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.

Recent accelerations in multi-modal applications have been made possible with the plethora of image and text data available online. However, the scarcity of analogous data in the medical field, specifically in histopathology, has halted comparable progress. To enable similar representation learning for histopathology, we turn to YouTube, an untapped resource of videos, offering 1,087 hours of valuable educational histopathology videos from expert clinicians. From YouTube, we curate Quilt: a large-scale vision-language dataset consisting of 768,826 image and text pairs. Quilt was automatically curated using a mixture of models, including large language models, handcrafted algorithms, human knowledge databases, and automatic speech recognition. In comparison, the most comprehensive datasets curated for histopathology amass only around 200K samples. We combine Quilt with datasets from other sources, including Twitter, research papers, and the internet in general, to create an even larger dataset: Quilt-1M, with 1M paired image-text samples, marking it as the largest vision-language histopathology dataset to date. We demonstrate the value of Quilt-1M by fine-tuning a pre-trained CLIP model. Our model outperforms state-of-the-art models on both zero-shot and linear probing tasks for classifying new histopathology images across 13 diverse patch-level datasets of 8 different sub-pathologies and cross-modal retrieval tasks.

In recent years, the integration of advanced imaging techniques and deep learning methods has significantly advanced computer-aided diagnosis (CAD) systems for breast cancer detection and classification. Transformers, which have shown great promise in computer vision, are now being applied to medical image analysis. However, their application to histopathological images presents challenges due to the need for extensive manual annotations of whole-slide images (WSIs), as these models require large amounts of data to work effectively, which is costly and time-consuming. Furthermore, the quadratic computational cost of Vision Transformers (ViTs) is particularly prohibitive for large, high-resolution histopathological images, especially on edge devices with limited computational resources. In this study, we introduce a novel lightweight breast cancer classification approach using transformers that operates effectively without large datasets. By incorporating parallel processing pathways for Discrete Cosine Transform (DCT) Attention and MobileConv, we convert image data from the spatial domain to the frequency domain to utilize the benefits such as filtering out high frequencies in the image, which reduces computational cost. This demonstrates the potential of our approach to improve breast cancer classification in histopathological images, offering a more efficient solution with reduced reliance on extensive annotated datasets. Our proposed model achieves an accuracy of 96.00% pm 0.48% for binary classification and 87.85% pm 0.93% for multiclass classification, which is comparable to state-of-the-art models while significantly reducing computational costs. This demonstrates the potential of our approach to improve breast cancer classification in histopathological images, offering a more efficient solution with reduced reliance on extensive annotated datasets.

Histopathological cancer diagnostics has become more complex, and the increasing number of biopsies is a challenge for most pathology laboratories. Thus, development of automatic methods for evaluation of histopathological cancer sections would be of value. In this study, we used 624 whole slide images (WSIs) of breast cancer from a Norwegian cohort. We propose a cascaded convolutional neural network design, called H2G-Net, for semantic segmentation of gigapixel histopathological images. The design involves a detection stage using a patch-wise method, and a refinement stage using a convolutional autoencoder. To validate the design, we conducted an ablation study to assess the impact of selected components in the pipeline on tumour segmentation. Guiding segmentation, using hierarchical sampling and deep heatmap refinement, proved to be beneficial when segmenting the histopathological images. We found a significant improvement when using a refinement network for postprocessing the generated tumour segmentation heatmaps. The overall best design achieved a Dice score of 0.933 on an independent test set of 90 WSIs. The design outperformed single-resolution approaches, such as cluster-guided, patch-wise high-resolution classification using MobileNetV2 (0.872) and a low-resolution U-Net (0.874). In addition, segmentation on a representative x400 WSI took ~58 seconds, using only the CPU. The findings demonstrate the potential of utilizing a refinement network to improve patch-wise predictions. The solution is efficient and does not require overlapping patch inference or ensembling. Furthermore, we showed that deep neural networks can be trained using a random sampling scheme that balances on multiple different labels simultaneously, without the need of storing patches on disk. Future work should involve more efficient patch generation and sampling, as well as improved clustering.

Feature vectors provided by pre-trained deep artificial neural networks have become a dominant source for image representation in recent literature. Their contribution to the performance of image analysis can be improved through finetuning. As an ultimate solution, one might even train a deep network from scratch with the domain-relevant images, a highly desirable option which is generally impeded in pathology by lack of labeled images and the computational expense. In this study, we propose a new network, namely KimiaNet, that employs the topology of the DenseNet with four dense blocks, fine-tuned and trained with histopathology images in different configurations. We used more than 240,000 image patches with 1000x1000 pixels acquired at 20x magnification through our proposed "highcellularity mosaic" approach to enable the usage of weak labels of 7,126 whole slide images of formalin-fixed paraffin-embedded human pathology samples publicly available through the The Cancer Genome Atlas (TCGA) repository. We tested KimiaNet using three public datasets, namely TCGA, endometrial cancer images, and colorectal cancer images by evaluating the performance of search and classification when corresponding features of different networks are used for image representation. As well, we designed and trained multiple convolutional batch-normalized ReLU (CBR) networks. The results show that KimiaNet provides superior results compared to the original DenseNet and smaller CBR networks when used as feature extractor to represent histopathology images.

Application of deep learning on histopathological whole slide images (WSIs) holds promise of improving diagnostic efficiency and reproducibility but is largely dependent on the ability to write computer code or purchase commercial solutions. We present a code-free pipeline utilizing free-to-use, open-source software (QuPath, DeepMIB, and FastPathology) for creating and deploying deep learning-based segmentation models for computational pathology. We demonstrate the pipeline on a use case of separating epithelium from stroma in colonic mucosa. A dataset of 251 annotated WSIs, comprising 140 hematoxylin-eosin (HE)-stained and 111 CD3 immunostained colon biopsy WSIs, were developed through active learning using the pipeline. On a hold-out test set of 36 HE and 21 CD3-stained WSIs a mean intersection over union score of 96.6% and 95.3% was achieved on epithelium segmentation. We demonstrate pathologist-level segmentation accuracy and clinical acceptable runtime performance and show that pathologists without programming experience can create near state-of-the-art segmentation solutions for histopathological WSIs using only free-to-use software. The study further demonstrates the strength of open-source solutions in its ability to create generalizable, open pipelines, of which trained models and predictions can seamlessly be exported in open formats and thereby used in external solutions. All scripts, trained models, a video tutorial, and the full dataset of 251 WSIs with ~31k epithelium annotations are made openly available at https://github.com/andreped/NoCodeSeg to accelerate research in the field.

This paper addresses complex challenges in histopathological image analysis through three key contributions. Firstly, it introduces a fast patch selection method, FPS, for whole-slide image (WSI) analysis, significantly reducing computational cost while maintaining accuracy. Secondly, it presents PathDino, a lightweight histopathology feature extractor with a minimal configuration of five Transformer blocks and only 9 million parameters, markedly fewer than alternatives. Thirdly, it introduces a rotation-agnostic representation learning paradigm using self-supervised learning, effectively mitigating overfitting. We also show that our compact model outperforms existing state-of-the-art histopathology-specific vision transformers on 12 diverse datasets, including both internal datasets spanning four sites (breast, liver, skin, and colorectal) and seven public datasets (PANDA, CAMELYON16, BRACS, DigestPath, Kather, PanNuke, and WSSS4LUAD). Notably, even with a training dataset of 6 million histopathology patches from The Cancer Genome Atlas (TCGA), our approach demonstrates an average 8.5% improvement in patch-level majority vote performance. These contributions provide a robust framework for enhancing image analysis in digital pathology, rigorously validated through extensive evaluation. Project Page: https://rhazeslab.github.io/PathDino-Page/

Tissue phenotyping is a fundamental task in learning objective characterizations of histopathologic biomarkers within the tumor-immune microenvironment in cancer pathology. However, whole-slide imaging (WSI) is a complex computer vision in which: 1) WSIs have enormous image resolutions with precludes large-scale pixel-level efforts in data curation, and 2) diversity of morphological phenotypes results in inter- and intra-observer variability in tissue labeling. To address these limitations, current efforts have proposed using pretrained image encoders (transfer learning from ImageNet, self-supervised pretraining) in extracting morphological features from pathology, but have not been extensively validated. In this work, we conduct a search for good representations in pathology by training a variety of self-supervised models with validation on a variety of weakly-supervised and patch-level tasks. Our key finding is in discovering that Vision Transformers using DINO-based knowledge distillation are able to learn data-efficient and interpretable features in histology images wherein the different attention heads learn distinct morphological phenotypes. We make evaluation code and pretrained weights publicly-available at: https://github.com/Richarizardd/Self-Supervised-ViT-Path.

Accurate and efficient segmentation of brain tumors is critical for diagnosis, treatment planning, and monitoring in clinical practice. In this study, we present an enhanced ResUNet architecture for automatic brain tumor segmentation, integrating an EfficientNetB0 encoder, a channel attention mechanism, and an Atrous Spatial Pyramid Pooling (ASPP) module. The EfficientNetB0 encoder leverages pre-trained features to improve feature extraction efficiency, while the channel attention mechanism enhances the model's focus on tumor-relevant features. ASPP enables multiscale contextual learning, crucial for handling tumors of varying sizes and shapes. The proposed model was evaluated on two benchmark datasets: TCGA LGG and BraTS 2020. Experimental results demonstrate that our method consistently outperforms the baseline ResUNet and its EfficientNet variant, achieving Dice coefficients of 0.903 and 0.851 and HD95 scores of 9.43 and 3.54 for whole tumor and tumor core regions on the BraTS 2020 dataset, respectively. compared with state-of-the-art methods, our approach shows competitive performance, particularly in whole tumor and tumor core segmentation. These results indicate that combining a powerful encoder with attention mechanisms and ASPP can significantly enhance brain tumor segmentation performance. The proposed approach holds promise for further optimization and application in other medical image segmentation tasks.

Despite extensive progress on image generation, common deep generative model architectures are not easily applied to lossless compression. For example, VAEs suffer from a compression cost overhead due to their latent variables. This overhead can only be partially eliminated with elaborate schemes such as bits-back coding, often resulting in poor single-sample compression rates. To overcome such problems, we establish a new class of tractable lossless compression models that permit efficient encoding and decoding: Probabilistic Circuits (PCs). These are a class of neural networks involving |p| computational units that support efficient marginalization over arbitrary subsets of the D feature dimensions, enabling efficient arithmetic coding. We derive efficient encoding and decoding schemes that both have time complexity O (log(D) cdot |p|), where a naive scheme would have linear costs in D and |p|, making the approach highly scalable. Empirically, our PC-based (de)compression algorithm runs 5-40 times faster than neural compression algorithms that achieve similar bitrates. By scaling up the traditional PC structure learning pipeline, we achieve state-of-the-art results on image datasets such as MNIST. Furthermore, PCs can be naturally integrated with existing neural compression algorithms to improve the performance of these base models on natural image datasets. Our results highlight the potential impact that non-standard learning architectures may have on neural data compression.

Task-specific deep learning models in histopathology offer promising opportunities for improving diagnosis, clinical research, and precision medicine. However, development of such models is often limited by availability of high-quality data. Foundation models in histopathology that learn general representations across a wide range of tissue types, diagnoses, and magnifications offer the potential to reduce the data, compute, and technical expertise necessary to develop task-specific deep learning models with the required level of model performance. In this work, we describe the development and evaluation of foundation models for histopathology via self-supervised learning (SSL). We first establish a diverse set of benchmark tasks involving 17 unique tissue types and 12 unique cancer types and spanning different optimal magnifications and task types. Next, we use this benchmark to explore and evaluate histopathology-specific SSL methods followed by further evaluation on held out patch-level and weakly supervised tasks. We found that standard SSL methods thoughtfully applied to histopathology images are performant across our benchmark tasks and that domain-specific methodological improvements can further increase performance. Our findings reinforce the value of using domain-specific SSL methods in pathology, and establish a set of high quality foundation models to enable further research across diverse applications.

Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem in which the large-scale image resolutions of WSIs and the enormous diversity of morphological phenotypes preclude large-scale data annotation. Current efforts have proposed using pretrained image encoders with either transfer learning from natural image datasets or self-supervised pretraining on publicly-available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using over 100 million tissue patches from over 100,000 diagnostic haematoxylin and eosin-stained WSIs across 20 major tissue types, and evaluated on 33 representative CPath clinical tasks in CPath of varying diagnostic difficulties. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree code classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient AI models that can generalize and transfer to a gamut of diagnostically-challenging tasks and clinical workflows in anatomic pathology.

Precise breast cancer classification on histopathological images has the potential to greatly improve the diagnosis and patient outcome in oncology. The data imbalance problem largely stems from the inherent imbalance within medical image datasets, where certain tumor subtypes may appear much less frequently. This constitutes a considerable limitation in biased model predictions that can overlook critical but rare classes. In this work, we adopted EfficientNet, a state-of-the-art convolutional neural network (CNN) model that balances high accuracy with computational cost efficiency. To address data imbalance, we introduce an intensive data augmentation pipeline and cost-sensitive learning, improving representation and ensuring that the model does not overly favor majority classes. This approach provides the ability to learn effectively from rare tumor types, improving its robustness. Additionally, we fine-tuned the model using transfer learning, where weights in the beginning trained on a binary classification task were adopted to multi-class classification, improving the capability to detect complex patterns within the BreakHis dataset. Our results underscore significant improvements in the binary classification performance, achieving an exceptional recall increase for benign cases from 0.92 to 0.95, alongside an accuracy enhancement from 97.35 % to 98.23%. Our approach improved the performance of multi-class tasks from 91.27% with regular augmentation to 94.54% with intensive augmentation, reaching 95.04% with transfer learning. This framework demonstrated substantial gains in precision in the minority classes, such as Mucinous carcinoma and Papillary carcinoma, while maintaining high recall consistently across these critical subtypes, as further confirmed by confusion matrix analysis.

The accelerated adoption of digital pathology and advances in deep learning have enabled the development of powerful models for various pathology tasks across a diverse array of diseases and patient cohorts. However, model training is often difficult due to label scarcity in the medical domain and the model's usage is limited by the specific task and disease for which it is trained. Additionally, most models in histopathology leverage only image data, a stark contrast to how humans teach each other and reason about histopathologic entities. We introduce CONtrastive learning from Captions for Histopathology (CONCH), a visual-language foundation model developed using diverse sources of histopathology images, biomedical text, and notably over 1.17 million image-caption pairs via task-agnostic pretraining. Evaluated on a suite of 13 diverse benchmarks, CONCH can be transferred to a wide range of downstream tasks involving either or both histopathology images and text, achieving state-of-the-art performance on histology image classification, segmentation, captioning, text-to-image and image-to-text retrieval. CONCH represents a substantial leap over concurrent visual-language pretrained systems for histopathology, with the potential to directly facilitate a wide array of machine learning-based workflows requiring minimal or no further supervised fine-tuning.

Foundation models in computational pathology promise to unlock the development of new clinical decision support systems and models for precision medicine. However, there is a mismatch between most clinical analysis, which is defined at the level of one or more whole slide images, and foundation models to date, which process the thousands of image tiles contained in a whole slide image separately. The requirement to train a network to aggregate information across a large number of tiles in multiple whole slide images limits these models' impact. In this work, we present a slide-level foundation model for H&E-stained histopathology, PRISM, that builds on Virchow tile embeddings and leverages clinical report text for pre-training. Using the tile embeddings, PRISM produces slide-level embeddings with the ability to generate clinical reports, resulting in several modes of use. Using text prompts, PRISM achieves zero-shot cancer detection and sub-typing performance approaching and surpassing that of a supervised aggregator model. Using the slide embeddings with linear classifiers, PRISM surpasses supervised aggregator models. Furthermore, we demonstrate that fine-tuning of the PRISM slide encoder yields label-efficient training for biomarker prediction, a task that typically suffers from low availability of training data; an aggregator initialized with PRISM and trained on as little as 10% of the training data can outperform a supervised baseline that uses all of the data.

Representation learning of pathology whole-slide images (WSIs) has been has primarily relied on weak supervision with Multiple Instance Learning (MIL). However, the slide representations resulting from this approach are highly tailored to specific clinical tasks, which limits their expressivity and generalization, particularly in scenarios with limited data. Instead, we hypothesize that morphological redundancy in tissue can be leveraged to build a task-agnostic slide representation in an unsupervised fashion. To this end, we introduce PANTHER, a prototype-based approach rooted in the Gaussian mixture model that summarizes the set of WSI patches into a much smaller set of morphological prototypes. Specifically, each patch is assumed to have been generated from a mixture distribution, where each mixture component represents a morphological exemplar. Utilizing the estimated mixture parameters, we then construct a compact slide representation that can be readily used for a wide range of downstream tasks. By performing an extensive evaluation of PANTHER on subtyping and survival tasks using 13 datasets, we show that 1) PANTHER outperforms or is on par with supervised MIL baselines and 2) the analysis of morphological prototypes brings new qualitative and quantitative insights into model interpretability.

This work contributes to breast cancer sub-type classification using histopathological images. We utilize masked autoencoders (MAEs) to learn a self-supervised embedding tailored for computer vision tasks in this domain. This embedding captures informative representations of histopathological data, facilitating feature learning without extensive labeled datasets. During pre-training, we investigate employing a random crop technique to generate a large dataset from WSIs automatically. Additionally, we assess the performance of linear probes for multi-class classification tasks of cancer sub-types using the representations learnt by the MAE. Our approach aims to achieve strong performance on downstream tasks by leveraging the complementary strengths of ViTs and autoencoders. We evaluate our model's performance on the BRACS dataset and compare it with existing benchmarks.

Computational pathology can lead to saving human lives, but models are annotation hungry and pathology images are notoriously expensive to annotate. Self-supervised learning has shown to be an effective method for utilizing unlabeled data, and its application to pathology could greatly benefit its downstream tasks. Yet, there are no principled studies that compare SSL methods and discuss how to adapt them for pathology. To address this need, we execute the largest-scale study of SSL pre-training on pathology image data, to date. Our study is conducted using 4 representative SSL methods on diverse downstream tasks. We establish that large-scale domain-aligned pre-training in pathology consistently out-performs ImageNet pre-training in standard SSL settings such as linear and fine-tuning evaluations, as well as in low-label regimes. Moreover, we propose a set of domain-specific techniques that we experimentally show leads to a performance boost. Lastly, for the first time, we apply SSL to the challenging task of nuclei instance segmentation and show large and consistent performance improvements under diverse settings.

To synthesize high-fidelity samples, diffusion models typically require auxiliary data to guide the generation process. However, it is impractical to procure the painstaking patch-level annotation effort required in specialized domains like histopathology and satellite imagery; it is often performed by domain experts and involves hundreds of millions of patches. Modern-day self-supervised learning (SSL) representations encode rich semantic and visual information. In this paper, we posit that such representations are expressive enough to act as proxies to fine-grained human labels. We introduce a novel approach that trains diffusion models conditioned on embeddings from SSL. Our diffusion models successfully project these features back to high-quality histopathology and remote sensing images. In addition, we construct larger images by assembling spatially consistent patches inferred from SSL embeddings, preserving long-range dependencies. Augmenting real data by generating variations of real images improves downstream classifier accuracy for patch-level and larger, image-scale classification tasks. Our models are effective even on datasets not encountered during training, demonstrating their robustness and generalizability. Generating images from learned embeddings is agnostic to the source of the embeddings. The SSL embeddings used to generate a large image can either be extracted from a reference image, or sampled from an auxiliary model conditioned on any related modality (e.g. class labels, text, genomic data). As proof of concept, we introduce the text-to-large image synthesis paradigm where we successfully synthesize large pathology and satellite images out of text descriptions.

Masked image modelling (MIM) is a powerful self-supervised representation learning paradigm, whose potential has not been widely demonstrated in medical image analysis. In this work, we show the capacity of MIM to capture rich semantic representations of Haemotoxylin & Eosin (H&E)-stained images at the nuclear level. Inspired by Bidirectional Encoder representation from Image Transformers (BEiT), we split the images into smaller patches and generate corresponding discrete visual tokens. In addition to the regular grid-based patches, typically used in visual Transformers, we introduce patches of individual cell nuclei. We propose positional encoding of the irregular distribution of these structures within an image. We pre-train the model in a self-supervised manner on H&E-stained whole-slide images of diffuse large B-cell lymphoma, where cell nuclei have been segmented. The pre-training objective is to recover the original discrete visual tokens of the masked image on the one hand, and to reconstruct the visual tokens of the masked object instances on the other. Coupling these two pre-training tasks allows us to build powerful, context-aware representations of nuclei. Our model generalizes well and can be fine-tuned on downstream classification tasks, achieving improved cell classification accuracy on PanNuke dataset by more than 5% compared to current instance segmentation methods.

