Yuyin Zhou

Yutong Bai, Zeyu Wang, Junfei Xiao et al. · berkeley

This paper studies the potential of distilling knowledge from pre-trained models, especially Masked Autoencoders. Our approach is simple: in addition to optimizing the pixel reconstruction loss on masked inputs, we minimize the distance between the intermediate feature map of the teacher model and that of the student model. This design leads to a computationally efficient knowledge distillation framework, given 1) only a small visible subset of patches is used, and 2) the (cumbersome) teacher model only needs to be partially executed, ie, forward propagate inputs through the first few layers, for obtaining intermediate feature maps. Compared to directly distilling fine-tuned models, distilling pre-trained models substantially improves downstream performance. For example, by distilling the knowledge from an MAE pre-trained ViT-L into a ViT-B, our method achieves 84.0% ImageNet top-1 accuracy, outperforming the baseline of directly distilling a fine-tuned ViT-L by 1.2%. More intriguingly, our method can robustly distill knowledge from teacher models even with extremely high masking ratios: e.g., with 95% masking ratio where merely TEN patches are visible during distillation, our ViT-B competitively attains a top-1 ImageNet accuracy of 83.6%; surprisingly, it can still secure 82.4% top-1 ImageNet accuracy by aggressively training with just FOUR visible patches (98% masking ratio). The code and models are publicly available at https://github.com/UCSC-VLAA/DMAE.

Yiqing Wang, Zihan Li, Jieru Mei et al. · uw

Recent advancements in large-scale Vision Transformers have made significant strides in improving pre-trained models for medical image segmentation. However, these methods face a notable challenge in acquiring a substantial amount of pre-training data, particularly within the medical field. To address this limitation, we present Masked Multi-view with Swin Transformers (SwinMM), a novel multi-view pipeline for enabling accurate and data-efficient self-supervised medical image analysis. Our strategy harnesses the potential of multi-view information by incorporating two principal components. In the pre-training phase, we deploy a masked multi-view encoder devised to concurrently train masked multi-view observations through a range of diverse proxy tasks. These tasks span image reconstruction, rotation, contrastive learning, and a novel task that employs a mutual learning paradigm. This new task capitalizes on the consistency between predictions from various perspectives, enabling the extraction of hidden multi-view information from 3D medical data. In the fine-tuning stage, a cross-view decoder is developed to aggregate the multi-view information through a cross-attention block. Compared with the previous state-of-the-art self-supervised learning method Swin UNETR, SwinMM demonstrates a notable advantage on several medical image segmentation tasks. It allows for a smooth integration of multi-view information, significantly boosting both the accuracy and data-efficiency of the model. Code and models are available at https://github.com/UCSC-VLAA/SwinMM/.

Zeyu Wang, Yutong Bai, Yuyin Zhou et al. · berkeley

The recent success of Vision Transformers is shaking the long dominance of Convolutional Neural Networks (CNNs) in image recognition for a decade. Specifically, in terms of robustness on out-of-distribution samples, recent research finds that Transformers are inherently more robust than CNNs, regardless of different training setups. Moreover, it is believed that such superiority of Transformers should largely be credited to their self-attention-like architectures per se. In this paper, we question that belief by closely examining the design of Transformers. Our findings lead to three highly effective architecture designs for boosting robustness, yet simple enough to be implemented in several lines of code, namely a) patchifying input images, b) enlarging kernel size, and c) reducing activation layers and normalization layers. Bringing these components together, we are able to build pure CNN architectures without any attention-like operations that are as robust as, or even more robust than, Transformers. We hope this work can help the community better understand the design of robust neural architectures. The code is publicly available at https://github.com/UCSC-VLAA/RobustCNN.

Rui Yan, Liangqiong Qu, Qingyue Wei et al.

