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Mar 13

RadGenome-Chest CT: A Grounded Vision-Language Dataset for Chest CT Analysis

Developing generalist foundation model has recently attracted tremendous attention among researchers in the field of AI for Medicine (AI4Medicine). A pivotal insight in developing these models is their reliance on dataset scaling, which emphasizes the requirements on developing open-source medical image datasets that incorporate diverse supervision signals across various imaging modalities. In this paper, we introduce RadGenome-Chest CT, a comprehensive, large-scale, region-guided 3D chest CT interpretation dataset based on CT-RATE. Specifically, we leverage the latest powerful universal segmentation and large language models, to extend the original datasets (over 25,692 non-contrast 3D chest CT volume and reports from 20,000 patients) from the following aspects: (i) organ-level segmentation masks covering 197 categories, which provide intermediate reasoning visual clues for interpretation; (ii) 665 K multi-granularity grounded reports, where each sentence of the report is linked to the corresponding anatomical region of CT volume in the form of a segmentation mask; (iii) 1.3 M grounded VQA pairs, where questions and answers are all linked with reference segmentation masks, enabling models to associate visual evidence with textual explanations. All grounded reports and VQA pairs in the validation set have gone through manual verification to ensure dataset quality. We believe that RadGenome-Chest CT can significantly advance the development of multimodal medical foundation models, by training to generate texts based on given segmentation regions, which is unattainable with previous relevant datasets. We will release all segmentation masks, grounded reports, and VQA pairs to facilitate further research and development in this field.

MAIRA-2: Grounded Radiology Report Generation

Radiology reporting is a complex task that requires detailed image understanding, integration of multiple inputs, including comparison with prior imaging, and precise language generation. This makes it ideal for the development and use of generative multimodal models. Here, we extend report generation to include the localisation of individual findings on the image - a task we call grounded report generation. Prior work indicates that grounding is important for clarifying image understanding and interpreting AI-generated text. Therefore, grounded reporting stands to improve the utility and transparency of automated report drafting. To enable evaluation of grounded reporting, we propose a novel evaluation framework - RadFact - leveraging the reasoning capabilities of large language models (LLMs). RadFact assesses the factuality of individual generated sentences, as well as correctness of generated spatial localisations when present. We introduce MAIRA-2, a large multimodal model combining a radiology-specific image encoder with a LLM, and trained for the new task of grounded report generation on chest X-rays. MAIRA-2 uses more comprehensive inputs than explored previously: the current frontal image, the current lateral image, the prior frontal image and prior report, as well as the Indication, Technique and Comparison sections of the current report. We demonstrate that these additions significantly improve report quality and reduce hallucinations, establishing a new state of the art on findings generation (without grounding) on MIMIC-CXR while demonstrating the feasibility of grounded reporting as a novel and richer task.

CLARA: Clinical Report Auto-completion

Generating clinical reports from raw recordings such as X-rays and electroencephalogram (EEG) is an essential and routine task for doctors. However, it is often time-consuming to write accurate and detailed reports. Most existing methods try to generate the whole reports from the raw input with limited success because 1) generated reports often contain errors that need manual review and correction, 2) it does not save time when doctors want to write additional information into the report, and 3) the generated reports are not customized based on individual doctors' preference. We propose {\it CL}inic{\it A}l {\it R}eport {\it A}uto-completion (CLARA), an interactive method that generates reports in a sentence by sentence fashion based on doctors' anchor words and partially completed sentences. CLARA searches for most relevant sentences from existing reports as the template for the current report. The retrieved sentences are sequentially modified by combining with the input feature representations to create the final report. In our experimental evaluation, CLARA achieved 0.393 CIDEr and 0.248 BLEU-4 on X-ray reports and 0.482 CIDEr and 0.491 BLEU-4 for EEG reports for sentence-level generation, which is up to 35% improvement over the best baseline. Also via our qualitative evaluation, CLARA is shown to produce reports which have a significantly higher level of approval by doctors in a user study (3.74 out of 5 for CLARA vs 2.52 out of 5 for the baseline).

