large language models to perform research independently and communicate their findings. We introduce The AI Scientist, which generates novel research ideas, writes code, executes experiments, visualizes results, describes its findings by writing a full scientific paper, and then runs a simulated review process for evaluation. In principle, this process can be repeated to iteratively develop ideas in an open-ended fashion, acting like the human scientific community. We demonstrate its versatility by applying it to three distinct subfields of machine learning: diffusion modeling, transformer-based language modeling, and learning dynamics. Each idea is implemented and developed into a full paper at a cost of less than $15 per paper. To evaluate the generated papers, we design and validate an automated reviewer, which we show achieves near-human performance in evaluating paper scores. The AI Scientist can produce papers that exceed the acceptance threshold at a top machine learning conference as judged by our automated reviewer. This approach signifies the beginning of a new era in scientific discovery in machine learning: bringing the transformative benefits of AI agents to the entire research process of AI itself, and taking us closer to a world where endless affordable creativity and innovation can be unleashed on the world's most challenging problems. Our code is open-sourced at https://github.com/SakanaAI/AI-Scientist

Deep neural networks are a promising tool for Audio Event Classification. In contrast to other data like natural images, there are many sensible and non-obvious representations for audio data, which could serve as input to these models. Due to their black-box nature, the effect of different input representations has so far mostly been investigated by measuring classification performance. In this work, we leverage eXplainable AI (XAI), to understand the underlying classification strategies of models trained on different input representations. Specifically, we compare two model architectures with regard to relevant input features used for Audio Event Detection: one directly processes the signal as the raw waveform, and the other takes in its time-frequency spectrogram representation. We show how relevance heatmaps obtained via "Siren"{Layer-wise Relevance Propagation} uncover representation-dependent decision strategies. With these insights, we can make a well-informed decision about the best input representation in terms of robustness and representativity and confirm that the model's classification strategies align with human requirements.

Deep learning models for natural language processing (NLP) are increasingly adopted and deployed by analysts without formal training in NLP or machine learning (ML). However, the documentation intended to convey the model's details and appropriate use is tailored primarily to individuals with ML or NLP expertise. To address this gap, we conduct a design inquiry into interactive model cards, which augment traditionally static model cards with affordances for exploring model documentation and interacting with the models themselves. Our investigation consists of an initial conceptual study with experts in ML, NLP, and AI Ethics, followed by a separate evaluative study with non-expert analysts who use ML models in their work. Using a semi-structured interview format coupled with a think-aloud protocol, we collected feedback from a total of 30 participants who engaged with different versions of standard and interactive model cards. Through a thematic analysis of the collected data, we identified several conceptual dimensions that summarize the strengths and limitations of standard and interactive model cards, including: stakeholders; design; guidance; understandability & interpretability; sensemaking & skepticism; and trust & safety. Our findings demonstrate the importance of carefully considered design and interactivity for orienting and supporting non-expert analysts using deep learning models, along with a need for consideration of broader sociotechnical contexts and organizational dynamics. We have also identified design elements, such as language, visual cues, and warnings, among others, that support interactivity and make non-interactive content accessible. We summarize our findings as design guidelines and discuss their implications for a human-centered approach towards AI/ML documentation.

To create rich visualizations, data analysts often need to iterate back and forth among data processing and chart specification to achieve their goals. To achieve this, analysts need not only proficiency in data transformation and visualization tools but also efforts to manage the branching history consisting of many different versions of data and charts. Recent LLM-powered AI systems have greatly improved visualization authoring experiences, for example by mitigating manual data transformation barriers via LLMs' code generation ability. However, these systems do not work well for iterative visualization authoring, because they often require analysts to provide, in a single turn, a text-only prompt that fully describes the complex visualization task to be performed, which is unrealistic to both users and models in many cases. In this paper, we present Data Formulator 2, an LLM-powered visualization system to address these challenges. With Data Formulator 2, users describe their visualization intent with blended UI and natural language inputs, and data transformation are delegated to AI. To support iteration, Data Formulator 2 lets users navigate their iteration history and reuse previous designs towards new ones so that they don't need to start from scratch every time. In a user study with eight participants, we observed that Data Formulator 2 allows participants to develop their own iteration strategies to complete challenging data exploration sessions.