The collection and curation of large-scale medical datasets from multiple institutions is essential for training accurate deep learning models, but privacy concerns often hinder data sharing. Federated learning (FL) is a promising solution that enables privacy-preserving collaborative learning among different institutions, but it generally suffers from performance deterioration due to heterogeneous data distributions and a lack of quality labeled data. In this paper, we present a robust and label-efficient self-supervised FL framework for medical image analysis. Our method introduces a novel Transformer-based self-supervised pre-training paradigm that pre-trains models directly on decentralized target task datasets using masked image modeling, to facilitate more robust representation learning on heterogeneous data and effective knowledge transfer to downstream models. Extensive empirical results on simulated and real-world medical imaging non-IID federated datasets show that masked image modeling with Transformers significantly improves the robustness of models against various degrees of data heterogeneity. Notably, under severe data heterogeneity, our method, without relying on any additional pre-training data, achieves an improvement of 5.06%, 1.53% and 4.58% in test accuracy on retinal, dermatology and chest X-ray classification compared to the supervised baseline with ImageNet pre-training. In addition, we show that our federated self-supervised pre-training methods yield models that generalize better to out-of-distribution data and perform more effectively when fine-tuning with limited labeled data, compared to existing FL algorithms. The code is available at https://github.com/rui-yan/SSL-FL.

Junyang Wu, Xianhang Li, Chen Wei et al.

This paper presents a simple and effective visual prompting method for adapting pre-trained models to downstream recognition tasks. Our method includes two key designs. First, rather than directly adding together the prompt and the image, we treat the prompt as an extra and independent learnable component. We show that the strategy of reconciling the prompt and the image matters, and find that warping the prompt around a properly shrinked image empirically works the best. Second, we re-introduce two "old tricks" commonly used in building transferable adversarial examples, i.e., input diversity and gradient normalization, into visual prompting. These techniques improve optimization and enable the prompt to generalize better. We provide extensive experimental results to demonstrate the effectiveness of our method. Using a CLIP model, our prompting method sets a new record of 82.8% average accuracy across 12 popular classification datasets, substantially surpassing the prior art by +5.6%. It is worth noting that this prompting performance already outperforms linear probing by +2.1% and can even match fully fine-tuning in certain datasets. In addition, our prompting method shows competitive performance across different data scales and against distribution shifts. The code is publicly available at https://github.com/UCSC-VLAA/EVP.

Sucheng Ren, Huiyu Wang, Zhengqi Gao et al.

Data mixing (e.g., Mixup, Cutmix, ResizeMix) is an essential component for advancing recognition models. In this paper, we focus on studying its effectiveness in the self-supervised setting. By noticing the mixed images that share the same source images are intrinsically related to each other, we hereby propose SDMP, short for $\textbf{S}$imple $\textbf{D}$ata $\textbf{M}$ixing $\textbf{P}$rior, to capture this straightforward yet essential prior, and position such mixed images as additional $\textbf{positive pairs}$ to facilitate self-supervised representation learning. Our experiments verify that the proposed SDMP enables data mixing to help a set of self-supervised learning frameworks (e.g., MoCo) achieve better accuracy and out-of-distribution robustness. More notably, our SDMP is the first method that successfully leverages data mixing to improve (rather than hurt) the performance of Vision Transformers in the self-supervised setting. Code is publicly available at https://github.com/OliverRensu/SDMP

Jiaqi Liu, Shi Qiu, Mairui Li et al.

Automating scientific discovery requires more than generating papers from ideas. Real research is iterative: hypotheses are challenged from multiple perspectives, experiments fail and inform the next attempt, and lessons accumulate across cycles. Existing autonomous research systems often model this process as a linear pipeline: they rely on single-agent reasoning, stop when execution fails, and do not carry experience across runs. We present AutoResearchClaw, a multi-agent autonomous research pipeline built on five mechanisms: structured multi-agent debate for hypothesis generation and result analysis, a self-healing executor with a \textsc{Pivot}/\textsc{Refine} decision loop that transforms failures into information, verifiable result reporting that prevents fabricated numbers and hallucinated citations, human-in-the-loop collaboration with seven intervention modes spanning full autonomy to step-by-step oversight, and cross-run evolution that converts past mistakes into future safeguards. On ARC-Bench, a 25-topic experiment-stage benchmark, AutoResearchClaw outperforms AI Scientist v2 by 54.7%. A human-in-the-loop ablation across seven intervention modes reveals that precise, targeted collaboration at high-leverage decision points consistently outperforms both full autonomy and exhaustive step-by-step oversight. We position AutoResearchClaw as a research amplifier that augments rather than replaces human scientific judgment. Code is available at https://github.com/aiming-lab/AutoResearchClaw.