Immunohistochemical (IHC) staining highlights the molecular information critical to diagnostics in tissue samples. However, compared to H&E staining, IHC staining can be much more expensive in terms of both labor and the laboratory equipment required. This motivates recent research that demonstrates that the correlations between the morphological information present in the H&E-stained slides and the molecular information in the IHC-stained slides can be used for H&E-to-IHC stain translation. However, due to a lack of pixel-perfect H&E-IHC groundtruth pairs, most existing methods have resorted to relying on expert annotations. To remedy this situation, we present a new loss function, Adaptive Supervised PatchNCE (ASP), to directly deal with the input to target inconsistencies in a proposed H&E-to-IHC image-to-image translation framework. The ASP loss is built upon a patch-based contrastive learning criterion, named Supervised PatchNCE (SP), and augments it further with weight scheduling to mitigate the negative impact of noisy supervision. Lastly, we introduce the Multi-IHC Stain Translation (MIST) dataset, which contains aligned H&E-IHC patches for 4 different IHC stains critical to breast cancer diagnosis. In our experiment, we demonstrate that our proposed method outperforms existing image-to-image translation methods for stain translation to multiple IHC stains. All of our code and datasets are available at https://github.com/lifangda01/AdaptiveSupervisedPatchNCE.

In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively.

Medical images are acquired at high resolutions with large fields of view in order to capture fine-grained features necessary for clinical decision-making. Consequently, training deep learning models on medical images can incur large computational costs. In this work, we address the challenge of downsizing medical images in order to improve downstream computational efficiency while preserving clinically-relevant features. We introduce MedVAE, a family of six large-scale 2D and 3D autoencoders capable of encoding medical images as downsized latent representations and decoding latent representations back to high-resolution images. We train MedVAE autoencoders using a novel two-stage training approach with 1,052,730 medical images. Across diverse tasks obtained from 20 medical image datasets, we demonstrate that (1) utilizing MedVAE latent representations in place of high-resolution images when training downstream models can lead to efficiency benefits (up to 70x improvement in throughput) while simultaneously preserving clinically-relevant features and (2) MedVAE can decode latent representations back to high-resolution images with high fidelity. Our work demonstrates that large-scale, generalizable autoencoders can help address critical efficiency challenges in the medical domain. Our code is available at https://github.com/StanfordMIMI/MedVAE.

While machine learning is currently transforming the field of histopathology, the domain lacks a comprehensive evaluation of state-of-the-art models based on essential but complementary quality requirements beyond a mere classification accuracy. In order to fill this gap, we developed a new methodology to extensively evaluate a wide range of classification models, including recent vision transformers, and convolutional neural networks such as: ConvNeXt, ResNet (BiT), Inception, ViT and Swin transformer, with and without supervised or self-supervised pretraining. We thoroughly tested the models on five widely used histopathology datasets containing whole slide images of breast, gastric, and colorectal cancer and developed a novel approach using an image-to-image translation model to assess the robustness of a cancer classification model against stain variations. Further, we extended existing interpretability methods to previously unstudied models and systematically reveal insights of the models' classifications strategies that can be transferred to future model architectures.

Gene expression can be used to subtype breast cancer with improved prediction of risk of recurrence and treatment responsiveness over that obtained using routine immunohistochemistry (IHC). However, in the clinic, molecular profiling is primarily used for ER+ breast cancer, which is costly, tissue destructive, requires specialized platforms and takes several weeks to obtain a result. Deep learning algorithms can effectively extract morphological patterns in digital histopathology images to predict molecular phenotypes quickly and cost-effectively. We propose a new, computationally efficient approach called hist2RNA inspired by bulk RNA-sequencing techniques to predict the expression of 138 genes (incorporated from six commercially available molecular profiling tests), including luminal PAM50 subtype, from hematoxylin and eosin (H&E) stained whole slide images (WSIs). The training phase involves the aggregation of extracted features for each patient from a pretrained model to predict gene expression at the patient level using annotated H&E images from The Cancer Genome Atlas (TCGA, n=335). We demonstrate successful gene prediction on a held-out test set (n = 160, corr = 0.82 across patients, corr = 0.29 across genes) and perform exploratory analysis on an external tissue microarray (TMA) dataset (n = 498) with known IHC and survival information. Our model is able to predict gene expression and luminal PAM50 subtype (Luminal A versus Luminal B) on the TMA dataset with prognostic significance for overall survival in univariate analysis (c-index = 0.56, hazard ratio = 2.16 (95% CI 1.12-3.06), p < 5 x 10-3), and independent significance in multivariate analysis incorporating standard clinicopathological variables (c-index = 0.65, hazard ratio = 1.85 (95% CI 1.30-2.68), p < 5 x 10-3).

The segmentation of cell nuclei in tissue images stained with the blood dye hematoxylin and eosin (H&E) is essential for various clinical applications and analyses. Due to the complex characteristics of cellular morphology, a large receptive field is considered crucial for generating high-quality segmentation. However, previous methods face challenges in achieving a balance between the receptive field and computational burden. To address this issue, we propose LKCell, a high-accuracy and efficient cell segmentation method. Its core insight lies in unleashing the potential of large convolution kernels to achieve computationally efficient large receptive fields. Specifically, (1) We transfer pre-trained large convolution kernel models to the medical domain for the first time, demonstrating their effectiveness in cell segmentation. (2) We analyze the redundancy of previous methods and design a new segmentation decoder based on large convolution kernels. It achieves higher performance while significantly reducing the number of parameters. We evaluate our method on the most challenging benchmark and achieve state-of-the-art results (0.5080 mPQ) in cell nuclei instance segmentation with only 21.6% FLOPs compared with the previous leading method. Our source code and models are available at https://github.com/hustvl/LKCell.

Efficient Human Epithelial-2 (HEp-2) cell image classification can facilitate the diagnosis of many autoimmune diseases. This paper presents an automatic framework for this classification task, by utilizing the deep convolutional neural networks (CNNs) which have recently attracted intensive attention in visual recognition. This paper elaborates the important components of this framework, discusses multiple key factors that impact the efficiency of training a deep CNN, and systematically compares this framework with the well-established image classification models in the literature. Experiments on benchmark datasets show that i) the proposed framework can effectively outperform existing models by properly applying data augmentation; ii) our CNN-based framework demonstrates excellent adaptability across different datasets, which is highly desirable for classification under varying laboratory settings. Our system is ranked high in the cell image classification competition hosted by ICPR 2014.

Digital pathology enables automatic analysis of histopathological sections using artificial intelligence (AI). Automatic evaluation could improve diagnostic efficiency and help find associations between morphological features and clinical outcome. For development of such prediction models, identifying invasive epithelial cells, and separating these from benign epithelial cells and in situ lesions would be the first step. In this study, we aimed to develop an AI model for segmentation of epithelial cells in sections from breast cancer. We generated epithelial ground truth masks by restaining hematoxylin and eosin (HE) sections with cytokeratin (CK) AE1/AE3, and by pathologists' annotations. HE/CK image pairs were used to train a convolutional neural network, and data augmentation was used to make the model more robust. Tissue microarrays (TMAs) from 839 patients, and whole slide images from two patients were used for training and evaluation of the models. The sections were derived from four cohorts of breast cancer patients. TMAs from 21 patients from a fifth cohort was used as a second test set. In quantitative evaluation, a mean Dice score of 0.70, 0.79, and 0.75 for invasive epithelial cells, benign epithelial cells, and in situ lesions, respectively, were achieved. In qualitative scoring (0-5) by pathologists, results were best for all epithelium and invasive epithelium, with scores of 4.7 and 4.4. Scores for benign epithelium and in situ lesions were 3.7 and 2.0. The proposed model segmented epithelial cells in HE stained breast cancer slides well, but further work is needed for accurate division between the classes. Immunohistochemistry, together with pathologists' annotations, enabled the creation of accurate ground truths. The model is made freely available in FastPathology and the code is available at https://github.com/AICAN-Research/breast-epithelium-segmentation

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

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.

The convolutional neural network-based methods have become more and more popular for medical image segmentation due to their outstanding performance. However, they struggle with capturing long-range dependencies, which are essential for accurately modeling global contextual correlations. Thanks to the ability to model long-range dependencies by expanding the receptive field, the transformer-based methods have gained prominence. Inspired by this, we propose an advanced 2D feature extraction method by combining the convolutional neural network and Transformer architectures. More specifically, we introduce a parallelized encoder structure, where one branch uses ResNet to extract local information from images, while the other branch uses Transformer to extract global information. Furthermore, we integrate pyramid structures into the Transformer to extract global information at varying resolutions, especially in intensive prediction tasks. To efficiently utilize the different information in the parallelized encoder at the decoder stage, we use a channel attention module to merge the features of the encoder and propagate them through skip connections and bottlenecks. Intensive numerical experiments are performed on both aortic vessel tree, cardiac, and multi-organ datasets. By comparing with state-of-the-art medical image segmentation methods, our method is shown with better segmentation accuracy, especially on small organs. The code is publicly available on https://github.com/HongkunSun/ParaTransCNN.

Vision transformer based models bring significant improvements for image segmentation tasks. Although these architectures offer powerful capabilities irrespective of specific segmentation tasks, their use of computational resources can be taxing on deployed devices. One way to overcome this challenge is by adapting the computation level to the specific needs of the input image rather than the current one-size-fits-all approach. To this end, we introduce ECO-M2F or EffiCient TransfOrmer Encoders for Mask2Former-style models. Noting that the encoder module of M2F-style models incur high resource-intensive computations, ECO-M2F provides a strategy to self-select the number of hidden layers in the encoder, conditioned on the input image. To enable this self-selection ability for providing a balance between performance and computational efficiency, we present a three step recipe. The first step is to train the parent architecture to enable early exiting from the encoder. The second step is to create an derived dataset of the ideal number of encoder layers required for each training example. The third step is to use the aforementioned derived dataset to train a gating network that predicts the number of encoder layers to be used, conditioned on the input image. Additionally, to change the computational-accuracy tradeoff, only steps two and three need to be repeated which significantly reduces retraining time. Experiments on the public datasets show that the proposed approach reduces expected encoder computational cost while maintaining performance, adapts to various user compute resources, is flexible in architecture configurations, and can be extended beyond the segmentation task to object detection.

Even though convolutional neural networks (CNNs) are driving progress in medical image segmentation, standard models still have some drawbacks. First, the use of multi-scale approaches, i.e., encoder-decoder architectures, leads to a redundant use of information, where similar low-level features are extracted multiple times at multiple scales. Second, long-range feature dependencies are not efficiently modeled, resulting in non-optimal discriminative feature representations associated with each semantic class. In this paper we attempt to overcome these limitations with the proposed architecture, by capturing richer contextual dependencies based on the use of guided self-attention mechanisms. This approach is able to integrate local features with their corresponding global dependencies, as well as highlight interdependent channel maps in an adaptive manner. Further, the additional loss between different modules guides the attention mechanisms to neglect irrelevant information and focus on more discriminant regions of the image by emphasizing relevant feature associations. We evaluate the proposed model in the context of semantic segmentation on three different datasets: abdominal organs, cardiovascular structures and brain tumors. A series of ablation experiments support the importance of these attention modules in the proposed architecture. In addition, compared to other state-of-the-art segmentation networks our model yields better segmentation performance, increasing the accuracy of the predictions while reducing the standard deviation. This demonstrates the efficiency of our approach to generate precise and reliable automatic segmentations of medical images. Our code is made publicly available at https://github.com/sinAshish/Multi-Scale-Attention

Efficiently quantifying renal structures can provide distinct spatial context and facilitate biomarker discovery for kidney morphology. However, the development and evaluation of the transformer model to segment the renal cortex, medulla, and collecting system remains challenging due to data inefficiency. Inspired by the hierarchical structures in vision transformer, we propose a novel method using a 3D block aggregation transformer for segmenting kidney components on contrast-enhanced CT scans. We construct the first cohort of renal substructures segmentation dataset with 116 subjects under institutional review board (IRB) approval. Our method yields the state-of-the-art performance (Dice of 0.8467) against the baseline approach of 0.8308 with the data-efficient design. The Pearson R achieves 0.9891 between the proposed method and manual standards and indicates the strong correlation and reproducibility for volumetric analysis. We extend the proposed method to the public KiTS dataset, the method leads to improved accuracy compared to transformer-based approaches. We show that the 3D block aggregation transformer can achieve local communication between sequence representations without modifying self-attention, and it can serve as an accurate and efficient quantification tool for characterizing renal structures.

Our approach, which we call Embeddings for Language/Image-aligned X-Rays, or ELIXR, leverages a language-aligned image encoder combined or grafted onto a fixed LLM, PaLM 2, to perform a broad range of tasks. We train this lightweight adapter architecture using images paired with corresponding free-text radiology reports from the MIMIC-CXR dataset. ELIXR achieved state-of-the-art performance on zero-shot chest X-ray (CXR) classification (mean AUC of 0.850 across 13 findings), data-efficient CXR classification (mean AUCs of 0.893 and 0.898 across five findings (atelectasis, cardiomegaly, consolidation, pleural effusion, and pulmonary edema) for 1% (~2,200 images) and 10% (~22,000 images) training data), and semantic search (0.76 normalized discounted cumulative gain (NDCG) across nineteen queries, including perfect retrieval on twelve of them). Compared to existing data-efficient methods including supervised contrastive learning (SupCon), ELIXR required two orders of magnitude less data to reach similar performance. ELIXR also showed promise on CXR vision-language tasks, demonstrating overall accuracies of 58.7% and 62.5% on visual question answering and report quality assurance tasks, respectively. These results suggest that ELIXR is a robust and versatile approach to CXR AI.

In this work, we explore a cost-effective framework for multilingual image generation. We find that, unlike models tuned on high-quality images with multilingual annotations, leveraging text encoders pre-trained on widely available, noisy Internet image-text pairs significantly enhances data efficiency in text-to-image (T2I) generation across multiple languages. Based on this insight, we introduce MuLan, Multi-Language adapter, a lightweight language adapter with fewer than 20M parameters, trained alongside a frozen text encoder and image diffusion model. Compared to previous multilingual T2I models, this framework offers: (1) Cost efficiency. Using readily accessible English data and off-the-shelf multilingual text encoders minimizes the training cost; (2) High performance. Achieving comparable generation capabilities in over 110 languages with CLIP similarity scores nearly matching those in English (38.61 for English vs. 37.61 for other languages); and (3) Broad applicability. Seamlessly integrating with compatible community tools like LoRA, LCM, ControlNet, and IP-Adapter, expanding its potential use cases.

Deep neural networks have introduced significant advancements in the field of machine learning-based analysis of digital pathology images including prostate tissue images. With the help of transfer learning, classification and segmentation performance of neural network models have been further increased. However, due to the absence of large, extensively annotated, publicly available prostate histopathology datasets, several previous studies employ datasets from well-studied computer vision tasks such as ImageNet dataset. In this work, we propose a transfer learning scheme from breast histopathology images to improve prostate cancer detection performance. We validate our approach on annotated prostate whole slide images by using a publicly available breast histopathology dataset as pre-training. We show that the proposed cross-cancer approach outperforms transfer learning from ImageNet dataset.

The field of computational pathology has been transformed with recent advances in foundation models that encode histopathology region-of-interests (ROIs) into versatile and transferable feature representations via self-supervised learning (SSL). However, translating these advancements to address complex clinical challenges at the patient and slide level remains constrained by limited clinical data in disease-specific cohorts, especially for rare clinical conditions. We propose TITAN, a multimodal whole slide foundation model pretrained using 335,645 WSIs via visual self-supervised learning and vision-language alignment with corresponding pathology reports and 423,122 synthetic captions generated from a multimodal generative AI copilot for pathology. Without any finetuning or requiring clinical labels, TITAN can extract general-purpose slide representations and generate pathology reports that generalize to resource-limited clinical scenarios such as rare disease retrieval and cancer prognosis. We evaluate TITAN on diverse clinical tasks and find that TITAN outperforms both ROI and slide foundation models across machine learning settings such as linear probing, few-shot and zero-shot classification, rare cancer retrieval and cross-modal retrieval, and pathology report generation.

Attention-based vision models, such as Vision Transformer (ViT) and its variants, have shown promising performance in various computer vision tasks. However, these emerging architectures suffer from large model sizes and high computational costs, calling for efficient model compression solutions. To date, pruning ViTs has been well studied, while other compression strategies that have been widely applied in CNN compression, e.g., model factorization, is little explored in the context of ViT compression. This paper explores an efficient method for compressing vision transformers to enrich the toolset for obtaining compact attention-based vision models. Based on the new insight on the multi-head attention layer, we develop a highly efficient ViT compression solution, which outperforms the state-of-the-art pruning methods. For compressing DeiT-small and DeiT-base models on ImageNet, our proposed approach can achieve 0.45% and 0.76% higher top-1 accuracy even with fewer parameters. Our finding can also be applied to improve the customization efficiency of text-to-image diffusion models, with much faster training (up to 2.6times speedup) and lower extra storage cost (up to 1927.5times reduction) than the existing works.

Nuclei detection and segmentation in hematoxylin and eosin-stained (H&E) tissue images are important clinical tasks and crucial for a wide range of applications. However, it is a challenging task due to nuclei variances in staining and size, overlapping boundaries, and nuclei clustering. While convolutional neural networks have been extensively used for this task, we explore the potential of Transformer-based networks in this domain. Therefore, we introduce a new method for automated instance segmentation of cell nuclei in digitized tissue samples using a deep learning architecture based on Vision Transformer called CellViT. CellViT is trained and evaluated on the PanNuke dataset, which is one of the most challenging nuclei instance segmentation datasets, consisting of nearly 200,000 annotated Nuclei into 5 clinically important classes in 19 tissue types. We demonstrate the superiority of large-scale in-domain and out-of-domain pre-trained Vision Transformers by leveraging the recently published Segment Anything Model and a ViT-encoder pre-trained on 104 million histological image patches - achieving state-of-the-art nuclei detection and instance segmentation performance on the PanNuke dataset with a mean panoptic quality of 0.50 and an F1-detection score of 0.83. The code is publicly available at https://github.com/TIO-IKIM/CellViT

Spatial transcriptomics (ST) enables interrogating the molecular composition of tissue with ever-increasing resolution, depth, and sensitivity. However, costs, rapidly evolving technology, and lack of standards have constrained computational methods in ST to narrow tasks and small cohorts. In addition, the underlying tissue morphology as reflected by H&E-stained whole slide images (WSIs) encodes rich information often overlooked in ST studies. Here, we introduce HEST-1k, a collection of 1,108 spatial transcriptomic profiles, each linked to a WSI and metadata. HEST-1k was assembled using HEST-Library from 131 public and internal cohorts encompassing 25 organs, two species (Homo Sapiens and Mus Musculus), and 320 cancer samples from 25 cancer types. HEST-1k processing enabled the identification of 1.5 million expression--morphology pairs and 60 million nuclei. HEST-1k is tested on three use cases: (1) benchmarking foundation models for histopathology (HEST-Benchmark), (2) biomarker identification, and (3) multimodal representation learning. HEST-1k, HEST-Library, and HEST-Benchmark can be freely accessed via https://github.com/mahmoodlab/hest.

Stain normalization algorithms aim to transform the color and intensity characteristics of a source multi-gigapixel histology image to match those of a target image, mitigating inconsistencies in the appearance of stains used to highlight cellular components in the images. We propose a new approach, StainFuser, which treats this problem as a style transfer task using a novel Conditional Latent Diffusion architecture, eliminating the need for handcrafted color components. With this method, we curate SPI-2M the largest stain normalization dataset to date of over 2 million histology images with neural style transfer for high-quality transformations. Trained on this data, StainFuser outperforms current state-of-the-art GAN and handcrafted methods in terms of the quality of normalized images. Additionally, compared to existing approaches, it improves the performance of nuclei instance segmentation and classification models when used as a test time augmentation method on the challenging CoNIC dataset. Finally, we apply StainFuser on multi-gigapixel Whole Slide Images (WSIs) and demonstrate improved performance in terms of computational efficiency, image quality and consistency across tiles over current methods.

Learned Image Compression (LIC) has shown remarkable progress in recent years. Existing works commonly employ CNN-based or self-attention-based modules as transform methods for compression. However, there is no prior research on neural transform that focuses on specific regions. In response, we introduce the class-agnostic segmentation masks (i.e. semantic masks without category labels) for extracting region-adaptive contextual information. Our proposed module, Region-Adaptive Transform, applies adaptive convolutions on different regions guided by the masks. Additionally, we introduce a plug-and-play module named Scale Affine Layer to incorporate rich contexts from various regions. While there have been prior image compression efforts that involve segmentation masks as additional intermediate inputs, our approach differs significantly from them. Our advantages lie in that, to avoid extra bitrate overhead, we treat these masks as privilege information, which is accessible during the model training stage but not required during the inference phase. To the best of our knowledge, we are the first to employ class-agnostic masks as privilege information and achieve superior performance in pixel-fidelity metrics, such as Peak Signal to Noise Ratio (PSNR). The experimental results demonstrate our improvement compared to previously well-performing methods, with about 8.2% bitrate saving compared to VTM-17.0. The source code is available at https://github.com/GityuxiLiu/SegPIC-for-Image-Compression.