Large Language Models (LLMs) and multi-agent systems have shown impressive capabilities in natural language tasks but face challenges in clinical trial applications, primarily due to limited access to external knowledge. Recognizing the potential of advanced clinical trial tools that aggregate and predict based on the latest medical data, we propose an integrated solution to enhance their accessibility and utility. We introduce Clinical Agent System (ClinicalAgent), a clinical multi-agent system designed for clinical trial tasks, leveraging GPT-4, multi-agent architectures, LEAST-TO-MOST, and ReAct reasoning technology. This integration not only boosts LLM performance in clinical contexts but also introduces novel functionalities. The proposed method achieves competitive predictive performance in clinical trial outcome prediction (0.7908 PR-AUC), obtaining a 0.3326 improvement over the standard prompt Method. Publicly available code can be found at https://anonymous.4open.science/r/ClinicalAgent-6671.

As machine intelligence evolves, the need to test and compare the problem-solving abilities of different AI models grows. However, current benchmarks are often overly simplistic, allowing models to perform uniformly well, making it difficult to distinguish their capabilities. Additionally, benchmarks typically rely on static question-answer pairs, which models might memorize or guess. To address these limitations, we introduce the Dynamic Intelligence Assessment (DIA), a novel methodology for testing AI models using dynamic question templates and improved metrics across multiple disciplines such as mathematics, cryptography, cybersecurity, and computer science. The accompanying DIA-Bench dataset, which includes 150 diverse and challenging task templates with mutable parameters, is presented in various formats such as text, PDFs, compiled binaries, and visual puzzles. Our framework introduces four new metrics to assess a model's reliability and confidence across multiple attempts. These metrics revealed that even simple questions are frequently answered incorrectly when posed in varying forms, highlighting significant gaps in models' reliability. Notably, models like GPT-4o tended to overestimate their mathematical abilities, while ChatGPT-4o demonstrated better decision-making and performance through effective tool usage. We evaluated eight state-of-the-art large language models (LLMs) using DIA-Bench, showing that current models struggle with complex tasks and often display unexpectedly low confidence, even with simpler questions. The DIA framework sets a new standard for assessing not only problem-solving but also a model's adaptive intelligence and ability to assess its own limitations. The dataset is publicly available on our project's website.

We find that large language models (LLMs) are more likely to modify human-written text than AI-generated text when tasked with rewriting. This tendency arises because LLMs often perceive AI-generated text as high-quality, leading to fewer modifications. We introduce a method to detect AI-generated content by prompting LLMs to rewrite text and calculating the editing distance of the output. We dubbed our geneRative AI Detection viA Rewriting method Raidar. Raidar significantly improves the F1 detection scores of existing AI content detection models -- both academic and commercial -- across various domains, including News, creative writing, student essays, code, Yelp reviews, and arXiv papers, with gains of up to 29 points. Operating solely on word symbols without high-dimensional features, our method is compatible with black box LLMs, and is inherently robust on new content. Our results illustrate the unique imprint of machine-generated text through the lens of the machines themselves.

Artificial intelligence has significantly impacted medical applications, particularly with the advent of Medical Large Vision Language Models (Med-LVLMs), sparking optimism for the future of automated and personalized healthcare. However, the trustworthiness of Med-LVLMs remains unverified, posing significant risks for future model deployment. In this paper, we introduce CARES and aim to comprehensively evaluate the Trustworthiness of Med-LVLMs across the medical domain. We assess the trustworthiness of Med-LVLMs across five dimensions, including trustfulness, fairness, safety, privacy, and robustness. CARES comprises about 41K question-answer pairs in both closed and open-ended formats, covering 16 medical image modalities and 27 anatomical regions. Our analysis reveals that the models consistently exhibit concerns regarding trustworthiness, often displaying factual inaccuracies and failing to maintain fairness across different demographic groups. Furthermore, they are vulnerable to attacks and demonstrate a lack of privacy awareness. We publicly release our benchmark and code in https://github.com/richard-peng-xia/CARES.