Xianhang Li, Huiyu Wang, Chen Wei et al.

Image pre-training, the current de-facto paradigm for a wide range of visual tasks, is generally less favored in the field of video recognition. By contrast, a common strategy is to directly train with spatiotemporal convolutional neural networks (CNNs) from scratch. Nonetheless, interestingly, by taking a closer look at these from-scratch learned CNNs, we note there exist certain 3D kernels that exhibit much stronger appearance modeling ability than others, arguably suggesting appearance information is already well disentangled in learning. Inspired by this observation, we hypothesize that the key to effectively leveraging image pre-training lies in the decomposition of learning spatial and temporal features, and revisiting image pre-training as the appearance prior to initializing 3D kernels. In addition, we propose Spatial-Temporal Separable (STS) convolution, which explicitly splits the feature channels into spatial and temporal groups, to further enable a more thorough decomposition of spatiotemporal features for fine-tuning 3D CNNs. Our experiments show that simply replacing 3D convolution with STS notably improves a wide range of 3D CNNs without increasing parameters and computation on both Kinetics-400 and Something-Something V2. Moreover, this new training pipeline consistently achieves better results on video recognition with significant speedup. For instance, we achieve +0.6% top-1 of Slowfast on Kinetics-400 over the strong 256-epoch 128-GPU baseline while fine-tuning for only 50 epochs with 4 GPUs. The code and models are available at https://github.com/UCSC-VLAA/Image-Pretraining-for-Video.

Yipeng Gao, Zeyu Wang, Wei-Shi Zheng et al.

Contrastive learning has emerged as a promising paradigm for 3D open-world understanding, i.e., aligning point cloud representation to image and text embedding space individually. In this paper, we introduce MixCon3D, a simple yet effective method aiming to sculpt holistic 3D representation in contrastive language-image-3D pre-training. In contrast to point cloud only, we develop the 3D object-level representation from complementary perspectives, e.g., multi-view rendered images with the point cloud. Then, MixCon3D performs language-3D contrastive learning, comprehensively depicting real-world 3D objects and bolstering text alignment. Additionally, we pioneer the first thorough investigation of various training recipes for the 3D contrastive learning paradigm, building a solid baseline with improved performance. Extensive experiments conducted on three representative benchmarks reveal that our method significantly improves over the baseline, surpassing the previous state-of-the-art performance on the challenging 1,156-category Objaverse-LVIS dataset by 5.7%. The versatility of MixCon3D is showcased in applications such as text-to-3D retrieval and point cloud captioning, further evidencing its efficacy in diverse scenarios. The code is available at https://github.com/UCSC-VLAA/MixCon3D.

Qingyue Wei, Lequan Yu, Xianhang Li et al.

Medical imaging has witnessed remarkable progress but usually requires a large amount of high-quality annotated data which is time-consuming and costly to obtain. To alleviate this burden, semi-supervised learning has garnered attention as a potential solution. In this paper, we present Meta-Learning for Bootstrapping Medical Image Segmentation (MLB-Seg), a novel method for tackling the challenge of semi-supervised medical image segmentation. Specifically, our approach first involves training a segmentation model on a small set of clean labeled images to generate initial labels for unlabeled data. To further optimize this bootstrapping process, we introduce a per-pixel weight mapping system that dynamically assigns weights to both the initialized labels and the model's own predictions. These weights are determined using a meta-process that prioritizes pixels with loss gradient directions closer to those of clean data, which is based on a small set of precisely annotated images. To facilitate the meta-learning process, we additionally introduce a consistency-based Pseudo Label Enhancement (PLE) scheme that improves the quality of the model's own predictions by ensembling predictions from various augmented versions of the same input. In order to improve the quality of the weight maps obtained through multiple augmentations of a single input, we introduce a mean teacher into the PLE scheme. This method helps to reduce noise in the weight maps and stabilize its generation process. Our extensive experimental results on public atrial and prostate segmentation datasets demonstrate that our proposed method achieves state-of-the-art results under semi-supervision. Our code is available at https://github.com/aijinrjinr/MLB-Seg.