In this paper, we present an efficient method for storing fine-tuned models by leveraging the low-rank properties of weight residuals. Our key observation is that weight residuals in large overparameterized models exhibit even stronger low-rank characteristics. Based on this insight, we propose Efficient Residual Encoding (ERE), a novel approach that achieves efficient storage of fine-tuned model weights by approximating the low-rank weight residuals. Furthermore, we analyze the robustness of weight residuals and push the limit of storage efficiency by utilizing additional quantization and layer-wise rank allocation. Our experimental results demonstrate that our method significantly reduces memory footprint while preserving performance in various tasks and modalities. We release our code.

We present Statistical Calibrated Activation Pruning (SCAP), a post-training activation pruning framework that (1) generalizes sparsification by input activations of Fully-Connected layers for generic and flexible application across Transformers, and (2) features a simple Mode-Centering technique to pre-calibrate activation distributions for maximizing post-training sparsity. Our results demonstrate robust Pareto efficiency compared to prior methods, translating to a 1.5x additional LLM decoding speedup against CATS at iso model quality. SCAP effectiveness is empirically verified across a wide range of models, including recent Transformer Decoders, MoE, Mamba2, Encoding Transformer, and pre-quantized models, highlighting its practicality and scalability. The code is available at: https://github.com/IntelLabs/SCAP.

Vision Language Models (VLMs) like CLIP have attracted substantial attention in pathology, serving as backbones for applications such as zero-shot image classification and Whole Slide Image (WSI) analysis. Additionally, they can function as vision encoders when combined with large language models (LLMs) to support broader capabilities. Current efforts to train pathology VLMs rely on pathology image-text pairs from platforms like PubMed, YouTube, and Twitter, which provide limited, unscalable data with generally suboptimal image quality. In this work, we leverage large-scale WSI datasets like TCGA to extract numerous high-quality image patches. We then train a large multimodal model to generate captions for these images, creating PathGen-1.6M, a dataset containing 1.6 million high-quality image-caption pairs. Our approach involves multiple agent models collaborating to extract representative WSI patches, generating and refining captions to obtain high-quality image-text pairs. Extensive experiments show that integrating these generated pairs with existing datasets to train a pathology-specific CLIP model, PathGen-CLIP, significantly enhances its ability to analyze pathological images, with substantial improvements across nine pathology-related zero-shot image classification tasks and three whole-slide image tasks. Furthermore, we construct 200K instruction-tuning data based on PathGen-1.6M and integrate PathGen-CLIP with the Vicuna LLM to create more powerful multimodal models through instruction tuning. Overall, we provide a scalable pathway for high-quality data generation in pathology, paving the way for next-generation general pathology models.

In recent years, the advent of foundation models (FM) for digital pathology has relied heavily on scaling the pre-training datasets and the model size, yielding large and powerful models. While it resulted in improving the performance on diverse downstream tasks, it also introduced increased computational cost and inference time. In this work, we explore the distillation of a large foundation model into a smaller one, reducing the number of parameters by several orders of magnitude. Leveraging distillation techniques, our distilled model, H0-mini, achieves nearly comparable performance to large FMs at a significantly reduced inference cost. It is evaluated on several public benchmarks, achieving 3rd place on the HEST benchmark and 5th place on the EVA benchmark. Additionally, a robustness analysis conducted on the PLISM dataset demonstrates that our distilled model reaches excellent robustness to variations in staining and scanning conditions, significantly outperforming other state-of-the art models. This opens new perspectives to design lightweight and robust models for digital pathology, without compromising on performance.

Large-scale text encoders in text-to-image (T2I) diffusion models have demonstrated exceptional performance in generating high-quality images from textual prompts. Unlike denoising modules that rely on multiple iterative steps, text encoders require only a single forward pass to produce text embeddings. However, despite their minimal contribution to total inference time and floating-point operations (FLOPs), text encoders demand significantly higher memory usage, up to eight times more than denoising modules. To address this inefficiency, we propose Skip and Re-use layers (Skrr), a simple yet effective pruning strategy specifically designed for text encoders in T2I diffusion models. Skrr exploits the inherent redundancy in transformer blocks by selectively skipping or reusing certain layers in a manner tailored for T2I tasks, thereby reducing memory consumption without compromising performance. Extensive experiments demonstrate that Skrr maintains image quality comparable to the original model even under high sparsity levels, outperforming existing blockwise pruning methods. Furthermore, Skrr achieves state-of-the-art memory efficiency while preserving performance across multiple evaluation metrics, including the FID, CLIP, DreamSim, and GenEval scores.

An increasing number of public datasets have shown a marked impact on automated organ segmentation and tumor detection. However, due to the small size and partially labeled problem of each dataset, as well as a limited investigation of diverse types of tumors, the resulting models are often limited to segmenting specific organs/tumors and ignore the semantics of anatomical structures, nor can they be extended to novel domains. To address these issues, we propose the CLIP-Driven Universal Model, which incorporates text embedding learned from Contrastive Language-Image Pre-training (CLIP) to segmentation models. This CLIP-based label encoding captures anatomical relationships, enabling the model to learn a structured feature embedding and segment 25 organs and 6 types of tumors. The proposed model is developed from an assembly of 14 datasets, using a total of 3,410 CT scans for training and then evaluated on 6,162 external CT scans from 3 additional datasets. We rank first on the Medical Segmentation Decathlon (MSD) public leaderboard and achieve state-of-the-art results on Beyond The Cranial Vault (BTCV). Additionally, the Universal Model is computationally more efficient (6x faster) compared with dataset-specific models, generalized better to CT scans from varying sites, and shows stronger transfer learning performance on novel tasks.

In this paper, a multi-scale visual transformer model, referred as GasHis-Transformer, is proposed for Gastric Histopathological Image Detection (GHID), which enables the automatic global detection of gastric cancer images. GasHis-Transformer model consists of two key modules designed to extract global and local information using a position-encoded transformer model and a convolutional neural network with local convolution, respectively. A publicly available hematoxylin and eosin (H&E) stained gastric histopathological image dataset is used in the experiment. Furthermore, a Dropconnect based lightweight network is proposed to reduce the model size and training time of GasHis-Transformer for clinical applications with improved confidence. Moreover, a series of contrast and extended experiments verify the robustness, extensibility and stability of GasHis-Transformer. In conclusion, GasHis-Transformer demonstrates high global detection performance and shows its significant potential in GHID task.

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.

Histopathology has played an essential role in cancer diagnosis. With the rapid advances in convolutional neural networks (CNN). Various CNN-based automated pathological image segmentation approaches have been developed in computer-assisted pathological image analysis. In the past few years, Transformer neural networks (Transformer) have shown the unique merit of capturing the global long-distance dependencies across the entire image as a new deep learning paradigm. Such merit is appealing for exploring spatially heterogeneous pathological images. However, there have been very few, if any, studies that have systematically evaluated the current Transformer-based approaches in pathological image segmentation. To assess the performance of Transformer segmentation models on whole slide images (WSI), we quantitatively evaluated six prevalent transformer-based models on tumor segmentation, using the widely used PAIP liver histopathological dataset. For a more comprehensive analysis, we also compare the transformer-based models with six major traditional CNN-based models. The results show that the Transformer-based models exhibit a general superior performance over the CNN-based models. In particular, Segmenter, Swin-Transformer and TransUNet-all transformer-based-came out as the best performers among the twelve evaluated models.

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.

Foundation models are rapidly being developed for computational pathology applications. However, it remains an open question which factors are most important for downstream performance with data scale and diversity, model size, and training algorithm all playing a role. In this work, we present the result of scaling both data and model size, surpassing previous studies in both dimensions, and introduce two new models: Virchow 2, a 632M parameter vision transformer, and Virchow 2G, a 1.85B parameter vision transformer, each trained with 3.1M histopathology whole slide images. To support this scale, we propose domain-inspired adaptations to the DINOv2 training algorithm, which is quickly becoming the default method in self-supervised learning for computational pathology. We achieve state of the art performance on twelve tile-level tasks, as compared to the top performing competing models. Our results suggest that data diversity and domain-specific training can outperform models that only scale in the number of parameters, but, on average, performance benefits from domain-tailoring, data scale, and model scale.

The recently introduced Segment Anything Model (SAM) combines a clever architecture and large quantities of training data to obtain remarkable image segmentation capabilities. However, it fails to reproduce such results for Out-Of-Distribution (OOD) domains such as medical images. Moreover, while SAM is conditioned on either a mask or a set of points, it may be desirable to have a fully automatic solution. In this work, we replace SAM's conditioning with an encoder that operates on the same input image. By adding this encoder and without further fine-tuning SAM, we obtain state-of-the-art results on multiple medical images and video benchmarks. This new encoder is trained via gradients provided by a frozen SAM. For inspecting the knowledge within it, and providing a lightweight segmentation solution, we also learn to decode it into a mask by a shallow deconvolution network.

Neural image compression methods have seen increasingly strong performance in recent years. However, they suffer orders of magnitude higher computational complexity compared to traditional codecs, which stands in the way of real-world deployment. This paper takes a step forward in closing this gap in decoding complexity by adopting shallow or even linear decoding transforms. To compensate for the resulting drop in compression performance, we exploit the often asymmetrical computation budget between encoding and decoding, by adopting more powerful encoder networks and iterative encoding. We theoretically formalize the intuition behind, and our experimental results establish a new frontier in the trade-off between rate-distortion and decoding complexity for neural image compression. Specifically, we achieve rate-distortion performance competitive with the established mean-scale hyperprior architecture of Minnen et al. (2018), while reducing the overall decoding complexity by 80 %, or over 90 % for the synthesis transform alone. Our code can be found at https://github.com/mandt-lab/shallow-ntc.

The use of artificial intelligence to enable precision medicine and decision support systems through the analysis of pathology images has the potential to revolutionize the diagnosis and treatment of cancer. Such applications will depend on models' abilities to capture the diverse patterns observed in pathology images. To address this challenge, we present Virchow, a foundation model for computational pathology. Using self-supervised learning empowered by the DINOv2 algorithm, Virchow is a vision transformer model with 632 million parameters trained on 1.5 million hematoxylin and eosin stained whole slide images from diverse tissue and specimen types, which is orders of magnitude more data than previous works. The Virchow model enables the development of a pan-cancer detection system with 0.949 overall specimen-level AUC across 17 different cancer types, while also achieving 0.937 AUC on 7 rare cancer types. The Virchow model sets the state-of-the-art on the internal and external image tile level benchmarks and slide level biomarker prediction tasks. The gains in performance highlight the importance of training on massive pathology image datasets, suggesting scaling up the data and network architecture can improve the accuracy for many high-impact computational pathology applications where limited amounts of training data are available.

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.

We extend first-order model agnostic meta-learning algorithms (including FOMAML and Reptile) to image segmentation, present a novel neural network architecture built for fast learning which we call EfficientLab, and leverage a formal definition of the test error of meta-learning algorithms to decrease error on out of distribution tasks. We show state of the art results on the FSS-1000 dataset by meta-training EfficientLab with FOMAML and using Bayesian optimization to infer the optimal test-time adaptation routine hyperparameters. We also construct a small benchmark dataset, FP-k, for the empirical study of how meta-learning systems perform in both few- and many-shot settings. On the FP-k dataset, we show that meta-learned initializations provide value for canonical few-shot image segmentation but their performance is quickly matched by conventional transfer learning with performance being equal beyond 10 labeled examples. Our code, meta-learned model, and the FP-k dataset are available at https://github.com/ml4ai/mliis .

We propose a new model for digital pathology segmentation, based on the observation that histopathology images are inherently symmetric under rotation and reflection. Utilizing recent findings on rotation equivariant CNNs, the proposed model leverages these symmetries in a principled manner. We present a visual analysis showing improved stability on predictions, and demonstrate that exploiting rotation equivariance significantly improves tumor detection performance on a challenging lymph node metastases dataset. We further present a novel derived dataset to enable principled comparison of machine learning models, in combination with an initial benchmark. Through this dataset, the task of histopathology diagnosis becomes accessible as a challenging benchmark for fundamental machine learning research.

Representation learning of pathology whole-slide images (WSIs) has primarily relied on weak supervision with Multiple Instance Learning (MIL). This approach leads to slide representations highly tailored to a specific clinical task. Self-supervised learning (SSL) has been successfully applied to train histopathology foundation models (FMs) for patch embedding generation. However, generating patient or slide level embeddings remains challenging. Existing approaches for slide representation learning extend the principles of SSL from patch level learning to entire slides by aligning different augmentations of the slide or by utilizing multimodal data. By integrating tile embeddings from multiple FMs, we propose a new single modality SSL method in feature space that generates useful slide representations. Our contrastive pretraining strategy, called COBRA, employs multiple FMs and an architecture based on Mamba-2. COBRA exceeds performance of state-of-the-art slide encoders on four different public CPTAC cohorts on average by at least +3.8% AUC, despite only being pretrained on 3048 WSIs from TCGA. Additionally, COBRA is readily compatible at inference time with previously unseen feature extractors.

Automatic organ segmentation is an important yet challenging problem for medical image analysis. The pancreas is an abdominal organ with very high anatomical variability. This inhibits previous segmentation methods from achieving high accuracies, especially compared to other organs such as the liver, heart or kidneys. In this paper, we present a probabilistic bottom-up approach for pancreas segmentation in abdominal computed tomography (CT) scans, using multi-level deep convolutional networks (ConvNets). We propose and evaluate several variations of deep ConvNets in the context of hierarchical, coarse-to-fine classification on image patches and regions, i.e. superpixels. We first present a dense labeling of local image patches via P{-}ConvNet and nearest neighbor fusion. Then we describe a regional ConvNet (R_1{-}ConvNet) that samples a set of bounding boxes around each image superpixel at different scales of contexts in a "zoom-out" fashion. Our ConvNets learn to assign class probabilities for each superpixel region of being pancreas. Last, we study a stacked R_2{-}ConvNet leveraging the joint space of CT intensities and the P{-}ConvNet dense probability maps. Both 3D Gaussian smoothing and 2D conditional random fields are exploited as structured predictions for post-processing. We evaluate on CT images of 82 patients in 4-fold cross-validation. We achieve a Dice Similarity Coefficient of 83.6pm6.3% in training and 71.8pm10.7% in testing.

Recent advancements in digital pathology have led to the development of numerous foundational models that utilize self-supervised learning on patches extracted from gigapixel whole slide images (WSIs). While this approach leverages vast amounts of unlabeled data, we have discovered a significant issue: features extracted from these self-supervised models tend to cluster by individual WSIs, a phenomenon we term WSI-specific feature collapse. This problem can potentially limit the model's generalization ability and performance on various downstream tasks. To address this issue, we introduce Stain Normalized Pathology Foundational Model, a novel foundational model trained on patches that have undergone stain normalization. Stain normalization helps reduce color variability arising from different laboratories and scanners, enabling the model to learn more consistent features. Stain Normalized Pathology Foundational Model is trained using 285,153,903 patches extracted from a total of 34,795 WSIs, combining data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. Our experiments demonstrate that Stain Normalized Pathology Foundational Model significantly mitigates the feature collapse problem, indicating that the model has learned more generalized features rather than overfitting to individual WSI characteristics. We compared Stain Normalized Pathology Foundational Model with state-of-the-art models across six downstream task datasets, and our results show that Stain Normalized Pathology Foundational Model achieves excellent performance relative to the number of WSIs used and the model's parameter count. This suggests that the application of stain normalization has substantially improved the model's efficiency and generalization capabilities.

Recently, most handwritten mathematical expression recognition (HMER) methods adopt the encoder-decoder networks, which directly predict the markup sequences from formula images with the attention mechanism. However, such methods may fail to accurately read formulas with complicated structure or generate long markup sequences, as the attention results are often inaccurate due to the large variance of writing styles or spatial layouts. To alleviate this problem, we propose an unconventional network for HMER named Counting-Aware Network (CAN), which jointly optimizes two tasks: HMER and symbol counting. Specifically, we design a weakly-supervised counting module that can predict the number of each symbol class without the symbol-level position annotations, and then plug it into a typical attention-based encoder-decoder model for HMER. Experiments on the benchmark datasets for HMER validate that both joint optimization and counting results are beneficial for correcting the prediction errors of encoder-decoder models, and CAN consistently outperforms the state-of-the-art methods. In particular, compared with an encoder-decoder model for HMER, the extra time cost caused by the proposed counting module is marginal. The source code is available at https://github.com/LBH1024/CAN.

Whole Slide Image (WSI) classification with multiple instance learning (MIL) in digital pathology faces significant computational challenges. Current methods mostly rely on extensive self-supervised learning (SSL) for satisfactory performance, requiring long training periods and considerable computational resources. At the same time, no pre-training affects performance due to domain shifts from natural images to WSIs. We introduce Snuffy architecture, a novel MIL-pooling method based on sparse transformers that mitigates performance loss with limited pre-training and enables continual few-shot pre-training as a competitive option. Our sparsity pattern is tailored for pathology and is theoretically proven to be a universal approximator with the tightest probabilistic sharp bound on the number of layers for sparse transformers, to date. We demonstrate Snuffy's effectiveness on CAMELYON16 and TCGA Lung cancer datasets, achieving superior WSI and patch-level accuracies. The code is available on https://github.com/jafarinia/snuffy.

The recent surge in performance for image analysis of digitised pathology slides can largely be attributed to the advances in deep learning. Deep models can be used to initially localise various structures in the tissue and hence facilitate the extraction of interpretable features for biomarker discovery. However, these models are typically trained for a single task and therefore scale poorly as we wish to adapt the model for an increasing number of different tasks. Also, supervised deep learning models are very data hungry and therefore rely on large amounts of training data to perform well. In this paper, we present a multi-task learning approach for segmentation and classification of nuclei, glands, lumina and different tissue regions that leverages data from multiple independent data sources. While ensuring that our tasks are aligned by the same tissue type and resolution, we enable meaningful simultaneous prediction with a single network. As a result of feature sharing, we also show that the learned representation can be used to improve the performance of additional tasks via transfer learning, including nuclear classification and signet ring cell detection. As part of this work, we train our developed Cerberus model on a huge amount of data, consisting of over 600K objects for segmentation and 440K patches for classification. We use our approach to process 599 colorectal whole-slide images from TCGA, where we localise 377 million, 900K and 2.1 million nuclei, glands and lumina, respectively and make the results available to the community for downstream analysis.

We present EfficientViT-SAM, a new family of accelerated segment anything models. We retain SAM's lightweight prompt encoder and mask decoder while replacing the heavy image encoder with EfficientViT. For the training, we begin with the knowledge distillation from the SAM-ViT-H image encoder to EfficientViT. Subsequently, we conduct end-to-end training on the SA-1B dataset. Benefiting from EfficientViT's efficiency and capacity, EfficientViT-SAM delivers 48.9x measured TensorRT speedup on A100 GPU over SAM-ViT-H without sacrificing performance. Our code and pre-trained models are released at https://github.com/mit-han-lab/efficientvit.

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyperparameters in different experimental settings. Here, we present a multi-modality cell segmentation benchmark, comprising over 1500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods, but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.

Foundation models are reshaping computational pathology by enabling transfer learning, where models pre-trained on vast datasets can be adapted for downstream diagnostic, prognostic, and therapeutic response tasks. Despite these advances, foundation models are still limited in their ability to encode the entire gigapixel whole-slide images without additional training and often lack complementary multimodal data. Here, we introduce Threads, a slide-level foundation model capable of generating universal representations of whole-slide images of any size. Threads was pre-trained using a multimodal learning approach on a diverse cohort of 47,171 hematoxylin and eosin (H&E)-stained tissue sections, paired with corresponding genomic and transcriptomic profiles - the largest such paired dataset to be used for foundation model development to date. This unique training paradigm enables Threads to capture the tissue's underlying molecular composition, yielding powerful representations applicable to a wide array of downstream tasks. In extensive benchmarking across 54 oncology tasks, including clinical subtyping, grading, mutation prediction, immunohistochemistry status determination, treatment response prediction, and survival prediction, Threads outperformed all baselines while demonstrating remarkable generalizability and label efficiency. It is particularly well suited for predicting rare events, further emphasizing its clinical utility. We intend to make the model publicly available for the broader community.