Recent advancements have positioned AI, and particularly Large Language Models (LLMs), as transformative tools for scientific research, capable of addressing complex tasks that require reasoning, problem-solving, and decision-making. Their exceptional capabilities suggest their potential as scientific research assistants but also highlight the need for holistic, rigorous, and domain-specific evaluation to assess effectiveness in real-world scientific applications. This paper describes a multifaceted methodology for Evaluating AI models as scientific Research Assistants (EAIRA) developed at Argonne National Laboratory. This methodology incorporates four primary classes of evaluations. 1) Multiple Choice Questions to assess factual recall; 2) Open Response to evaluate advanced reasoning and problem-solving skills; 3) Lab-Style Experiments involving detailed analysis of capabilities as research assistants in controlled environments; and 4) Field-Style Experiments to capture researcher-LLM interactions at scale in a wide range of scientific domains and applications. These complementary methods enable a comprehensive analysis of LLM strengths and weaknesses with respect to their scientific knowledge, reasoning abilities, and adaptability. Recognizing the rapid pace of LLM advancements, we designed the methodology to evolve and adapt so as to ensure its continued relevance and applicability. This paper describes the methodology state at the end of February 2025. Although developed within a subset of scientific domains, the methodology is designed to be generalizable to a wide range of scientific domains.

Training new engineers in digital design is a challenge, particularly when it comes to teaching the complex electronic design automation (EDA) tooling used in this domain. Learners will typically deploy designs in the Verilog and VHDL hardware description languages to Field Programmable Gate Arrays (FPGAs) from Altera (Intel) and Xilinx (AMD) via proprietary closed-source toolchains (Quartus Prime and Vivado, respectively). These tools are complex and difficult to use -- yet, as they are the tools used in industry, they are an essential first step in this space. In this work, we examine how recent advances in artificial intelligence may be leveraged to address aspects of this challenge. Specifically, we investigate if Large Language Models (LLMs), which have demonstrated text comprehension and question-answering capabilities, can be used to generate novice-friendly explanations of compile-time synthesis error messages from Quartus Prime and Vivado. To perform this study we generate 936 error message explanations using three OpenAI LLMs over 21 different buggy code samples. These are then graded for relevance and correctness, and we find that in approximately 71% of cases the LLMs give correct & complete explanations suitable for novice learners.

Recent advancements in tool-equipped Agents (LLMs) have enabled complex tasks like secure database interactions and multi-agent code development. However, scaling tool capacity beyond agent reasoning or model limits remains a challenge. In this paper, we address these challenges by introducing Toolshed Knowledge Bases, a tool knowledge base (vector database) designed to store enhanced tool representations and optimize tool selection for large-scale tool-equipped Agents. Additionally, we propose Advanced RAG-Tool Fusion, a novel ensemble of tool-applied advanced retrieval-augmented generation (RAG) techniques across the pre-retrieval, intra-retrieval, and post-retrieval phases, without requiring model fine-tuning. During pre-retrieval, tool documents are enhanced with key information and stored in the Toolshed Knowledge Base. Intra-retrieval focuses on query planning and transformation to increase retrieval accuracy. Post-retrieval refines the retrieved tool documents and enables self-reflection. Furthermore, by varying both the total number of tools (tool-M) an Agent has access to and the tool selection threshold (top-k), we address trade-offs between retrieval accuracy, agent performance, and token cost. Our approach achieves 46%, 56%, and 47% absolute improvements on the ToolE single-tool, ToolE multi-tool and Seal-Tools benchmark datasets, respectively (Recall@5).

The advent of Industry 4.0 has precipitated the incorporation of Artificial Intelligence (AI) methods within industrial contexts, aiming to realize intelligent manufacturing, operation as well as maintenance, also known as industrial intelligence. However, intricate industrial milieus, particularly those relating to energy exploration and production, frequently encompass data characterized by long-tailed class distribution, sample imbalance, and domain shift. These attributes pose noteworthy challenges to data-centric Deep Learning (DL) techniques, crucial for the realization of industrial intelligence. The present study centers on the intricate and distinctive industrial scenarios of Nuclear Power Generation (NPG), meticulously scrutinizing the application of DL techniques under the constraints of finite data samples. Initially, the paper expounds on potential employment scenarios for AI across the full life-cycle of NPG. Subsequently, we delve into an evaluative exposition of DL's advancement, grounded in the finite sample perspective. This encompasses aspects such as small-sample learning, few-shot learning, zero-shot learning, and open-set recognition, also referring to the unique data characteristics of NPG. The paper then proceeds to present two specific case studies. The first revolves around the automatic recognition of zirconium alloy metallography, while the second pertains to open-set recognition for signal diagnosis of machinery sensors. These cases, spanning the entirety of NPG's life-cycle, are accompanied by constructive outcomes and insightful deliberations. By exploring and applying DL methodologies within the constraints of finite sample availability, this paper not only furnishes a robust technical foundation but also introduces a fresh perspective toward the secure and efficient advancement and exploitation of this advanced energy source.