Detailed Annotations of Chest X-Rays via CT Projection for Report Understanding

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

Measuring Large Language Models Capacity to Annotate Journalistic Sourcing

Since the launch of ChatGPT in late 2022, the capacities of Large Language Models and their evaluation have been in constant discussion and evaluation both in academic research and in the industry. Scenarios and benchmarks have been developed in several areas such as law, medicine and math (Bommasani et al., 2023) and there is continuous evaluation of model variants. One area that has not received sufficient scenario development attention is journalism, and in particular journalistic sourcing and ethics. Journalism is a crucial truth-determination function in democracy (Vincent, 2023), and sourcing is a crucial pillar to all original journalistic output. Evaluating the capacities of LLMs to annotate stories for the different signals of sourcing and how reporters justify them is a crucial scenario that warrants a benchmark approach. It offers potential to build automated systems to contrast more transparent and ethically rigorous forms of journalism with everyday fare. In this paper we lay out a scenario to evaluate LLM performance on identifying and annotating sourcing in news stories on a five-category schema inspired from journalism studies (Gans, 2004). We offer the use case, our dataset and metrics and as the first step towards systematic benchmarking. Our accuracy findings indicate LLM-based approaches have more catching to do in identifying all the sourced statements in a story, and equally, in matching the type of sources. An even harder task is spotting source justifications.

CsFEVER and CTKFacts: Acquiring Czech data for fact verification

In this paper, we examine several methods of acquiring Czech data for automated fact-checking, which is a task commonly modeled as a classification of textual claim veracity w.r.t. a corpus of trusted ground truths. We attempt to collect sets of data in form of a factual claim, evidence within the ground truth corpus, and its veracity label (supported, refuted or not enough info). As a first attempt, we generate a Czech version of the large-scale FEVER dataset built on top of Wikipedia corpus. We take a hybrid approach of machine translation and document alignment; the approach and the tools we provide can be easily applied to other languages. We discuss its weaknesses and inaccuracies, propose a future approach for their cleaning and publish the 127k resulting translations, as well as a version of such dataset reliably applicable for the Natural Language Inference task - the CsFEVER-NLI. Furthermore, we collect a novel dataset of 3,097 claims, which is annotated using the corpus of 2.2M articles of Czech News Agency. We present its extended annotation methodology based on the FEVER approach, and, as the underlying corpus is kept a trade secret, we also publish a standalone version of the dataset for the task of Natural Language Inference we call CTKFactsNLI. We analyze both acquired datasets for spurious cues - annotation patterns leading to model overfitting. CTKFacts is further examined for inter-annotator agreement, thoroughly cleaned, and a typology of common annotator errors is extracted. Finally, we provide baseline models for all stages of the fact-checking pipeline and publish the NLI datasets, as well as our annotation platform and other experimental data.

Grounded Decoding: Guiding Text Generation with Grounded Models for Robot Control

Recent progress in large language models (LLMs) has demonstrated the ability to learn and leverage Internet-scale knowledge through pre-training with autoregressive models. Unfortunately, applying such models to settings with embodied agents, such as robots, is challenging due to their lack of experience with the physical world, inability to parse non-language observations, and ignorance of rewards or safety constraints that robots may require. On the other hand, language-conditioned robotic policies that learn from interaction data can provide the necessary grounding that allows the agent to be correctly situated in the real world, but such policies are limited by the lack of high-level semantic understanding due to the limited breadth of the interaction data available for training them. Thus, if we want to make use of the semantic knowledge in a language model while still situating it in an embodied setting, we must construct an action sequence that is both likely according to the language model and also realizable according to grounded models of the environment. We frame this as a problem similar to probabilistic filtering: decode a sequence that both has high probability under the language model and high probability under a set of grounded model objectives. We demonstrate this guided decoding strategy is able to solve complex, long-horizon embodiment tasks in a robotic setting by leveraging the knowledge of both models. The project's website can be found at grounded-decoding.github.io.

Data Cards: Purposeful and Transparent Dataset Documentation for Responsible AI

As research and industry moves towards large-scale models capable of numerous downstream tasks, the complexity of understanding multi-modal datasets that give nuance to models rapidly increases. A clear and thorough understanding of a dataset's origins, development, intent, ethical considerations and evolution becomes a necessary step for the responsible and informed deployment of models, especially those in people-facing contexts and high-risk domains. However, the burden of this understanding often falls on the intelligibility, conciseness, and comprehensiveness of the documentation. It requires consistency and comparability across the documentation of all datasets involved, and as such documentation must be treated as a user-centric product in and of itself. In this paper, we propose Data Cards for fostering transparent, purposeful and human-centered documentation of datasets within the practical contexts of industry and research. Data Cards are structured summaries of essential facts about various aspects of ML datasets needed by stakeholders across a dataset's lifecycle for responsible AI development. These summaries provide explanations of processes and rationales that shape the data and consequently the models, such as upstream sources, data collection and annotation methods; training and evaluation methods, intended use; or decisions affecting model performance. We also present frameworks that ground Data Cards in real-world utility and human-centricity. Using two case studies, we report on desirable characteristics that support adoption across domains, organizational structures, and audience groups. Finally, we present lessons learned from deploying over 20 Data Cards.