Multimodal Large Language Models (MLLMs) have experienced significant advancements recently. Nevertheless, challenges persist in the accurate recognition and comprehension of intricate details within high-resolution images. Despite being indispensable for the development of robust MLLMs, this area remains underinvestigated. To tackle this challenge, our work introduces InfiMM-HD, a novel architecture specifically designed for processing images of different resolutions with low computational overhead. This innovation facilitates the enlargement of MLLMs to higher-resolution capabilities. InfiMM-HD incorporates a cross-attention module and visual windows to reduce computation costs. By integrating this architectural design with a four-stage training pipeline, our model attains improved visual perception efficiently and cost-effectively. Empirical study underscores the robustness and effectiveness of InfiMM-HD, opening new avenues for exploration in related areas. Codes and models can be found at https://huggingface.co/Infi-MM/infimm-hd

Domain generalization is critical for real-world applications of machine learning to microscopy images, including histopathology and fluorescence imaging. Artifacts in these modalities arise through a complex combination of factors relating to tissue collection and laboratory processing, as well as factors intrinsic to patient samples. In fluorescence imaging, these artifacts stem from variations across experimental batches. The complexity and subtlety of these artifacts make the enumeration of data domains intractable. Therefore, augmentation-based methods of domain generalization that require domain identifiers and manual fine-tuning are inadequate in this setting. To overcome this challenge, we introduce ContriMix, a domain generalization technique that learns to generate synthetic images by disentangling and permuting the biological content ("content") and technical variations ("attributes") in microscopy images. ContriMix does not rely on domain identifiers or handcrafted augmentations and makes no assumptions about the input characteristics of images. We assess the performance of ContriMix on two pathology datasets dealing with patch classification and Whole Slide Image label prediction tasks respectively (Camelyon17-WILDS and RCC subtyping), and one fluorescence microscopy dataset (RxRx1-WILDS). Without any access to domain identifiers at train or test time, ContriMix performs similar or better than current state-of-the-art methods in all these datasets, motivating its usage for microscopy image analysis in real-world settings where domain information is hard to come by. The code for ContriMix can be found at https://gitlab.com/huutan86/contrimix

Contemporary lossy image and video coding standards rely on transform coding, the process through which pixels are mapped to an alternative representation to facilitate efficient data compression. Despite impressive performance of end-to-end optimized compression with deep neural networks, the high computational and space demands of these models has prevented them from superseding the relatively simple transform coding found in conventional video codecs. In this study, we propose learned transforms and entropy coding that may either serve as (non)linear drop-in replacements, or enhancements for linear transforms in existing codecs. These transforms can be multi-rate, allowing a single model to operate along the entire rate-distortion curve. To demonstrate the utility of our framework, we augmented the DCT with learned quantization matrices and adaptive entropy coding to compress intra-frame AV1 block prediction residuals. We report substantial BD-rate and perceptual quality improvements over more complex nonlinear transforms at a fraction of the computational cost.

In this paper, we introduce a novel unsupervised network to denoise microscopy videos featured by image sequences captured by a fixed location microscopy camera. Specifically, we propose a DeepTemporal Interpolation method, leveraging a temporal signal filter integrated into the bottom CNN layers, to restore microscopy videos corrupted by unknown noise types. Our unsupervised denoising architecture is distinguished by its ability to adapt to multiple noise conditions without the need for pre-existing noise distribution knowledge, addressing a significant challenge in real-world medical applications. Furthermore, we evaluate our denoising framework using both real microscopy recordings and simulated data, validating our outperforming video denoising performance across a broad spectrum of noise scenarios. Extensive experiments demonstrate that our unsupervised model consistently outperforms state-of-the-art supervised and unsupervised video denoising techniques, proving especially effective for microscopy videos.

We present Deep Compression Autoencoder (DC-AE), a new family of autoencoder models for accelerating high-resolution diffusion models. Existing autoencoder models have demonstrated impressive results at a moderate spatial compression ratio (e.g., 8x), but fail to maintain satisfactory reconstruction accuracy for high spatial compression ratios (e.g., 64x). We address this challenge by introducing two key techniques: (1) Residual Autoencoding, where we design our models to learn residuals based on the space-to-channel transformed features to alleviate the optimization difficulty of high spatial-compression autoencoders; (2) Decoupled High-Resolution Adaptation, an efficient decoupled three-phases training strategy for mitigating the generalization penalty of high spatial-compression autoencoders. With these designs, we improve the autoencoder's spatial compression ratio up to 128 while maintaining the reconstruction quality. Applying our DC-AE to latent diffusion models, we achieve significant speedup without accuracy drop. For example, on ImageNet 512x512, our DC-AE provides 19.1x inference speedup and 17.9x training speedup on H100 GPU for UViT-H while achieving a better FID, compared with the widely used SD-VAE-f8 autoencoder. Our code is available at https://github.com/mit-han-lab/efficientvit.

The task of recognising Handwritten Mathematical Expressions (HMER) is crucial in the fields of digital education and scholarly research. However, it is difficult to accurately determine the length and complex spatial relationships among symbols in handwritten mathematical expressions. In this study, we present a novel encoder-decoder architecture (DenseBAM-GI) for HMER, where the encoder has a Bottleneck Attention Module (BAM) to improve feature representation and the decoder has a Gated Input-GRU (GI-GRU) unit with an extra gate to make decoding long and complex expressions easier. The proposed model is an efficient and lightweight architecture with performance equivalent to state-of-the-art models in terms of Expression Recognition Rate (exprate). It also performs better in terms of top 1, 2, and 3 error accuracy across the CROHME 2014, 2016, and 2019 datasets. DenseBAM-GI achieves the best exprate among all models on the CROHME 2019 dataset. Importantly, these successes are accomplished with a drop in the complexity of the calculation and a reduction in the need for GPU memory.

Prevailing Multimodal Large Language Models (MLLMs) encode the input image(s) as vision tokens and feed them into the language backbone, similar to how Large Language Models (LLMs) process the text tokens. However, the number of vision tokens increases quadratically as the image resolutions, leading to huge computational costs. In this paper, we consider improving MLLM's efficiency from two scenarios, (I) Reducing computational cost without degrading the performance. (II) Improving the performance with given budgets. We start with our main finding that the ranking of each vision token sorted by attention scores is similar in each layer except the first layer. Based on it, we assume that the number of essential top vision tokens does not increase along layers. Accordingly, for Scenario I, we propose a greedy search algorithm (G-Search) to find the least number of vision tokens to keep at each layer from the shallow to the deep. Interestingly, G-Search is able to reach the optimal reduction strategy based on our assumption. For Scenario II, based on the reduction strategy from G-Search, we design a parametric sigmoid function (P-Sigmoid) to guide the reduction at each layer of the MLLM, whose parameters are optimized by Bayesian Optimization. Extensive experiments demonstrate that our approach can significantly accelerate those popular MLLMs, e.g. LLaVA, and InternVL2 models, by more than 2 times without performance drops. Our approach also far outperforms other token reduction methods when budgets are limited, achieving a better trade-off between efficiency and effectiveness.

We introduce Sana, a text-to-image framework that can efficiently generate images up to 4096times4096 resolution. Sana can synthesize high-resolution, high-quality images with strong text-image alignment at a remarkably fast speed, deployable on laptop GPU. Core designs include: (1) Deep compression autoencoder: unlike traditional AEs, which compress images only 8times, we trained an AE that can compress images 32times, effectively reducing the number of latent tokens. (2) Linear DiT: we replace all vanilla attention in DiT with linear attention, which is more efficient at high resolutions without sacrificing quality. (3) Decoder-only text encoder: we replaced T5 with modern decoder-only small LLM as the text encoder and designed complex human instruction with in-context learning to enhance the image-text alignment. (4) Efficient training and sampling: we propose Flow-DPM-Solver to reduce sampling steps, with efficient caption labeling and selection to accelerate convergence. As a result, Sana-0.6B is very competitive with modern giant diffusion model (e.g. Flux-12B), being 20 times smaller and 100+ times faster in measured throughput. Moreover, Sana-0.6B can be deployed on a 16GB laptop GPU, taking less than 1 second to generate a 1024times1024 resolution image. Sana enables content creation at low cost. Code and model will be publicly released.

Domain adaptation (DA) has drawn high interest for its capacity to adapt a model trained on labeled source data to perform well on unlabeled or weakly labeled target data from a different domain. Most common DA techniques require concurrent access to the input images of both the source and target domains. However, in practice, privacy concerns often impede the availability of source images in the adaptation phase. This is a very frequent DA scenario in medical imaging, where, for instance, the source and target images could come from different clinical sites. We introduce a source-free domain adaptation for image segmentation. Our formulation is based on minimizing a label-free entropy loss defined over target-domain data, which we further guide with a domain-invariant prior on the segmentation regions. Many priors can be derived from anatomical information. Here, a class ratio prior is estimated from anatomical knowledge and integrated in the form of a Kullback Leibler (KL) divergence in our overall loss function. Furthermore, we motivate our overall loss with an interesting link to maximizing the mutual information between the target images and their label predictions. We show the effectiveness of our prior aware entropy minimization in a variety of domain-adaptation scenarios, with different modalities and applications, including spine, prostate, and cardiac segmentation. Our method yields comparable results to several state of the art adaptation techniques, despite having access to much less information, as the source images are entirely absent in our adaptation phase. Our straightforward adaptation strategy uses only one network, contrary to popular adversarial techniques, which are not applicable to a source-free DA setting. Our framework can be readily used in a breadth of segmentation problems, and our code is publicly available: https://github.com/mathilde-b/SFDA

Advancing AI in computational pathology requires large, high-quality, and diverse datasets, yet existing public datasets are often limited in organ diversity, class coverage, or annotation quality. To bridge this gap, we introduce SPIDER (Supervised Pathology Image-DEscription Repository), the largest publicly available patch-level dataset covering multiple organ types, including Skin, Colorectal, and Thorax, with comprehensive class coverage for each organ. SPIDER provides high-quality annotations verified by expert pathologists and includes surrounding context patches, which enhance classification performance by providing spatial context. Alongside the dataset, we present baseline models trained on SPIDER using the Hibou-L foundation model as a feature extractor combined with an attention-based classification head. The models achieve state-of-the-art performance across multiple tissue categories and serve as strong benchmarks for future digital pathology research. Beyond patch classification, the model enables rapid identification of significant areas, quantitative tissue metrics, and establishes a foundation for multimodal approaches. Both the dataset and trained models are publicly available to advance research, reproducibility, and AI-driven pathology development. Access them at: https://github.com/HistAI/SPIDER

Single cell analysis of human skeletal muscle (SM) tissue cross-sections is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be automatic and precise. Biomedical scientists in this field currently rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to fine-tune segmentation. We believe that fully automated, precise, reproducible segmentation is possible by training ML models. However, in this important biomedical domain, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human SM tissue cross-sections from both healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include > 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibre segmentations, annotating reasons for rejecting low quality myofibres and low quality regions in SM tissue images, making these annotations completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

Anatomical segmentation is a fundamental task in medical image computing, generally tackled with fully convolutional neural networks which produce dense segmentation masks. These models are often trained with loss functions such as cross-entropy or Dice, which assume pixels to be independent of each other, thus ignoring topological errors and anatomical inconsistencies. We address this limitation by moving from pixel-level to graph representations, which allow to naturally incorporate anatomical constraints by construction. To this end, we introduce HybridGNet, an encoder-decoder neural architecture that leverages standard convolutions for image feature encoding and graph convolutional neural networks (GCNNs) to decode plausible representations of anatomical structures. We also propose a novel image-to-graph skip connection layer which allows localized features to flow from standard convolutional blocks to GCNN blocks, and show that it improves segmentation accuracy. The proposed architecture is extensively evaluated in a variety of domain shift and image occlusion scenarios, and audited considering different types of demographic domain shift. Our comprehensive experimental setup compares HybridGNet with other landmark and pixel-based models for anatomical segmentation in chest x-ray images, and shows that it produces anatomically plausible results in challenging scenarios where other models tend to fail.

We introduce a radiology-focused visual language model designed to generate radiology reports from chest X-rays. Building on previous findings that large language models (LLMs) can acquire multimodal capabilities when aligned with pretrained vision encoders, we demonstrate similar potential with chest X-ray images. This integration enhances the ability of model to understand and describe chest X-ray images. Our model combines an image encoder with a fine-tuned LLM based on the Vicuna-7B architecture, enabling it to generate different sections of a radiology report with notable accuracy. The training process involves a two-stage approach: (i) initial alignment of chest X-ray features with the LLM (ii) followed by fine-tuning for radiology report generation.

We present a self-supervised U-Net-based masked autoencoder and noise removal model designed to reconstruct original images. Once adequately trained, this model extracts high-level features, which are then combined with features from the EfficientNet B7 model. These integrated features are subsequently fed into dense layers for classification. Among the approaches of masked input and Gaussian noise removal, we selected the best U-Net reconstruction model. Additionally, we explored various configurations, including EfficientNet with attention, attention fusion of the autoencoder, and classification utilizing U-Net encoder features. The best performance was achieved with EfficientNet B7 combined with U-Net encoder features. We employed the Adam optimizer with a learning rate of 0.0001, achieving a top accuracy of 0.94 on the validation set.

Cell instance segmentation in cytology images has significant importance for biology analysis and cancer screening, while remains challenging due to 1) the extensive overlapping translucent cell clusters that cause the ambiguous boundaries, and 2) the confusion of mimics and debris as nuclei. In this work, we proposed a De-overlapping Network (DoNet) in a decompose-and-recombined strategy. A Dual-path Region Segmentation Module (DRM) explicitly decomposes the cell clusters into intersection and complement regions, followed by a Semantic Consistency-guided Recombination Module (CRM) for integration. To further introduce the containment relationship of the nucleus in the cytoplasm, we design a Mask-guided Region Proposal Strategy (MRP) that integrates the cell attention maps for inner-cell instance prediction. We validate the proposed approach on ISBI2014 and CPS datasets. Experiments show that our proposed DoNet significantly outperforms other state-of-the-art (SOTA) cell instance segmentation methods. The code is available at https://github.com/DeepDoNet/DoNet.

In healthcare, medical image segmentation is crucial for accurate disease diagnosis and the development of effective treatment strategies. Early detection can significantly aid in managing diseases and potentially prevent their progression. Machine learning, particularly deep convolutional neural networks, has emerged as a promising approach to addressing segmentation challenges. Traditional methods like U-Net use encoding blocks for local representation modeling and decoding blocks to uncover semantic relationships. However, these models often struggle with multi-scale objects exhibiting significant variations in texture and shape, and they frequently fail to capture long-range dependencies in the input data. Transformers designed for sequence-to-sequence predictions have been proposed as alternatives, utilizing global self-attention mechanisms. Yet, they can sometimes lack precise localization due to insufficient granular details. To overcome these limitations, we introduce TransDAE: a novel approach that reimagines the self-attention mechanism to include both spatial and channel-wise associations across the entire feature space, while maintaining computational efficiency. Additionally, TransDAE enhances the skip connection pathway with an inter-scale interaction module, promoting feature reuse and improving localization accuracy. Remarkably, TransDAE outperforms existing state-of-the-art methods on the Synaps multi-organ dataset, even without relying on pre-trained weights.

Recent work on mini-batch consistency (MBC) for set functions has brought attention to the need for sequentially processing and aggregating chunks of a partitioned set while guaranteeing the same output for all partitions. However, existing constraints on MBC architectures lead to models with limited expressive power. Additionally, prior work has not addressed how to deal with large sets during training when the full set gradient is required. To address these issues, we propose a Universally MBC (UMBC) class of set functions which can be used in conjunction with arbitrary non-MBC components while still satisfying MBC, enabling a wider range of function classes to be used in MBC settings. Furthermore, we propose an efficient MBC training algorithm which gives an unbiased approximation of the full set gradient and has a constant memory overhead for any set size for both train- and test-time. We conduct extensive experiments including image completion, text classification, unsupervised clustering, and cancer detection on high-resolution images to verify the efficiency and efficacy of our scalable set encoding framework. Our code is available at github.com/jeffwillette/umbc

Utilizing massive web-scale datasets has led to unprecedented performance gains in machine learning models, but also imposes outlandish compute requirements for their training. In order to improve training and data efficiency, we here push the limits of pruning large-scale multimodal datasets for training CLIP-style models. Today's most effective pruning method on ImageNet clusters data samples into separate concepts according to their embedding and prunes away the most prototypical samples. We scale this approach to LAION and improve it by noting that the pruning rate should be concept-specific and adapted to the complexity of the concept. Using a simple and intuitive complexity measure, we are able to reduce the training cost to a quarter of regular training. By filtering from the LAION dataset, we find that training on a smaller set of high-quality data can lead to higher performance with significantly lower training costs. More specifically, we are able to outperform the LAION-trained OpenCLIP-ViT-B32 model on ImageNet zero-shot accuracy by 1.1p.p. while only using 27.7% of the data and training compute. Despite a strong reduction in training cost, we also see improvements on ImageNet dist. shifts, retrieval tasks and VTAB. On the DataComp Medium benchmark, we achieve a new state-of-the-art ImageNet zero-shot accuracy and a competitive average zero-shot accuracy on 38 evaluation tasks.

In the domain of computer vision, Parameter-Efficient Tuning (PET) is increasingly replacing the traditional paradigm of pre-training followed by full fine-tuning. PET is particularly favored for its effectiveness in large foundation models, as it streamlines transfer learning costs and optimizes hardware utilization. However, the current PET methods are mainly designed for single-modal optimization. While some pioneering studies have undertaken preliminary explorations, they still remain at the level of aligned encoders (e.g., CLIP) and lack exploration of misaligned encoders. These methods show sub-optimal performance with misaligned encoders, as they fail to effectively align the multimodal features during fine-tuning. In this paper, we introduce DETRIS, a parameter-efficient tuning framework designed to enhance low-rank visual feature propagation by establishing dense interconnections between each layer and all preceding layers, which enables effective cross-modal feature interaction and adaptation to misaligned encoders. We also suggest using text adapters to improve textual features. Our simple yet efficient approach greatly surpasses state-of-the-art methods with 0.9% to 1.8% backbone parameter updates, evaluated on challenging benchmarks. Our project is available at https://github.com/jiaqihuang01/DETRIS.

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

We need billion-scale images to achieve more generalizable and ground-breaking vision models, as well as massive dataset storage to ship the images (e.g., the LAION-4B dataset needs 240TB storage space). However, it has become challenging to deal with unlimited dataset storage with limited storage infrastructure. A number of storage-efficient training methods have been proposed to tackle the problem, but they are rarely scalable or suffer from severe damage to performance. In this paper, we propose a storage-efficient training strategy for vision classifiers for large-scale datasets (e.g., ImageNet) that only uses 1024 tokens per instance without using the raw level pixels; our token storage only needs <1% of the original JPEG-compressed raw pixels. We also propose token augmentations and a Stem-adaptor module to make our approach able to use the same architecture as pixel-based approaches with only minimal modifications on the stem layer and the carefully tuned optimization settings. Our experimental results on ImageNet-1k show that our method significantly outperforms other storage-efficient training methods with a large gap. We further show the effectiveness of our method in other practical scenarios, storage-efficient pre-training, and continual learning. Code is available at https://github.com/naver-ai/seit

We study neural image compression based on the Sparse Visual Representation (SVR), where images are embedded into a discrete latent space spanned by learned visual codebooks. By sharing codebooks with the decoder, the encoder transfers integer codeword indices that are efficient and cross-platform robust, and the decoder retrieves the embedded latent feature using the indices for reconstruction. Previous SVR-based compression lacks effective mechanism for rate-distortion tradeoffs, where one can only pursue either high reconstruction quality or low transmission bitrate. We propose a Masked Adaptive Codebook learning (M-AdaCode) method that applies masks to the latent feature subspace to balance bitrate and reconstruction quality. A set of semantic-class-dependent basis codebooks are learned, which are weighted combined to generate a rich latent feature for high-quality reconstruction. The combining weights are adaptively derived from each input image, providing fidelity information with additional transmission costs. By masking out unimportant weights in the encoder and recovering them in the decoder, we can trade off reconstruction quality for transmission bits, and the masking rate controls the balance between bitrate and distortion. Experiments over the standard JPEG-AI dataset demonstrate the effectiveness of our M-AdaCode approach.

Visual encoding constitutes the basis of large multimodal models (LMMs) in understanding the visual world. Conventional LMMs process images in fixed sizes and limited resolutions, while recent explorations in this direction are limited in adaptivity, efficiency, and even correctness. In this work, we first take GPT-4V and LLaVA-1.5 as representative examples and expose systematic flaws rooted in their visual encoding strategy. To address the challenges, we present LLaVA-UHD, a large multimodal model that can efficiently perceive images in any aspect ratio and high resolution. LLaVA-UHD includes three key components: (1) An image modularization strategy that divides native-resolution images into smaller variable-sized slices for efficient and extensible encoding, (2) a compression module that further condenses image tokens from visual encoders, and (3) a spatial schema to organize slice tokens for LLMs. Comprehensive experiments show that LLaVA-UHD outperforms established LMMs trained with 2-3 orders of magnitude more data on 9 benchmarks. Notably, our model built on LLaVA-1.5 336x336 supports 6 times larger (i.e., 672x1088) resolution images using only 94% inference computation, and achieves 6.4 accuracy improvement on TextVQA. Moreover, the model can be efficiently trained in academic settings, within 23 hours on 8 A100 GPUs (vs. 26 hours of LLaVA-1.5). We make the data and code publicly available at https://github.com/thunlp/LLaVA-UHD.

This paper investigates the capability of plain Vision Transformers (ViTs) for semantic segmentation using the encoder-decoder framework and introduces SegViTv2. In this study, we introduce a novel Attention-to-Mask (\atm) module to design a lightweight decoder effective for plain ViT. The proposed ATM converts the global attention map into semantic masks for high-quality segmentation results. Our decoder outperforms the popular decoder UPerNet using various ViT backbones while consuming only about 5% of the computational cost. For the encoder, we address the concern of the relatively high computational cost in the ViT-based encoders and propose a Shrunk++ structure that incorporates edge-aware query-based down-sampling (EQD) and query-based upsampling (QU) modules. The Shrunk++ structure reduces the computational cost of the encoder by up to 50% while maintaining competitive performance. Furthermore, we propose to adapt SegViT for continual semantic segmentation, demonstrating nearly zero forgetting of previously learned knowledge. Experiments show that our proposed SegViTv2 surpasses recent segmentation methods on three popular benchmarks including ADE20k, COCO-Stuff-10k and PASCAL-Context datasets. The code is available through the following link: https://github.com/zbwxp/SegVit.

Instance-level image classification tasks have traditionally relied on single-instance labels to train models, e.g., few-shot learning and transfer learning. However, set-level coarse-grained labels that capture relationships among instances can provide richer information in real-world scenarios. In this paper, we present a novel approach to enhance instance-level image classification by leveraging set-level labels. We provide a theoretical analysis of the proposed method, including recognition conditions for fast excess risk rate, shedding light on the theoretical foundations of our approach. We conducted experiments on two distinct categories of datasets: natural image datasets and histopathology image datasets. Our experimental results demonstrate the effectiveness of our approach, showcasing improved classification performance compared to traditional single-instance label-based methods. Notably, our algorithm achieves 13% improvement in classification accuracy compared to the strongest baseline on the histopathology image classification benchmarks. Importantly, our experimental findings align with the theoretical analysis, reinforcing the robustness and reliability of our proposed method. This work bridges the gap between instance-level and set-level image classification, offering a promising avenue for advancing the capabilities of image classification models with set-level coarse-grained labels.

Modern sensors produce increasingly rich streams of high-resolution data. Due to resource constraints, machine learning systems discard the vast majority of this information via resolution reduction. Compressed-domain learning allows models to operate on compact latent representations, allowing higher effective resolution for the same budget. However, existing compression systems are not ideal for compressed learning. Linear transform coding and end-to-end learned compression systems reduce bitrate, but do not uniformly reduce dimensionality; thus, they do not meaningfully increase efficiency. Generative autoencoders reduce dimensionality, but their adversarial or perceptual objectives lead to significant information loss. To address these limitations, we introduce WaLLoC (Wavelet Learned Lossy Compression), a neural codec architecture that combines linear transform coding with nonlinear dimensionality-reducing autoencoders. WaLLoC sandwiches a shallow, asymmetric autoencoder and entropy bottleneck between an invertible wavelet packet transform. Across several key metrics, WaLLoC outperforms the autoencoders used in state-of-the-art latent diffusion models. WaLLoC does not require perceptual or adversarial losses to represent high-frequency detail, providing compatibility with modalities beyond RGB images and stereo audio. WaLLoC's encoder consists almost entirely of linear operations, making it exceptionally efficient and suitable for mobile computing, remote sensing, and learning directly from compressed data. We demonstrate WaLLoC's capability for compressed-domain learning across several tasks, including image classification, colorization, document understanding, and music source separation. Our code, experiments, and pre-trained audio and image codecs are available at https://ut-sysml.org/walloc

Recent advances on Multi-modal Large Language Models have demonstrated that high-resolution image input is crucial for model capabilities, especially for fine-grained tasks. However, high-resolution images lead to a quadratic increase in the number of visual tokens input into LLMs, resulting in significant computational costs. Current work develop visual token compression methods to achieve efficiency improvements, often at the expense of performance. We argue that removing visual redundancy can simultaneously improve both efficiency and performance. We build a coarse-to-fine visual token compression method, with a vision-guided sampler for compressing redundant regions with low information density, and a text-guided sampler for selecting visual tokens that are strongly correlated with the user instructions.With these two modules, the proposed FocusLLaVA achieves improvements in both efficiency and performance. We validate the effectiveness of our approach on a wide range of evaluation datasets.

Non-linear manifold learning enables high-dimensional data analysis, but requires out-of-sample-extension methods to process new data points. In this paper, we propose a manifold learning algorithm based on deep learning to create an encoder, which maps a high-dimensional dataset and its low-dimensional embedding, and a decoder, which takes the embedded data back to the high-dimensional space. Stacking the encoder and decoder together constructs an autoencoder, which we term a diffusion net, that performs out-of-sample-extension as well as outlier detection. We introduce new neural net constraints for the encoder, which preserves the local geometry of the points, and we prove rates of convergence for the encoder. Also, our approach is efficient in both computational complexity and memory requirements, as opposed to previous methods that require storage of all training points in both the high-dimensional and the low-dimensional spaces to calculate the out-of-sample-extension and the pre-image.

We present an efficient encoder-free approach for video-language understanding that achieves competitive performance while significantly reducing computational overhead. Current video-language models typically rely on heavyweight image encoders (300M-1.1B parameters) or video encoders (1B-1.4B parameters), creating a substantial computational burden when processing multi-frame videos. Our method introduces a novel Spatio-Temporal Alignment Block (STAB) that directly processes video inputs without requiring pre-trained encoders while using only 45M parameters for visual processing - at least a 6.5times reduction compared to traditional approaches. The STAB architecture combines Local Spatio-Temporal Encoding for fine-grained feature extraction, efficient spatial downsampling through learned attention and separate mechanisms for modeling frame-level and video-level relationships. Our model achieves comparable or superior performance to encoder-based approaches for open-ended video question answering on standard benchmarks. The fine-grained video question-answering evaluation demonstrates our model's effectiveness, outperforming the encoder-based approaches Video-ChatGPT and Video-LLaVA in key aspects like correctness and temporal understanding. Extensive ablation studies validate our architectural choices and demonstrate the effectiveness of our spatio-temporal modeling approach while achieving 3-4times faster processing speeds than previous methods. Code is available at https://github.com/jh-yi/Video-Panda.

To build scalable models for challenging real-world tasks, it is important to learn from diverse, multi-modal data in various forms (e.g., videos, text, and images). Among the existing works, a plethora of them have focused on leveraging large but cumbersome cross-modal architectures. Regardless of their effectiveness, larger architectures unavoidably prevent the models from being extended to real-world applications, so building a lightweight VL architecture and an efficient learning schema is of great practical value. In this paper, we propose an Efficient Video-Language Model (dubbed as E-ViLM) and a masked video modeling (MVM) schema, assisted with a semantic vector-quantized tokenizer. In particular, our E-ViLM learns to reconstruct the semantic labels of masked video regions, produced by the pre-trained vector-quantized tokenizer, which discretizes the continuous visual signals into labels. We show that with our simple MVM task and regular VL pre-training modelings, our E-ViLM, despite its compactness, is able to learn expressive representations from Video-Language corpus and generalize well to extensive Video-Language tasks including video question answering, text-to-video retrieval, etc. In particular, our E-ViLM obtains obvious efficiency improvements by reaching competing performances with faster inference speed, i.e., our model reaches 39.3% Top-1 accuracy on the MSRVTT benchmark, retaining 91.4% of the accuracy of state-of-the-art larger VL architecture with only 15% parameters and 94.8% fewer GFLOPs. We also provide extensive ablative studies that validate the effectiveness of our proposed learning schema for E-ViLM.

Implicit neural representations store videos as neural networks and have performed well for various vision tasks such as video compression and denoising. With frame index or positional index as input, implicit representations (NeRV, E-NeRV, \etc) reconstruct video from fixed and content-agnostic embeddings. Such embedding largely limits the regression capacity and internal generalization for video interpolation. In this paper, we propose a Hybrid Neural Representation for Videos (HNeRV), where a learnable encoder generates content-adaptive embeddings, which act as the decoder input. Besides the input embedding, we introduce HNeRV blocks, which ensure model parameters are evenly distributed across the entire network, such that higher layers (layers near the output) can have more capacity to store high-resolution content and video details. With content-adaptive embeddings and re-designed architecture, HNeRV outperforms implicit methods in video regression tasks for both reconstruction quality (+4.7 PSNR) and convergence speed (16times faster), and shows better internal generalization. As a simple and efficient video representation, HNeRV also shows decoding advantages for speed, flexibility, and deployment, compared to traditional codecs~(H.264, H.265) and learning-based compression methods. Finally, we explore the effectiveness of HNeRV on downstream tasks such as video compression and video inpainting. We provide project page at https://haochen-rye.github.io/HNeRV, and Code at https://github.com/haochen-rye/HNeRV

With applications ranging from metabolomics to histopathology, quantitative phase microscopy (QPM) is a powerful label-free imaging modality. Despite significant advances in fast multiplexed imaging sensors and deep-learning-based inverse solvers, the throughput of QPM is currently limited by the speed of electronic hardware. Complementarily, to improve throughput further, here we propose to acquire images in a compressed form such that more information can be transferred beyond the existing electronic hardware bottleneck. To this end, we present a learnable optical compression-decompression framework that learns content-specific features. The proposed differentiable quantitative phase microscopy (partial mu) first uses learnable optical feature extractors as image compressors. The intensity representation produced by these networks is then captured by the imaging sensor. Finally, a reconstruction network running on electronic hardware decompresses the QPM images. In numerical experiments, the proposed system achieves compression of times 64 while maintaining the SSIM of sim 0.90 and PSNR of sim 30 dB on cells. The results demonstrated by our experiments open up a new pathway for achieving end-to-end optimized (i.e., optics and electronic) compact QPM systems that may provide unprecedented throughput improvements.

Although purely transformer-based architectures showed promising performance in many computer vision tasks, many hybrid models consisting of CNN and transformer blocks are introduced to fit more specialized tasks. Nevertheless, despite the performance gain of both pure and hybrid transformer-based architectures compared to CNNs in medical imaging segmentation, their high training cost and complexity make it challenging to use them in real scenarios. In this work, we propose simple architectures based on purely convolutional layers, and show that by just taking advantage of the attention map visualizations obtained from a self-supervised pretrained vision transformer network (e.g., DINO) one can outperform complex transformer-based networks with much less computation costs. The proposed architecture is composed of two encoder branches with the original image as input in one branch and the attention map visualizations of the same image from multiple self-attention heads from a pre-trained DINO model (as multiple channels) in the other branch. The results of our experiments on two publicly available medical imaging datasets show that the proposed pipeline outperforms U-Net and the state-of-the-art medical image segmentation models.

Neural fields, also known as implicit neural representations (INRs), have shown a remarkable capability of representing, generating, and manipulating various data types, allowing for continuous data reconstruction at a low memory footprint. Though promising, INRs applied to video compression still need to improve their rate-distortion performance by a large margin, and require a huge number of parameters and long training iterations to capture high-frequency details, limiting their wider applicability. Resolving this problem remains a quite challenging task, which would make INRs more accessible in compression tasks. We take a step towards resolving these shortcomings by introducing neural representations for videos NeRV++, an enhanced implicit neural video representation, as more straightforward yet effective enhancement over the original NeRV decoder architecture, featuring separable conv2d residual blocks (SCRBs) that sandwiches the upsampling block (UB), and a bilinear interpolation skip layer for improved feature representation. NeRV++ allows videos to be directly represented as a function approximated by a neural network, and significantly enhance the representation capacity beyond current INR-based video codecs. We evaluate our method on UVG, MCL JVC, and Bunny datasets, achieving competitive results for video compression with INRs. This achievement narrows the gap to autoencoder-based video coding, marking a significant stride in INR-based video compression research.

There has been much interest in deploying deep learning algorithms on low-powered devices, including smartphones, drones, and medical sensors. However, full-scale deep neural networks are often too resource-intensive in terms of energy and storage. As a result, the bulk part of the machine learning operation is therefore often carried out on an edge server, where the data is compressed and transmitted. However, compressing data (such as images) leads to transmitting information irrelevant to the supervised task. Another popular approach is to split the deep network between the device and the server while compressing intermediate features. To date, however, such split computing strategies have barely outperformed the aforementioned naive data compression baselines due to their inefficient approaches to feature compression. This paper adopts ideas from knowledge distillation and neural image compression to compress intermediate feature representations more efficiently. Our supervised compression approach uses a teacher model and a student model with a stochastic bottleneck and learnable prior for entropy coding (Entropic Student). We compare our approach to various neural image and feature compression baselines in three vision tasks and found that it achieves better supervised rate-distortion performance while maintaining smaller end-to-end latency. We furthermore show that the learned feature representations can be tuned to serve multiple downstream tasks.

We introduce a novel cost aggregation network, dubbed Volumetric Aggregation with Transformers (VAT), to tackle the few-shot segmentation task by using both convolutions and transformers to efficiently handle high dimensional correlation maps between query and support. In specific, we propose our encoder consisting of volume embedding module to not only transform the correlation maps into more tractable size but also inject some convolutional inductive bias and volumetric transformer module for the cost aggregation. Our encoder has a pyramidal structure to let the coarser level aggregation to guide the finer level and enforce to learn complementary matching scores. We then feed the output into our affinity-aware decoder along with the projected feature maps for guiding the segmentation process. Combining these components, we conduct experiments to demonstrate the effectiveness of the proposed method, and our method sets a new state-of-the-art for all the standard benchmarks in few-shot segmentation task. Furthermore, we find that the proposed method attains state-of-the-art performance even for the standard benchmarks in semantic correspondence task although not specifically designed for this task. We also provide an extensive ablation study to validate our architectural choices. The trained weights and codes are available at: https://seokju-cho.github.io/VAT/.

Learned Image Compression (LIC) has achieved dramatic progress regarding objective and subjective metrics. MSE-based models aim to improve objective metrics while generative models are leveraged to improve visual quality measured by subjective metrics. However, they all suffer from blurring or deformation at low bit rates, especially at below 0.2bpp. Besides, deformation on human faces and text is unacceptable for visual quality assessment, and the problem becomes more prominent on small faces and text. To solve this problem, we combine the advantage of MSE-based models and generative models by utilizing region of interest (ROI). We propose Hierarchical-ROI (H-ROI), to split images into several foreground regions and one background region to improve the reconstruction of regions containing faces, text, and complex textures. Further, we propose adaptive quantization by non-linear mapping within the channel dimension to constrain the bit rate while maintaining the visual quality. Exhaustive experiments demonstrate that our methods achieve better visual quality on small faces and text with lower bit rates, e.g., 0.7X bits of HiFiC and 0.5X bits of BPG.

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.

Developing self-supervised learning (SSL) models that can learn universal and transferable representations of H&E gigapixel whole-slide images (WSIs) is becoming increasingly valuable in computational pathology. These models hold the potential to advance critical tasks such as few-shot classification, slide retrieval, and patient stratification. Existing approaches for slide representation learning extend the principles of SSL from small images (e.g., 224 x 224 patches) to entire slides, usually by aligning two different augmentations (or views) of the slide. Yet the resulting representation remains constrained by the limited clinical and biological diversity of the views. Instead, we postulate that slides stained with multiple markers, such as immunohistochemistry, can be used as different views to form a rich task-agnostic training signal. To this end, we introduce Madeleine, a multimodal pretraining strategy for slide representation learning. Madeleine is trained with a dual global-local cross-stain alignment objective on large cohorts of breast cancer samples (N=4,211 WSIs across five stains) and kidney transplant samples (N=12,070 WSIs across four stains). We demonstrate the quality of slide representations learned by Madeleine on various downstream evaluations, ranging from morphological and molecular classification to prognostic prediction, comprising 21 tasks using 7,299 WSIs from multiple medical centers. Code is available at https://github.com/mahmoodlab/MADELEINE.

The retroperitoneum hosts a variety of tumors, including rare benign and malignant types, which pose diagnostic and treatment challenges due to their infrequency and proximity to vital structures. Estimating tumor volume is difficult due to their irregular shapes, and manual segmentation is time-consuming. Automatic segmentation using U-Net and its variants, incorporating Vision Transformer (ViT) elements, has shown promising results but struggles with high computational demands. To address this, architectures like the Mamba State Space Model (SSM) and Extended Long-Short Term Memory (xLSTM) offer efficient solutions by handling long-range dependencies with lower resource consumption. This study evaluates U-Net enhancements, including CNN, ViT, Mamba, and xLSTM, on a new in-house CT dataset and a public organ segmentation dataset. The proposed ViLU-Net model integrates Vi-blocks for improved segmentation. Results highlight xLSTM's efficiency in the U-Net framework. The code is publicly accessible on GitHub.

Transformers have achieved the state-of-the-art performance on solving the inverse problem of Snapshot Compressive Imaging (SCI) for video, whose ill-posedness is rooted in the mixed degradation of spatial masking and temporal aliasing. However, previous Transformers lack an insight into the degradation and thus have limited performance and efficiency. In this work, we tailor an efficient reconstruction architecture without temporal aggregation in early layers and Hierarchical Separable Video Transformer (HiSViT) as building block. HiSViT is built by multiple groups of Cross-Scale Separable Multi-head Self-Attention (CSS-MSA) and Gated Self-Modulated Feed-Forward Network (GSM-FFN) with dense connections, each of which is conducted within a separate channel portions at a different scale, for multi-scale interactions and long-range modeling. By separating spatial operations from temporal ones, CSS-MSA introduces an inductive bias of paying more attention within frames instead of between frames while saving computational overheads. GSM-FFN further enhances the locality via gated mechanism and factorized spatial-temporal convolutions. Extensive experiments demonstrate that our method outperforms previous methods by !>!0.5 dB with comparable or fewer parameters and complexity. The source codes and pretrained models are released at https://github.com/pwangcs/HiSViT.

Prostate cancer, a growing global health concern, necessitates precise diagnostic tools, with Magnetic Resonance Imaging (MRI) offering high-resolution soft tissue imaging that significantly enhances diagnostic accuracy. Recent advancements in explainable AI and representation learning have significantly improved prostate cancer diagnosis by enabling automated and precise lesion classification. However, existing explainable AI methods, particularly those based on frameworks like generative adversarial networks (GANs), are predominantly developed for natural image generation, and their application to medical imaging often leads to suboptimal performance due to the unique characteristics and complexity of medical image. To address these challenges, our paper introduces three key contributions. First, we propose ProjectedEx, a generative framework that provides interpretable, multi-attribute explanations, effectively linking medical image features to classifier decisions. Second, we enhance the encoder module by incorporating feature pyramids, which enables multiscale feedback to refine the latent space and improves the quality of generated explanations. Additionally, we conduct comprehensive experiments on both the generator and classifier, demonstrating the clinical relevance and effectiveness of ProjectedEx in enhancing interpretability and supporting the adoption of AI in medical settings. Code will be released at https://github.com/Richardqiyi/ProjectedEx

Transformer-based image restoration methods in adverse weather have achieved significant progress. Most of them use self-attention along the channel dimension or within spatially fixed-range blocks to reduce computational load. However, such a compromise results in limitations in capturing long-range spatial features. Inspired by the observation that the weather-induced degradation factors mainly cause similar occlusion and brightness, in this work, we propose an efficient Histogram Transformer (Histoformer) for restoring images affected by adverse weather. It is powered by a mechanism dubbed histogram self-attention, which sorts and segments spatial features into intensity-based bins. Self-attention is then applied across bins or within each bin to selectively focus on spatial features of dynamic range and process similar degraded pixels of the long range together. To boost histogram self-attention, we present a dynamic-range convolution enabling conventional convolution to conduct operation over similar pixels rather than neighbor pixels. We also observe that the common pixel-wise losses neglect linear association and correlation between output and ground-truth. Thus, we propose to leverage the Pearson correlation coefficient as a loss function to enforce the recovered pixels following the identical order as ground-truth. Extensive experiments demonstrate the efficacy and superiority of our proposed method. We have released the codes in Github.

COMpression with Bayesian Implicit NEural Representations (COMBINER) is a recent data compression method that addresses a key inefficiency of previous Implicit Neural Representation (INR)-based approaches: it avoids quantization and enables direct optimization of the rate-distortion performance. However, COMBINER still has significant limitations: 1) it uses factorized priors and posterior approximations that lack flexibility; 2) it cannot effectively adapt to local deviations from global patterns in the data; and 3) its performance can be susceptible to modeling choices and the variational parameters' initializations. Our proposed method, Robust and Enhanced COMBINER (RECOMBINER), addresses these issues by 1) enriching the variational approximation while retaining a low computational cost via a linear reparameterization of the INR weights, 2) augmenting our INRs with learnable positional encodings that enable them to adapt to local details and 3) splitting high-resolution data into patches to increase robustness and utilizing expressive hierarchical priors to capture dependency across patches. We conduct extensive experiments across several data modalities, showcasing that RECOMBINER achieves competitive results with the best INR-based methods and even outperforms autoencoder-based codecs on low-resolution images at low bitrates. Our PyTorch implementation is available at https://github.com/cambridge-mlg/RECOMBINER/.

Recently, the scale of transformers has grown rapidly, which introduces considerable challenges in terms of training overhead and inference efficiency in the scope of task adaptation. Existing works, namely Parameter-Efficient Fine-Tuning (PEFT) and model compression, have separately investigated the challenges. However, PEFT cannot guarantee the inference efficiency of the original backbone, especially for large-scale models. Model compression requires significant training costs for structure searching and re-training. Consequently, a simple combination of them cannot guarantee accomplishing both training efficiency and inference efficiency with minimal costs. In this paper, we propose a novel Parallel Yielding Re-Activation (PYRA) method for such a challenge of training-inference efficient task adaptation. PYRA first utilizes parallel yielding adaptive weights to comprehensively perceive the data distribution in downstream tasks. A re-activation strategy for token modulation is then applied for tokens to be merged, leading to calibrated token features. Extensive experiments demonstrate that PYRA outperforms all competing methods under both low compression rate and high compression rate, demonstrating its effectiveness and superiority in maintaining both training efficiency and inference efficiency for large-scale foundation models. Our code will be released to the public.

Prior research on deep video compression (DVC) for machine tasks typically necessitates training a unique codec for each specific task, mandating a dedicated decoder per task. In contrast, traditional video codecs employ a flexible encoder controller, enabling the adaptation of a single codec to different tasks through mechanisms like mode prediction. Drawing inspiration from this, we introduce an innovative encoder controller for deep video compression for machines. This controller features a mode prediction and a Group of Pictures (GoP) selection module. Our approach centralizes control at the encoding stage, allowing for adaptable encoder adjustments across different tasks, such as detection and tracking, while maintaining compatibility with a standard pre-trained DVC decoder. Empirical evidence demonstrates that our method is applicable across multiple tasks with various existing pre-trained DVCs. Moreover, extensive experiments demonstrate that our method outperforms previous DVC by about 25% bitrate for different tasks, with only one pre-trained decoder.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

Pathology plays a critical role in diagnosing a wide range of diseases, yet existing approaches often rely heavily on task-specific models trained on extensive, well-labeled datasets. These methods face sustainability challenges due to the diversity of pathologies and the labor-intensive nature of data collection. To address these limitations, we highlight the need for universal multimodal embeddings that can support multiple downstream tasks. Previous approaches often involve fine-tuning CLIP-based models, which handle images and text separately, limiting their ability to capture complex multimodal relationships. Additionally, these models are evaluated across diverse datasets without a unified benchmark for assessing multimodal embeddings in pathology. To address these challenges, we propose MLLM4PUE, a novel framework that leverages Multimodal Large Language Models (MLLMs) to generate Pathology Universal Embeddings. The MLLM4PUE framework not only facilitates robust integration of images and text but also enhances understanding and fusion capabilities across various tasks. We further introduce the Pathology Multimodal Embedding Benchmark (PMEB), a comprehensive benchmark designed to assess the quality of pathology multimodal embeddings. PMEB comprises 15 original tasks drawn from 14 datasets, organized into three meta-tasks: retrieval, classification, and composed retrieval. Experimental results demonstrate the superiority of MLLM4PUE, illustrating MLLM-based models can effectively support a wide range of downstream tasks and unify the research direction for foundation models in pathology.

A range of recent works addresses the problem of compression of sequence of tokens into a shorter sequence of real-valued vectors to be used as inputs instead of token embeddings or key-value cache. These approaches allow to reduce the amount of compute in existing language models. Despite relying on powerful models as encoders, the maximum attainable lossless compression ratio is typically not higher than x10. This fact is highly intriguing because, in theory, the maximum information capacity of large real-valued vectors is far beyond the presented rates even for 16-bit precision and a modest vector size. In this work, we explore the limits of compression by replacing the encoder with a per-sample optimization procedure. We show that vectors with compression ratios up to x1500 exist, which highlights two orders of magnitude gap between existing and practically attainable solutions. Furthermore, we empirically show that the compression limits are determined not by the length of the input but by the amount of uncertainty to be reduced, namely, the cross-entropy loss on this sequence without any conditioning. The obtained limits highlight the substantial gap between the theoretical capacity of input embeddings and their practical utilization, suggesting significant room for optimization in model design.

Unlike color photography images, which are consistently encoded into RGB channels, biological images encompass various modalities, where the type of microscopy and the meaning of each channel varies with each experiment. Importantly, the number of channels can range from one to a dozen and their correlation is often comparatively much lower than RGB, as each of them brings specific information content. This aspect is largely overlooked by methods designed out of the bioimage field, and current solutions mostly focus on intra-channel spatial attention, often ignoring the relationship between channels, yet crucial in most biological applications. Importantly, the variable channel type and count prevent the projection of several experiments to a unified representation for large scale pre-training. In this study, we propose ChAda-ViT, a novel Channel Adaptive Vision Transformer architecture employing an Inter-Channel Attention mechanism on images with an arbitrary number, order and type of channels. We also introduce IDRCell100k, a bioimage dataset with a rich set of 79 experiments covering 7 microscope modalities, with a multitude of channel types, and channel counts varying from 1 to 10 per experiment. Our proposed architecture, trained in a self-supervised manner, outperforms existing approaches in several biologically relevant downstream tasks. Additionally, it can be used to bridge the gap for the first time between assays with different microscopes, channel numbers or types by embedding various image and experimental modalities into a unified biological image representation. The latter should facilitate interdisciplinary studies and pave the way for better adoption of deep learning in biological image-based analyses. Code and Data to be released soon.

High-resolution Vision-Language Models (VLMs) have been widely used in multimodal tasks to enhance accuracy by preserving detailed image information. However, these models often generate excessive visual tokens due to encoding multiple partitions of the input image. Processing these excessive visual tokens is computationally challenging, especially in resource-constrained environments with commodity GPUs. To support high-resolution images while meeting resource constraints, we propose High-Resolution Early Dropping (HiRED), a token-dropping scheme that operates within a fixed token budget before the Large Language Model (LLM) stage. HiRED can be integrated with existing high-resolution VLMs in a plug-and-play manner, as it requires no additional training while still maintaining superior accuracy. We strategically use the vision encoder's attention in the initial layers to assess the visual content of each image partition and allocate the token budget accordingly. Then, using the attention in the final layer, we select the most important visual tokens from each partition within the allocated budget, dropping the rest. Empirically, when applied to LLaVA-Next-7B on NVIDIA TESLA P40 GPU, HiRED with a 20% token budget increases token generation throughput by 4.7, reduces first-token generation latency by 15 seconds, and saves 2.3 GB of GPU memory for a single inference.

The emergence of large multimodal models has unlocked remarkable potential in AI, particularly in pathology. However, the lack of specialized, high-quality benchmark impeded their development and precise evaluation. To address this, we introduce PathMMU, the largest and highest-quality expert-validated pathology benchmark for LMMs. It comprises 33,573 multimodal multi-choice questions and 21,599 images from various sources, and an explanation for the correct answer accompanies each question. The construction of PathMMU capitalizes on the robust capabilities of GPT-4V, utilizing approximately 30,000 gathered image-caption pairs to generate Q\&As. Significantly, to maximize PathMMU's authority, we invite six pathologists to scrutinize each question under strict standards in PathMMU's validation and test sets, while simultaneously setting an expert-level performance benchmark for PathMMU. We conduct extensive evaluations, including zero-shot assessments of 14 open-sourced and three closed-sourced LMMs and their robustness to image corruption. We also fine-tune representative LMMs to assess their adaptability to PathMMU. The empirical findings indicate that advanced LMMs struggle with the challenging PathMMU benchmark, with the top-performing LMM, GPT-4V, achieving only a 51.7\% zero-shot performance, significantly lower than the 71.4\% demonstrated by human pathologists. After fine-tuning, even open-sourced LMMs can surpass GPT-4V with a performance of over 60\%, but still fall short of the expertise shown by pathologists. We hope that the PathMMU will offer valuable insights and foster the development of more specialized, next-generation LLMs for pathology.

The cost of deploying vision transformers increasingly represents a barrier to wider industrial adoption. Existing compression requires additional end-to-end fine-tuning or incurs a significant drawback to runtime, thus making them ill-suited for online inference. We introduce the Visual Word Tokenizer (VWT), a training-free method for reducing energy costs while retaining performance and runtime. The VWT groups patches (visual subwords) that are frequently used into visual words while infrequent ones remain intact. To do so, intra-image or inter-image statistics are leveraged to identify similar visual concepts for compression. Experimentally, we demonstrate a reduction in wattage of up to 19% with only a 20% increase in runtime at most. Comparative approaches of 8-bit quantization and token merging achieve a lower or similar energy efficiency but exact a higher toll on runtime (up to 2times or more). Our results indicate that VWTs are well-suited for efficient online inference with a marginal compromise on performance.

As convolution has empowered many smart applications, dynamic convolution further equips it with the ability to adapt to diverse inputs. However, the static and dynamic convolutions are either layout-agnostic or computation-heavy, making it inappropriate for layout-specific applications, e.g., face recognition and medical image segmentation. We observe that these applications naturally exhibit the characteristics of large intra-image (spatial) variance and small cross-image variance. This observation motivates our efficient translation variant convolution (TVConv) for layout-aware visual processing. Technically, TVConv is composed of affinity maps and a weight-generating block. While affinity maps depict pixel-paired relationships gracefully, the weight-generating block can be explicitly overparameterized for better training while maintaining efficient inference. Although conceptually simple, TVConv significantly improves the efficiency of the convolution and can be readily plugged into various network architectures. Extensive experiments on face recognition show that TVConv reduces the computational cost by up to 3.1x and improves the corresponding throughput by 2.3x while maintaining a high accuracy compared to the depthwise convolution. Moreover, for the same computation cost, we boost the mean accuracy by up to 4.21%. We also conduct experiments on the optic disc/cup segmentation task and obtain better generalization performance, which helps mitigate the critical data scarcity issue. Code is available at https://github.com/JierunChen/TVConv.

Existing neural audio codecs usually sacrifice computational complexity for audio quality. They build the feature transformation layers mainly on convolutional blocks, which are not inherently appropriate for capturing local redundancies of audio signals. As compensation, either adversarial losses from a discriminator or a large number of model parameters are required to improve the codec. To that end, we propose Efficient Speech Codec (ESC), a lightweight parameter-efficient codec laid on cross-scale residual vector quantization and transformers. Our model leverages mirrored hierarchical window-attention transformer blocks and performs step-wise decoding from coarse-to-fine feature representations. To enhance codebook utilization, we design a learning paradigm that involves a pre-training stage to assist with codec training. Extensive results show that ESC can achieve high audio quality with much lower complexity, which is a prospective alternative in place of existing codecs.

Implicit Neural Representations (INR) have recently shown to be powerful tool for high-quality video compression. However, existing works are limiting as they do not explicitly exploit the temporal redundancy in videos, leading to a long encoding time. Additionally, these methods have fixed architectures which do not scale to longer videos or higher resolutions. To address these issues, we propose NIRVANA, which treats videos as groups of frames and fits separate networks to each group performing patch-wise prediction. This design shares computation within each group, in the spatial and temporal dimensions, resulting in reduced encoding time of the video. The video representation is modeled autoregressively, with networks fit on a current group initialized using weights from the previous group's model. To further enhance efficiency, we perform quantization of the network parameters during training, requiring no post-hoc pruning or quantization. When compared with previous works on the benchmark UVG dataset, NIRVANA improves encoding quality from 37.36 to 37.70 (in terms of PSNR) and the encoding speed by 12X, while maintaining the same compression rate. In contrast to prior video INR works which struggle with larger resolution and longer videos, we show that our algorithm is highly flexible and scales naturally due to its patch-wise and autoregressive designs. Moreover, our method achieves variable bitrate compression by adapting to videos with varying inter-frame motion. NIRVANA achieves 6X decoding speed and scales well with more GPUs, making it practical for various deployment scenarios.

This work introduces a new framework, ProtoSAM, for one-shot medical image segmentation. It combines the use of prototypical networks, known for few-shot segmentation, with SAM - a natural image foundation model. The method proposed creates an initial coarse segmentation mask using the ALPnet prototypical network, augmented with a DINOv2 encoder. Following the extraction of an initial mask, prompts are extracted, such as points and bounding boxes, which are then input into the Segment Anything Model (SAM). State-of-the-art results are shown on several medical image datasets and demonstrate automated segmentation capabilities using a single image example (one shot) with no need for fine-tuning of the foundation model. Our code is available at: https://github.com/levayz/ProtoSAM

Large-scale foundation models have demonstrated exceptional performance in language and vision tasks. However, the numerous dense matrix-vector operations involved in these large networks pose significant computational challenges during inference. To address these challenges, we introduce the Block-Level Adaptive STructured (BLAST) matrix, designed to learn and leverage efficient structures prevalent in the weight matrices of linear layers within deep learning models. Compared to existing structured matrices, the BLAST matrix offers substantial flexibility, as it can represent various types of structures that are either learned from data or computed from pre-existing weight matrices. We demonstrate the efficiency of using the BLAST matrix for compressing both language and vision tasks, showing that (i) for medium-sized models such as ViT and GPT-2, training with BLAST weights boosts performance while reducing complexity by 70% and 40%, respectively; and (ii) for large foundation models such as Llama-7B and DiT-XL, the BLAST matrix achieves a 2x compression while exhibiting the lowest performance degradation among all tested structured matrices. Our code is available at https://github.com/changwoolee/BLAST.

Computer-aided medical image segmentation has been applied widely in diagnosis and treatment to obtain clinically useful information of shapes and volumes of target organs and tissues. In the past several years, convolutional neural network (CNN) based methods (e.g., U-Net) have dominated this area, but still suffered from inadequate long-range information capturing. Hence, recent work presented computer vision Transformer variants for medical image segmentation tasks and obtained promising performances. Such Transformers model long-range dependency by computing pair-wise patch relations. However, they incur prohibitive computational costs, especially on 3D medical images (e.g., CT and MRI). In this paper, we propose a new method called Dilated Transformer, which conducts self-attention for pair-wise patch relations captured alternately in local and global scopes. Inspired by dilated convolution kernels, we conduct the global self-attention in a dilated manner, enlarging receptive fields without increasing the patches involved and thus reducing computational costs. Based on this design of Dilated Transformer, we construct a U-shaped encoder-decoder hierarchical architecture called D-Former for 3D medical image segmentation. Experiments on the Synapse and ACDC datasets show that our D-Former model, trained from scratch, outperforms various competitive CNN-based or Transformer-based segmentation models at a low computational cost without time-consuming per-training process.

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.

We present an Encoder-Decoder Attention Transformer, EDAFormer, which consists of the Embedding-Free Transformer (EFT) encoder and the all-attention decoder leveraging our Embedding-Free Attention (EFA) structure. The proposed EFA is a novel global context modeling mechanism that focuses on functioning the global non-linearity, not the specific roles of the query, key and value. For the decoder, we explore the optimized structure for considering the globality, which can improve the semantic segmentation performance. In addition, we propose a novel Inference Spatial Reduction (ISR) method for the computational efficiency. Different from the previous spatial reduction attention methods, our ISR method further reduces the key-value resolution at the inference phase, which can mitigate the computation-performance trade-off gap for the efficient semantic segmentation. Our EDAFormer shows the state-of-the-art performance with the efficient computation compared to the existing transformer-based semantic segmentation models in three public benchmarks, including ADE20K, Cityscapes and COCO-Stuff. Furthermore, our ISR method reduces the computational cost by up to 61% with minimal mIoU performance degradation on Cityscapes dataset. The code is available at https://github.com/hyunwoo137/EDAFormer.

Though the state-of-the architectures for semantic segmentation, such as HRNet, demonstrate impressive accuracy, the complexity arising from their salient design choices hinders a range of model acceleration tools, and further they make use of operations that are inefficient on current hardware. This paper demonstrates that a simple encoder-decoder architecture with a ResNet-like backbone and a small multi-scale head, performs on-par or better than complex semantic segmentation architectures such as HRNet, FANet and DDRNets. Naively applying deep backbones designed for Image Classification to the task of Semantic Segmentation leads to sub-par results, owing to a much smaller effective receptive field of these backbones. Implicit among the various design choices put forth in works like HRNet, DDRNet, and FANet are networks with a large effective receptive field. It is natural to ask if a simple encoder-decoder architecture would compare favorably if comprised of backbones that have a larger effective receptive field, though without the use of inefficient operations like dilated convolutions. We show that with minor and inexpensive modifications to ResNets, enlarging the receptive field, very simple and competitive baselines can be created for Semantic Segmentation. We present a family of such simple architectures for desktop as well as mobile targets, which match or exceed the performance of complex models on the Cityscapes dataset. We hope that our work provides simple yet effective baselines for practitioners to develop efficient semantic segmentation models.

Data used for analytics and machine learning often take the form of tables with categorical entries. We introduce a family of lossless compression algorithms for such data that proceed in four steps: (i) Estimate latent variables associated to rows and columns; (ii) Partition the table in blocks according to the row/column latents; (iii) Apply a sequential (e.g. Lempel-Ziv) coder to each of the blocks; (iv) Append a compressed encoding of the latents. We evaluate it on several benchmark datasets, and study optimal compression in a probabilistic model for that tabular data, whereby latent values are independent and table entries are conditionally independent given the latent values. We prove that the model has a well defined entropy rate and satisfies an asymptotic equipartition property. We also prove that classical compression schemes such as Lempel-Ziv and finite-state encoders do not achieve this rate. On the other hand, the latent estimation strategy outlined above achieves the optimal rate.

Scale is the primary factor for building a powerful foundation model that could well generalize to a variety of downstream tasks. However, it is still challenging to train video foundation models with billions of parameters. This paper shows that video masked autoencoder (VideoMAE) is a scalable and general self-supervised pre-trainer for building video foundation models. We scale the VideoMAE in both model and data with a core design. Specifically, we present a dual masking strategy for efficient pre-training, with an encoder operating on a subset of video tokens and a decoder processing another subset of video tokens. Although VideoMAE is very efficient due to high masking ratio in encoder, masking decoder can still further reduce the overall computational cost. This enables the efficient pre-training of billion-level models in video. We also use a progressive training paradigm that involves an initial pre-training on a diverse multi-sourced unlabeled dataset, followed by a post-pre-training on a mixed labeled dataset. Finally, we successfully train a video ViT model with a billion parameters, which achieves a new state-of-the-art performance on the datasets of Kinetics (90.0% on K400 and 89.9% on K600) and Something-Something (68.7% on V1 and 77.0% on V2). In addition, we extensively verify the pre-trained video ViT models on a variety of downstream tasks, demonstrating its effectiveness as a general video representation learner. The code and model is available at https://github.com/OpenGVLab/VideoMAEv2.

Commercial video generation models have exhibited realistic, high-fidelity results but are still restricted to limited access. One crucial obstacle for large-scale applications is the expensive training and inference cost. In this paper, we argue that videos contain much more redundant information than images, thus can be encoded by very few motion latents based on a content image. Towards this goal, we design an image-conditioned VAE to encode a video to an extremely compressed motion latent space. This magic Reducio charm enables 64x reduction of latents compared to a common 2D VAE, without sacrificing the quality. Training diffusion models on such a compact representation easily allows for generating 1K resolution videos. We then adopt a two-stage video generation paradigm, which performs text-to-image and text-image-to-video sequentially. Extensive experiments show that our Reducio-DiT achieves strong performance in evaluation, though trained with limited GPU resources. More importantly, our method significantly boost the efficiency of video LDMs both in training and inference. We train Reducio-DiT in around 3.2K training hours in total and generate a 16-frame 1024*1024 video clip within 15.5 seconds on a single A100 GPU. Code released at https://github.com/microsoft/Reducio-VAE .

We show that Transformer encoder architectures can be sped up, with limited accuracy costs, by replacing the self-attention sublayers with simple linear transformations that "mix" input tokens. These linear mixers, along with standard nonlinearities in feed-forward layers, prove competent at modeling semantic relationships in several text classification tasks. Most surprisingly, we find that replacing the self-attention sublayer in a Transformer encoder with a standard, unparameterized Fourier Transform achieves 92-97% of the accuracy of BERT counterparts on the GLUE benchmark, but trains 80% faster on GPUs and 70% faster on TPUs at standard 512 input lengths. At longer input lengths, our FNet model is significantly faster: when compared to the "efficient" Transformers on the Long Range Arena benchmark, FNet matches the accuracy of the most accurate models, while outpacing the fastest models across all sequence lengths on GPUs (and across relatively shorter lengths on TPUs). Finally, FNet has a light memory footprint and is particularly efficient at smaller model sizes; for a fixed speed and accuracy budget, small FNet models outperform Transformer counterparts.

In this work we address the problem of landmark-based segmentation for anatomical structures. We propose HybridGNet, an encoder-decoder neural architecture which combines standard convolutions for image feature encoding, with graph convolutional neural networks to decode plausible representations of anatomical structures. We benchmark the proposed architecture considering other standard landmark and pixel-based models for anatomical segmentation in chest x-ray images, and found that HybridGNet is more robust to image occlusions. We also show that it can be used to construct landmark-based segmentations from pixel level annotations. Our experimental results suggest that HybridGNet produces accurate and anatomically plausible landmark-based segmentations, by naturally incorporating shape constraints within the decoding process via spectral convolutions.

Important information that relates to a specific topic in a document is often organized in tabular format to assist readers with information retrieval and comparison, which may be difficult to provide in natural language. However, tabular data in unstructured digital documents, e.g., Portable Document Format (PDF) and images, are difficult to parse into structured machine-readable format, due to complexity and diversity in their structure and style. To facilitate image-based table recognition with deep learning, we develop the largest publicly available table recognition dataset PubTabNet (https://github.com/ibm-aur-nlp/PubTabNet), containing 568k table images with corresponding structured HTML representation. PubTabNet is automatically generated by matching the XML and PDF representations of the scientific articles in PubMed Central Open Access Subset (PMCOA). We also propose a novel attention-based encoder-dual-decoder (EDD) architecture that converts images of tables into HTML code. The model has a structure decoder which reconstructs the table structure and helps the cell decoder to recognize cell content. In addition, we propose a new Tree-Edit-Distance-based Similarity (TEDS) metric for table recognition, which more appropriately captures multi-hop cell misalignment and OCR errors than the pre-established metric. The experiments demonstrate that the EDD model can accurately recognize complex tables solely relying on the image representation, outperforming the state-of-the-art by 9.7% absolute TEDS score.

Mixture of Experts (MoE) is able to scale up vision transformers effectively. However, it requires prohibiting computation resources to train a large MoE transformer. In this paper, we propose Residual Mixture of Experts (RMoE), an efficient training pipeline for MoE vision transformers on downstream tasks, such as segmentation and detection. RMoE achieves comparable results with the upper-bound MoE training, while only introducing minor additional training cost than the lower-bound non-MoE training pipelines. The efficiency is supported by our key observation: the weights of an MoE transformer can be factored into an input-independent core and an input-dependent residual. Compared with the weight core, the weight residual can be efficiently trained with much less computation resource, e.g., finetuning on the downstream data. We show that, compared with the current MoE training pipeline, we get comparable results while saving over 30% training cost. When compared with state-of-the-art non- MoE transformers, such as Swin-T / CvT-13 / Swin-L, we get +1.1 / 0.9 / 1.0 mIoU gain on ADE20K segmentation and +1.4 / 1.6 / 0.6 AP gain on MS-COCO object detection task with less than 3% additional training cost.

We present a radiology-specific multimodal model for the task for generating radiological reports from chest X-rays (CXRs). Our work builds on the idea that large language model(s) can be equipped with multimodal capabilities through alignment with pre-trained vision encoders. On natural images, this has been shown to allow multimodal models to gain image understanding and description capabilities. Our proposed model (MAIRA-1) leverages a CXR-specific image encoder in conjunction with a fine-tuned large language model based on Vicuna-7B, and text-based data augmentation, to produce reports with state-of-the-art quality. In particular, MAIRA-1 significantly improves on the radiologist-aligned RadCliQ metric and across all lexical metrics considered. Manual review of model outputs demonstrates promising fluency and accuracy of generated reports while uncovering failure modes not captured by existing evaluation practices. More information and resources can be found on the project website: https://aka.ms/maira.

Language-supervised pre-training has proven to be a valuable method for extracting semantically meaningful features from images, serving as a foundational element in multimodal systems within the computer vision and medical imaging domains. However, resulting features are limited by the information contained within the text. This is particularly problematic in medical imaging, where radiologists' written findings focus on specific observations; a challenge compounded by the scarcity of paired imaging-text data due to concerns over leakage of personal health information. In this work, we fundamentally challenge the prevailing reliance on language supervision for learning general purpose biomedical imaging encoders. We introduce RAD-DINO, a biomedical image encoder pre-trained solely on unimodal biomedical imaging data that obtains similar or greater performance than state-of-the-art biomedical language supervised models on a diverse range of benchmarks. Specifically, the quality of learned representations is evaluated on standard imaging tasks (classification and semantic segmentation), and a vision-language alignment task (text report generation from images). To further demonstrate the drawback of language supervision, we show that features from RAD-DINO correlate with other medical records (e.g., sex or age) better than language-supervised models, which are generally not mentioned in radiology reports. Finally, we conduct a series of ablations determining the factors in RAD-DINO's performance; notably, we observe that RAD-DINO's downstream performance scales well with the quantity and diversity of training data, demonstrating that image-only supervision is a scalable approach for training a foundational biomedical image encoder.

Lossy image compression aims to represent images in as few bits as possible while maintaining fidelity to the original. Theoretical results indicate that optimizing distortion metrics such as PSNR or MS-SSIM necessarily leads to a discrepancy in the statistics of original images from those of reconstructions, in particular at low bitrates, often manifested by the blurring of the compressed images. Previous work has leveraged adversarial discriminators to improve statistical fidelity. Yet these binary discriminators adopted from generative modeling tasks may not be ideal for image compression. In this paper, we introduce a non-binary discriminator that is conditioned on quantized local image representations obtained via VQ-VAE autoencoders. Our evaluations on the CLIC2020, DIV2K and Kodak datasets show that our discriminator is more effective for jointly optimizing distortion (e.g., PSNR) and statistical fidelity (e.g., FID) than the state-of-the-art HiFiC model. On the CLIC2020 test set, we obtain the same FID as HiFiC with 30-40% fewer bits.

Featurizing microscopy images for use in biological research remains a significant challenge, especially for large-scale experiments spanning millions of images. This work explores the scaling properties of weakly supervised classifiers and self-supervised masked autoencoders (MAEs) when training with increasingly larger model backbones and microscopy datasets. Our results show that ViT-based MAEs outperform weakly supervised classifiers on a variety of tasks, achieving as much as a 11.5% relative improvement when recalling known biological relationships curated from public databases. Additionally, we develop a new channel-agnostic MAE architecture (CA-MAE) that allows for inputting images of different numbers and orders of channels at inference time. We demonstrate that CA-MAEs effectively generalize by inferring and evaluating on a microscopy image dataset (JUMP-CP) generated under different experimental conditions with a different channel structure than our pretraining data (RPI-93M). Our findings motivate continued research into scaling self-supervised learning on microscopy data in order to create powerful foundation models of cellular biology that have the potential to catalyze advancements in drug discovery and beyond.

Neural network (NN) compression via techniques such as pruning, quantization requires setting compression hyperparameters (e.g., number of channels to be pruned, bitwidths for quantization) for each layer either manually or via neural architecture search (NAS) which can be computationally expensive. We address this problem by providing an end-to-end technique that optimizes for model's Floating Point Operations (FLOPs) or for on-device latency via a novel ell_1{ell_2} latency surrogate. Our algorithm is versatile and can be used with many popular compression methods including pruning, low-rank factorization, and quantization. Crucially, it is fast and runs in almost the same amount of time as single model training; which is a significant training speed-up over standard NAS methods. For BERT compression on GLUE fine-tuning tasks, we achieve 50% reduction in FLOPs with only 1% drop in performance. For compressing MobileNetV3 on ImageNet-1K, we achieve 15% reduction in FLOPs, and 11% reduction in on-device latency without drop in accuracy, while still requiring 3times less training compute than SOTA compression techniques. Finally, for transfer learning on smaller datasets, our technique identifies 1.2times-1.4times cheaper architectures than standard MobileNetV3, EfficientNet suite of architectures at almost the same training cost and accuracy.

Computed tomography (CT) serves as an effective tool for lung cancer screening, diagnosis, treatment, and prognosis, providing a rich source of features to quantify temporal and spatial tumor changes. Nonetheless, the diversity of CT scanners and customized acquisition protocols can introduce significant inconsistencies in texture features, even when assessing the same patient. This variability poses a fundamental challenge for subsequent research that relies on consistent image features. Existing CT image standardization models predominantly utilize GAN-based supervised or semi-supervised learning, but their performance remains limited. We present DiffusionCT, an innovative score-based DDPM model that operates in the latent space to transform disparate non-standard distributions into a standardized form. The architecture comprises a U-Net-based encoder-decoder, augmented by a DDPM model integrated at the bottleneck position. First, the encoder-decoder is trained independently, without embedding DDPM, to capture the latent representation of the input data. Second, the latent DDPM model is trained while keeping the encoder-decoder parameters fixed. Finally, the decoder uses the transformed latent representation to generate a standardized CT image, providing a more consistent basis for downstream analysis. Empirical tests on patient CT images indicate notable improvements in image standardization using DiffusionCT. Additionally, the model significantly reduces image noise in SPAD images, further validating the effectiveness of DiffusionCT for advanced imaging tasks.

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.

Transformer-based end-to-end speech recognition has achieved great success. However, the large footprint and computational overhead make it difficult to deploy these models in some real-world applications. Model compression techniques can reduce the model size and speed up inference, but the compressed model has a fixed architecture which might be suboptimal. We propose a novel Transformer encoder with Input-Dependent Dynamic Depth (I3D) to achieve strong performance-efficiency trade-offs. With a similar number of layers at inference time, I3D-based models outperform the vanilla Transformer and the static pruned model via iterative layer pruning. We also present interesting analysis on the gate probabilities and the input-dependency, which helps us better understand deep encoders.

We propose a one-stage framework for real-time multi-person 3D human mesh estimation from a single RGB image. While current one-stage methods, which follow a DETR-style pipeline, achieve state-of-the-art (SOTA) performance with high-resolution inputs, we observe that this particularly benefits the estimation of individuals in smaller scales of the image (e.g., those far from the camera), but at the cost of significantly increased computation overhead. To address this, we introduce scale-adaptive tokens that are dynamically adjusted based on the relative scale of each individual in the image within the DETR framework. Specifically, individuals in smaller scales are processed at higher resolutions, larger ones at lower resolutions, and background regions are further distilled. These scale-adaptive tokens more efficiently encode the image features, facilitating subsequent decoding to regress the human mesh, while allowing the model to allocate computational resources more effectively and focus on more challenging cases. Experiments show that our method preserves the accuracy benefits of high-resolution processing while substantially reducing computational cost, achieving real-time inference with performance comparable to SOTA methods.

Convolutional neural networks (CNNs) have been the consensus for medical image segmentation tasks. However, they suffer from the limitation in modeling long-range dependencies and spatial correlations due to the nature of convolution operation. Although transformers were first developed to address this issue, they fail to capture low-level features. In contrast, it is demonstrated that both local and global features are crucial for dense prediction, such as segmenting in challenging contexts. In this paper, we propose HiFormer, a novel method that efficiently bridges a CNN and a transformer for medical image segmentation. Specifically, we design two multi-scale feature representations using the seminal Swin Transformer module and a CNN-based encoder. To secure a fine fusion of global and local features obtained from the two aforementioned representations, we propose a Double-Level Fusion (DLF) module in the skip connection of the encoder-decoder structure. Extensive experiments on various medical image segmentation datasets demonstrate the effectiveness of HiFormer over other CNN-based, transformer-based, and hybrid methods in terms of computational complexity, and quantitative and qualitative results. Our code is publicly available at: https://github.com/amirhossein-kz/HiFormer

Neural Radiance Fields (NeRF) have achieved huge success in effectively capturing and representing 3D objects and scenes. However, to establish a ubiquitous presence in everyday media formats, such as images and videos, we need to fulfill three key objectives: 1. fast encoding and decoding time, 2. compact model sizes, and 3. high-quality renderings. Despite recent advancements, a comprehensive algorithm that adequately addresses all objectives has yet to be fully realized. In this work, we present CodecNeRF, a neural codec for NeRF representations, consisting of an encoder and decoder architecture that can generate a NeRF representation in a single forward pass. Furthermore, inspired by the recent parameter-efficient finetuning approaches, we propose a finetuning method to efficiently adapt the generated NeRF representations to a new test instance, leading to high-quality image renderings and compact code sizes. The proposed CodecNeRF, a newly suggested encoding-decoding-finetuning pipeline for NeRF, achieved unprecedented compression performance of more than 100x and remarkable reduction in encoding time while maintaining (or improving) the image quality on widely used 3D object datasets.

We present DeepCABAC, a novel context-adaptive binary arithmetic coder for compressing deep neural networks. It quantizes each weight parameter by minimizing a weighted rate-distortion function, which implicitly takes the impact of quantization on to the accuracy of the network into account. Subsequently, it compresses the quantized values into a bitstream representation with minimal redundancies. We show that DeepCABAC is able to reach very high compression ratios across a wide set of different network architectures and datasets. For instance, we are able to compress by x63.6 the VGG16 ImageNet model with no loss of accuracy, thus being able to represent the entire network with merely 8.7MB.

Diffusion transformers have shown significant effectiveness in both image and video synthesis at the expense of huge computation costs. To address this problem, feature caching methods have been introduced to accelerate diffusion transformers by caching the features in previous timesteps and reusing them in the following timesteps. However, previous caching methods ignore that different tokens exhibit different sensitivities to feature caching, and feature caching on some tokens may lead to 10times more destruction to the overall generation quality compared with other tokens. In this paper, we introduce token-wise feature caching, allowing us to adaptively select the most suitable tokens for caching, and further enable us to apply different caching ratios to neural layers in different types and depths. Extensive experiments on PixArt-alpha, OpenSora, and DiT demonstrate our effectiveness in both image and video generation with no requirements for training. For instance, 2.36times and 1.93times acceleration are achieved on OpenSora and PixArt-alpha with almost no drop in generation quality.

The previous advancements in pathology image understanding primarily involved developing models tailored to specific tasks. Recent studies has demonstrated that the large vision-language model can enhance the performance of various downstream tasks in medical image understanding. In this study, we developed a domain-specific large language-vision assistant (PA-LLaVA) for pathology image understanding. Specifically, (1) we first construct a human pathology image-text dataset by cleaning the public medical image-text data for domain-specific alignment; (2) Using the proposed image-text data, we first train a pathology language-image pretraining (PLIP) model as the specialized visual encoder for pathology image, and then we developed scale-invariant connector to avoid the information loss caused by image scaling; (3) We adopt two-stage learning to train PA-LLaVA, first stage for domain alignment, and second stage for end to end visual question \& answering (VQA) task. In experiments, we evaluate our PA-LLaVA on both supervised and zero-shot VQA datasets, our model achieved the best overall performance among multimodal models of similar scale. The ablation experiments also confirmed the effectiveness of our design. We posit that our PA-LLaVA model and the datasets presented in this work can promote research in field of computational pathology. All codes are available at: https://github.com/ddw2AIGROUP2CQUPT/PA-LLaVA}{https://github.com/ddw2AIGROUP2CQUPT/PA-LLaVA

We present STAT: a simple algorithm to prune transformer models without any fine-tuning. STAT eliminates both attention heads and neurons from the network, while preserving accuracy by calculating a correction to the weights of the next layer. Each layer block in the network is compressed using a series of principled matrix factorizations that preserve the network structure. Our entire algorithm takes minutes to compress BERT, and less than three hours to compress models with 7B parameters using a single GPU. Using only several hundred data examples, STAT preserves the output of the network and improves upon existing gradient-free pruning methods. It is even competitive with methods that include significant fine-tuning. We demonstrate our method on both encoder and decoder architectures, including BERT, DistilBERT, and Llama-2 using benchmarks such as GLUE, Squad, WikiText2.

Categorical encoders transform categorical features into numerical representations that are indispensable for a wide range of machine learning models. Existing encoder benchmark studies lack generalizability because of their limited choice of (1) encoders, (2) experimental factors, and (3) datasets. Additionally, inconsistencies arise from the adoption of varying aggregation strategies. This paper is the most comprehensive benchmark of categorical encoders to date, including an extensive evaluation of 32 configurations of encoders from diverse families, with 36 combinations of experimental factors, and on 50 datasets. The study shows the profound influence of dataset selection, experimental factors, and aggregation strategies on the benchmark's conclusions -- aspects disregarded in previous encoder benchmarks.

Transformer models are deployed in a wide range of settings, from multi-accelerator clusters to standalone mobile phones. The diverse inference constraints in these scenarios necessitate practitioners to train foundation models such as PaLM 2, Llama, & ViTs as a series of models of varying sizes. Due to significant training costs, only a select few model sizes are trained and supported, limiting more fine-grained control over relevant tradeoffs, including latency, cost, and accuracy. This work introduces MatFormer, a nested Transformer architecture designed to offer elasticity in a variety of deployment constraints. Each Feed Forward Network (FFN) block of a MatFormer model is jointly optimized with a few nested smaller FFN blocks. This training procedure allows for the Mix'n'Match of model granularities across layers -- i.e., a trained universal MatFormer model enables extraction of hundreds of accurate smaller models, which were never explicitly optimized. We empirically demonstrate MatFormer's effectiveness across different model classes (decoders & encoders), modalities (language & vision), and scales (up to 2.6B parameters). We find that a 2.6B decoder-only MatFormer language model (MatLM) allows us to extract smaller models spanning from 1.5B to 2.6B, each exhibiting comparable validation loss and one-shot downstream evaluations to their independently trained counterparts. Furthermore, we observe that smaller encoders extracted from a universal MatFormer-based ViT (MatViT) encoder preserve the metric-space structure for adaptive large-scale retrieval. Finally, we showcase that speculative decoding with the accurate and consistent submodels extracted from MatFormer can further reduce inference latency.

The scaling laws and extraordinary performance of large foundation models motivate the development and utilization of such models in biomedicine. However, despite early promising results on some biomedical benchmarks, there are still major challenges that need to be addressed before these models can be used in real-world clinics. Frontier general-domain models such as GPT-4V still have significant performance gaps in multimodal biomedical applications. More importantly, less-acknowledged pragmatic issues, including accessibility, model cost, and tedious manual evaluation make it hard for clinicians to use state-of-the-art large models directly on private patient data. Here, we explore training open-source small multimodal models (SMMs) to bridge competency gaps for unmet clinical needs in radiology. To maximize data efficiency, we adopt a modular approach by incorporating state-of-the-art pre-trained models for image and text modalities, and focusing on training a lightweight adapter to ground each modality to the text embedding space, as exemplified by LLaVA-Med. For training, we assemble a large dataset of over 697 thousand radiology image-text pairs. For evaluation, we propose CheXprompt, a GPT-4-based metric for factuality evaluation, and demonstrate its parity with expert evaluation. For best practice, we conduct a systematic ablation study on various choices in data engineering and multimodal training. The resulting LlaVA-Rad (7B) model attains state-of-the-art results on standard radiology tasks such as report generation and cross-modal retrieval, even outperforming much larger models such as GPT-4V and Med-PaLM M (84B). The inference of LlaVA-Rad is fast and can be performed on a single V100 GPU in private settings, offering a promising state-of-the-art tool for real-world clinical applications.

Nucleus instance segmentation in histology images is crucial for a broad spectrum of clinical applications. Current dominant algorithms rely on regression of nuclear proxy maps. Distinguishing nucleus instances from the estimated maps requires carefully curated post-processing, which is error-prone and parameter-sensitive. Recently, the Segment Anything Model (SAM) has earned huge attention in medical image segmentation, owing to its impressive generalization ability and promptable property. Nevertheless, its potential on nucleus instance segmentation remains largely underexplored. In this paper, we present a novel prompt-driven framework that consists of a nucleus prompter and SAM for automatic nucleus instance segmentation. Specifically, the prompter learns to generate a unique point prompt for each nucleus while the SAM is fine-tuned to output the corresponding mask for the prompted nucleus. Furthermore, we propose the inclusion of adjacent nuclei as negative prompts to enhance the model's capability to identify overlapping nuclei. Without complicated post-processing, our proposed method sets a new state-of-the-art performance on three challenging benchmarks. Code is available at github.com/windygoo/PromptNucSeg

Convolutional Neural Networks (CNNs) and Transformers have been the most popular architectures for biomedical image segmentation, but both of them have limited ability to handle long-range dependencies because of inherent locality or computational complexity. To address this challenge, we introduce U-Mamba, a general-purpose network for biomedical image segmentation. Inspired by the State Space Sequence Models (SSMs), a new family of deep sequence models known for their strong capability in handling long sequences, we design a hybrid CNN-SSM block that integrates the local feature extraction power of convolutional layers with the abilities of SSMs for capturing the long-range dependency. Moreover, U-Mamba enjoys a self-configuring mechanism, allowing it to automatically adapt to various datasets without manual intervention. We conduct extensive experiments on four diverse tasks, including the 3D abdominal organ segmentation in CT and MR images, instrument segmentation in endoscopy images, and cell segmentation in microscopy images. The results reveal that U-Mamba outperforms state-of-the-art CNN-based and Transformer-based segmentation networks across all tasks. This opens new avenues for efficient long-range dependency modeling in biomedical image analysis. The code, models, and data are publicly available at https://wanglab.ai/u-mamba.html.

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

Diffusion models have achieved great success in image generation, with the backbone evolving from U-Net to Vision Transformers. However, the computational cost of Transformers is quadratic to the number of tokens, leading to significant challenges when dealing with high-resolution images. In this work, we propose Diffusion Mamba (DiM), which combines the efficiency of Mamba, a sequence model based on State Space Models (SSM), with the expressive power of diffusion models for efficient high-resolution image synthesis. To address the challenge that Mamba cannot generalize to 2D signals, we make several architecture designs including multi-directional scans, learnable padding tokens at the end of each row and column, and lightweight local feature enhancement. Our DiM architecture achieves inference-time efficiency for high-resolution images. In addition, to further improve training efficiency for high-resolution image generation with DiM, we investigate ``weak-to-strong'' training strategy that pretrains DiM on low-resolution images (256times 256) and then finetune it on high-resolution images (512 times 512). We further explore training-free upsampling strategies to enable the model to generate higher-resolution images (e.g., 1024times 1024 and 1536times 1536) without further fine-tuning. Experiments demonstrate the effectiveness and efficiency of our DiM.

Visual tokenization via auto-encoding empowers state-of-the-art image and video generative models by compressing pixels into a latent space. Although scaling Transformer-based generators has been central to recent advances, the tokenizer component itself is rarely scaled, leaving open questions about how auto-encoder design choices influence both its objective of reconstruction and downstream generative performance. Our work aims to conduct an exploration of scaling in auto-encoders to fill in this blank. To facilitate this exploration, we replace the typical convolutional backbone with an enhanced Vision Transformer architecture for Tokenization (ViTok). We train ViTok on large-scale image and video datasets far exceeding ImageNet-1K, removing data constraints on tokenizer scaling. We first study how scaling the auto-encoder bottleneck affects both reconstruction and generation -- and find that while it is highly correlated with reconstruction, its relationship with generation is more complex. We next explored the effect of separately scaling the auto-encoders' encoder and decoder on reconstruction and generation performance. Crucially, we find that scaling the encoder yields minimal gains for either reconstruction or generation, while scaling the decoder boosts reconstruction but the benefits for generation are mixed. Building on our exploration, we design ViTok as a lightweight auto-encoder that achieves competitive performance with state-of-the-art auto-encoders on ImageNet-1K and COCO reconstruction tasks (256p and 512p) while outperforming existing auto-encoders on 16-frame 128p video reconstruction for UCF-101, all with 2-5x fewer FLOPs. When integrated with Diffusion Transformers, ViTok demonstrates competitive performance on image generation for ImageNet-1K and sets new state-of-the-art benchmarks for class-conditional video generation on UCF-101.

Pathology, the microscopic examination of diseased tissue, is critical for diagnosing various medical conditions, particularly cancers. Traditional methods are labor-intensive and prone to human error. Digital pathology, which converts glass slides into high-resolution digital images for analysis by computer algorithms, revolutionizes the field by enhancing diagnostic accuracy, consistency, and efficiency through automated image analysis and large-scale data processing. Foundational transformer pretraining is crucial for developing robust, generalizable models as it enables learning from vast amounts of unannotated data. This paper introduces the Hibou family of foundational vision transformers for pathology, leveraging the DINOv2 framework to pretrain two model variants, Hibou-B and Hibou-L, on a proprietary dataset of over 1 million whole slide images (WSIs) representing diverse tissue types and staining techniques. Our pretrained models demonstrate superior performance on both patch-level and slide-level benchmarks, surpassing existing state-of-the-art methods. Notably, Hibou-L achieves the highest average accuracy across multiple benchmark datasets. To support further research and application in the field, we have open-sourced the Hibou-B model, which can be accessed at https://github.com/HistAI/hibou

This paper introduces a network for volumetric segmentation that learns from sparsely annotated volumetric images. We outline two attractive use cases of this method: (1) In a semi-automated setup, the user annotates some slices in the volume to be segmented. The network learns from these sparse annotations and provides a dense 3D segmentation. (2) In a fully-automated setup, we assume that a representative, sparsely annotated training set exists. Trained on this data set, the network densely segments new volumetric images. The proposed network extends the previous u-net architecture from Ronneberger et al. by replacing all 2D operations with their 3D counterparts. The implementation performs on-the-fly elastic deformations for efficient data augmentation during training. It is trained end-to-end from scratch, i.e., no pre-trained network is required. We test the performance of the proposed method on a complex, highly variable 3D structure, the Xenopus kidney, and achieve good results for both use cases.

Training visual embeddings with labeled data supervision has been the de facto setup for representation learning in computer vision. Inspired by recent success of adopting masked image modeling (MIM) in self-supervised representation learning, we propose a simple yet effective setup that can easily integrate MIM into existing supervised training paradigms. In our design, in addition to the original classification task applied to a vision transformer image encoder, we add a shallow transformer-based decoder on top of the encoder and introduce an MIM task which tries to reconstruct image tokens based on masked image inputs. We show with minimal change in architecture and no overhead in inference that this setup is able to improve the quality of the learned representations for downstream tasks such as classification, image retrieval, and semantic segmentation. We conduct a comprehensive study and evaluation of our setup on public benchmarks. On ImageNet-1k, our ViT-B/14 model achieves 81.72% validation accuracy, 2.01% higher than the baseline model. On K-Nearest-Neighbor image retrieval evaluation with ImageNet-1k, the same model outperforms the baseline by 1.32%. We also show that this setup can be easily scaled to larger models and datasets. Code and checkpoints will be released.

Despite the progress made by multimodal large language models (MLLMs) in computational pathology, they remain limited by a predominant focus on patch-level analysis, missing essential contextual information at the whole-slide level. The lack of large-scale instruction datasets and the gigapixel scale of whole slide images (WSIs) pose significant developmental challenges. In this paper, we present SlideChat, the first vision-language assistant capable of understanding gigapixel whole-slide images, exhibiting excellent multimodal conversational capability and response complex instruction across diverse pathology scenarios. To support its development, we created SlideInstruction, the largest instruction-following dataset for WSIs consisting of 4.2K WSI captions and 176K VQA pairs with multiple categories. Furthermore, we propose SlideBench, a multimodal benchmark that incorporates captioning and VQA tasks to assess SlideChat's capabilities in varied clinical settings such as microscopy, diagnosis. Compared to both general and specialized MLLMs, SlideChat exhibits exceptional capabilities achieving state-of-the-art performance on 18 of 22 tasks. For example, it achieved an overall accuracy of 81.17% on SlideBench-VQA (TCGA), and 54.15% on SlideBench-VQA (BCNB). We will fully release SlideChat, SlideInstruction and SlideBench as open-source resources to facilitate research and development in computational pathology.

In this work, we present efficient modulation, a novel design for efficient vision networks. We revisit the modulation mechanism, which operates input through convolutional context modeling and feature projection layers, and fuses features via element-wise multiplication and an MLP block. We demonstrate that the modulation mechanism is particularly well suited for efficient networks and further tailor the modulation design by proposing the efficient modulation (EfficientMod) block, which is considered the essential building block for our networks. Benefiting from the prominent representational ability of modulation mechanism and the proposed efficient design, our network can accomplish better trade-offs between accuracy and efficiency and set new state-of-the-art performance in the zoo of efficient networks. When integrating EfficientMod with the vanilla self-attention block, we obtain the hybrid architecture which further improves the performance without loss of efficiency. We carry out comprehensive experiments to verify EfficientMod's performance. With fewer parameters, our EfficientMod-s performs 0.6 top-1 accuracy better than EfficientFormerV2-s2 and is 25% faster on GPU, and 2.9 better than MobileViTv2-1.0 at the same GPU latency. Additionally, our method presents a notable improvement in downstream tasks, outperforming EfficientFormerV2-s by 3.6 mIoU on the ADE20K benchmark. Code and checkpoints are available at https://github.com/ma-xu/EfficientMod.

We present a neural network architecture designed to naturally learn a positional embedding and overcome the spectral bias towards lower frequencies faced by conventional implicit neural representation networks. Our proposed architecture, SPDER, is a simple MLP that uses an activation function composed of a sinusoidal multiplied by a sublinear function, called the damping function. The sinusoidal enables the network to automatically learn the positional embedding of an input coordinate while the damping passes on the actual coordinate value by preventing it from being projected down to within a finite range of values. Our results indicate that SPDERs speed up training by 10x and converge to losses 1,500-50,000x lower than that of the state-of-the-art for image representation. SPDER is also state-of-the-art in audio representation. The superior representation capability allows SPDER to also excel on multiple downstream tasks such as image super-resolution and video frame interpolation. We provide intuition as to why SPDER significantly improves fitting compared to that of other INR methods while requiring no hyperparameter tuning or preprocessing.

Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1,149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with 15,000-30,000 dimensional gene expressions. With 4,293,195 pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.

Despite that deep learning has achieved state-of-the-art performance for medical image segmentation, its success relies on a large set of manually annotated images for training that are expensive to acquire. In this paper, we propose an annotation-efficient learning framework for segmentation tasks that avoids annotations of training images, where we use an improved Cycle-Consistent Generative Adversarial Network (GAN) to learn from a set of unpaired medical images and auxiliary masks obtained either from a shape model or public datasets. We first use the GAN to generate pseudo labels for our training images under the implicit high-level shape constraint represented by a Variational Auto-encoder (VAE)-based discriminator with the help of the auxiliary masks, and build a Discriminator-guided Generator Channel Calibration (DGCC) module which employs our discriminator's feedback to calibrate the generator for better pseudo labels. To learn from the pseudo labels that are noisy, we further introduce a noise-robust iterative learning method using noise-weighted Dice loss. We validated our framework with two situations: objects with a simple shape model like optic disc in fundus images and fetal head in ultrasound images, and complex structures like lung in X-Ray images and liver in CT images. Experimental results demonstrated that 1) Our VAE-based discriminator and DGCC module help to obtain high-quality pseudo labels. 2) Our proposed noise-robust learning method can effectively overcome the effect of noisy pseudo labels. 3) The segmentation performance of our method without using annotations of training images is close or even comparable to that of learning from human annotations.

Recent advancements in subject-driven image generation have led to zero-shot generation, yet precise selection and focus on crucial subject representations remain challenging. Addressing this, we introduce the SSR-Encoder, a novel architecture designed for selectively capturing any subject from single or multiple reference images. It responds to various query modalities including text and masks, without necessitating test-time fine-tuning. The SSR-Encoder combines a Token-to-Patch Aligner that aligns query inputs with image patches and a Detail-Preserving Subject Encoder for extracting and preserving fine features of the subjects, thereby generating subject embeddings. These embeddings, used in conjunction with original text embeddings, condition the generation process. Characterized by its model generalizability and efficiency, the SSR-Encoder adapts to a range of custom models and control modules. Enhanced by the Embedding Consistency Regularization Loss for improved training, our extensive experiments demonstrate its effectiveness in versatile and high-quality image generation, indicating its broad applicability. Project page: https://ssr-encoder.github.io

Modeling latent variables with priors and hyperpriors is an essential problem in variational image compression. Formally, trade-off between rate and distortion is handled well if priors and hyperpriors precisely describe latent variables. Current practices only adopt univariate priors and process each variable individually. However, we find inter-correlations and intra-correlations exist when observing latent variables in a vectorized perspective. These findings reveal visual redundancies to improve rate-distortion performance and parallel processing ability to speed up compression. This encourages us to propose a novel vectorized prior. Specifically, a multivariate Gaussian mixture is proposed with means and covariances to be estimated. Then, a novel probabilistic vector quantization is utilized to effectively approximate means, and remaining covariances are further induced to a unified mixture and solved by cascaded estimation without context models involved. Furthermore, codebooks involved in quantization are extended to multi-codebooks for complexity reduction, which formulates an efficient compression procedure. Extensive experiments on benchmark datasets against state-of-the-art indicate our model has better rate-distortion performance and an impressive 3.18times compression speed up, giving us the ability to perform real-time, high-quality variational image compression in practice. Our source code is publicly available at https://github.com/xiaosu-zhu/McQuic.

Accurate segmentation of brain tumors plays a key role in the diagnosis and treatment of brain tumor diseases. It serves as a critical technology for quantifying tumors and extracting their features. With the increasing application of deep learning methods, the computational burden has become progressively heavier. To achieve a lightweight model with good segmentation performance, this study proposes the MBDRes-U-Net model using the three-dimensional (3D) U-Net codec framework, which integrates multibranch residual blocks and fused attention into the model. The computational burden of the model is reduced by the branch strategy, which effectively uses the rich local features in multimodal images and enhances the segmentation performance of subtumor regions. Additionally, during encoding, an adaptive weighted expansion convolution layer is introduced into the multi-branch residual block, which enriches the feature expression and improves the segmentation accuracy of the model. Experiments on the Brain Tumor Segmentation (BraTS) Challenge 2018 and 2019 datasets show that the architecture could maintain a high precision of brain tumor segmentation while considerably reducing the calculation overhead.Our code is released at https://github.com/Huaibei-normal-university-cv-laboratory/mbdresunet

The visual projector serves as an essential bridge between the visual encoder and the Large Language Model (LLM) in a Multimodal LLM (MLLM). Typically, MLLMs adopt a simple MLP to preserve all visual contexts via one-to-one transformation. However, the visual tokens are redundant and can be considerably increased when dealing with high-resolution images, impairing the efficiency of MLLMs significantly. Some recent works have introduced resampler or abstractor to reduce the number of resulting visual tokens. Unfortunately, they fail to capture finer details and undermine the visual reasoning capabilities of MLLMs. In this work, we propose a novel visual projector, which adopts a coarse-to-fine scheme to inject the enriched characteristics to generate the condensed visual tokens. In specific, we first interpolate the visual features as a low-resolution point query, providing the overall visual representation as the foundation. Then, we introduce a region-to-point injection module that utilizes high-resolution, multi-level region-based cues as fine-grained reference keys and values, allowing them to be fully absorbed within the corresponding local context region. This step effectively updates the coarse point query, transforming it into an enriched one for the subsequent LLM reasoning. Extensive experiments demonstrate that our approach compresses the visual tokens by 75%~89%, while achieves comparable or even better performance across diverse benchmarks with significantly higher efficiency. The source codes can be found at https://github.com/CircleRadon/TokenPacker.

In this paper, we contend that a natural objective of representation learning is to compress and transform the distribution of the data, say sets of tokens, towards a low-dimensional Gaussian mixture supported on incoherent subspaces. The goodness of such a representation can be evaluated by a principled measure, called sparse rate reduction, that simultaneously maximizes the intrinsic information gain and extrinsic sparsity of the learned representation. From this perspective, popular deep network architectures, including transformers, can be viewed as realizing iterative schemes to optimize this measure. Particularly, we derive a transformer block from alternating optimization on parts of this objective: the multi-head self-attention operator compresses the representation by implementing an approximate gradient descent step on the coding rate of the features, and the subsequent multi-layer perceptron sparsifies the features. This leads to a family of white-box transformer-like deep network architectures, named CRATE, which are mathematically fully interpretable. We show, by way of a novel connection between denoising and compression, that the inverse to the aforementioned compressive encoding can be realized by the same class of CRATE architectures. Thus, the so-derived white-box architectures are universal to both encoders and decoders. Experiments show that these networks, despite their simplicity, indeed learn to compress and sparsify representations of large-scale real-world image and text datasets, and achieve performance very close to highly engineered transformer-based models: ViT, MAE, DINO, BERT, and GPT2. We believe the proposed computational framework demonstrates great potential in bridging the gap between theory and practice of deep learning, from a unified perspective of data compression. Code is available at: https://ma-lab-berkeley.github.io/CRATE .

In this paper, we present CAD2Program, a new method for reconstructing 3D parametric models from 2D CAD drawings. Our proposed method is inspired by recent successes in vision-language models (VLMs), and departs from traditional methods which rely on task-specific data representations and/or algorithms. Specifically, on the input side, we simply treat the 2D CAD drawing as a raster image, regardless of its original format, and encode the image with a standard ViT model. We show that such an encoding scheme achieves competitive performance against existing methods that operate on vector-graphics inputs, while imposing substantially fewer restrictions on the 2D drawings. On the output side, our method auto-regressively predicts a general-purpose language describing 3D parametric models in text form. Compared to other sequence modeling methods for CAD which use domain-specific sequence representations with fixed-size slots, our text-based representation is more flexible, and can be easily extended to arbitrary geometric entities and semantic or functional properties. Experimental results on a large-scale dataset of cabinet models demonstrate the effectiveness of our method.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

Multimodal models trained on large natural image-text pair datasets have exhibited astounding abilities in generating high-quality images. Medical imaging data is fundamentally different to natural images, and the language used to succinctly capture relevant details in medical data uses a different, narrow but semantically rich, domain-specific vocabulary. Not surprisingly, multi-modal models trained on natural image-text pairs do not tend to generalize well to the medical domain. Developing generative imaging models faithfully representing medical concepts while providing compositional diversity could mitigate the existing paucity of high-quality, annotated medical imaging datasets. In this work, we develop a strategy to overcome the large natural-medical distributional shift by adapting a pre-trained latent diffusion model on a corpus of publicly available chest x-rays (CXR) and their corresponding radiology (text) reports. We investigate the model's ability to generate high-fidelity, diverse synthetic CXR conditioned on text prompts. We assess the model outputs quantitatively using image quality metrics, and evaluate image quality and text-image alignment by human domain experts. We present evidence that the resulting model (RoentGen) is able to create visually convincing, diverse synthetic CXR images, and that the output can be controlled to a new extent by using free-form text prompts including radiology-specific language. Fine-tuning this model on a fixed training set and using it as a data augmentation method, we measure a 5% improvement of a classifier trained jointly on synthetic and real images, and a 3% improvement when trained on a larger but purely synthetic training set. Finally, we observe that this fine-tuning distills in-domain knowledge in the text-encoder and can improve its representation capabilities of certain diseases like pneumothorax by 25%.

The development of Multi-modal Large Language Models (MLLMs) enhances Large Language Models (LLMs) with the ability to perceive data formats beyond text, significantly advancing a range of downstream applications, such as visual question answering and image captioning. However, the substantial computational costs associated with processing high-resolution images and videos pose a barrier to their broader adoption. To address this challenge, compressing vision tokens in MLLMs has emerged as a promising approach to reduce inference costs. While existing methods conduct token reduction in the feature alignment phase. In this paper, we introduce VisToG, a novel grouping mechanism that leverages the capabilities of pre-trained vision encoders to group similar image segments without the need for segmentation masks. Specifically, we concatenate semantic tokens to represent image semantic segments after the linear projection layer before feeding into the vision encoder. Besides, with the isolated attention we adopt, VisToG can identify and eliminate redundant visual tokens utilizing the prior knowledge in the pre-trained vision encoder, which effectively reduces computational demands. Extensive experiments demonstrate the effectiveness of VisToG, maintaining 98.1% of the original performance while achieving a reduction of over 27\% inference time.