Ayush Singla, Qingyu Zhao, Daniel K. Do et al.

For the first time, we propose using a multiple instance learning based convolution-free transformer model, called Multiple Instance Neuroimage Transformer (MINiT), for the classification of T1weighted (T1w) MRIs. We first present several variants of transformer models adopted for neuroimages. These models extract non-overlapping 3D blocks from the input volume and perform multi-headed self-attention on a sequence of their linear projections. MINiT, on the other hand, treats each of the non-overlapping 3D blocks of the input MRI as its own instance, splitting it further into non-overlapping 3D patches, on which multi-headed self-attention is computed. As a proof-of-concept, we evaluate the efficacy of our model by training it to identify sex from T1w-MRIs of two public datasets: Adolescent Brain Cognitive Development (ABCD) and the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA). The learned attention maps highlight voxels contributing to identifying sex differences in brain morphometry. The code is available at https://github.com/singlaayush/MINIT.

Zichao Li, Li Liu, Zeyu Wang et al.

Adversarial training (AT) with samples generated by Fast Gradient Sign Method (FGSM), also known as FGSM-AT, is a computationally simple method to train robust networks. However, during its training procedure, an unstable mode of "catastrophic overfitting" has been identified in arXiv:2001.03994 [cs.LG], where the robust accuracy abruptly drops to zero within a single training step. Existing methods use gradient regularizers or random initialization tricks to attenuate this issue, whereas they either take high computational cost or lead to lower robust accuracy. In this work, we provide the first study, which thoroughly examines a collection of tricks from three perspectives: Data Initialization, Network Structure, and Optimization, to overcome the catastrophic overfitting in FGSM-AT. Surprisingly, we find that simple tricks, i.e., a) masking partial pixels (even without randomness), b) setting a large convolution stride and smooth activation functions, or c) regularizing the weights of the first convolutional layer, can effectively tackle the overfitting issue. Extensive results on a range of network architectures validate the effectiveness of each proposed trick, and the combinations of tricks are also investigated. For example, trained with PreActResNet-18 on CIFAR-10, our method attains 49.8% accuracy against PGD-50 attacker and 46.4% accuracy against AutoAttack, demonstrating that pure FGSM-AT is capable of enabling robust learners. The code and models are publicly available at https://github.com/UCSC-VLAA/Bag-of-Tricks-for-FGSM-AT.

Fuying Wang, Yuyin Zhou, Shujun Wang et al.

Learning medical visual representations directly from paired radiology reports has become an emerging topic in representation learning. However, existing medical image-text joint learning methods are limited by instance or local supervision analysis, ignoring disease-level semantic correspondences. In this paper, we present a novel Multi-Granularity Cross-modal Alignment (MGCA) framework for generalized medical visual representation learning by harnessing the naturally exhibited semantic correspondences between medical image and radiology reports at three different levels, i.e., pathological region-level, instance-level, and disease-level. Specifically, we first incorporate the instance-wise alignment module by maximizing the agreement between image-report pairs. Further, for token-wise alignment, we introduce a bidirectional cross-attention strategy to explicitly learn the matching between fine-grained visual tokens and text tokens, followed by contrastive learning to align them. More important, to leverage the high-level inter-subject relationship semantic (e.g., disease) correspondences, we design a novel cross-modal disease-level alignment paradigm to enforce the cross-modal cluster assignment consistency. Extensive experimental results on seven downstream medical image datasets covering image classification, object detection, and semantic segmentation tasks demonstrate the stable and superior performance of our framework.

Peiran Xu, Zeyu Wang, Jieru Mei et al.

Federated learning (FL) is an emerging paradigm in machine learning, where a shared model is collaboratively learned using data from multiple devices to mitigate the risk of data leakage. While recent studies posit that Vision Transformer (ViT) outperforms Convolutional Neural Networks (CNNs) in addressing data heterogeneity in FL, the specific architectural components that underpin this advantage have yet to be elucidated. In this paper, we systematically investigate the impact of different architectural elements, such as activation functions and normalization layers, on the performance within heterogeneous FL. Through rigorous empirical analyses, we are able to offer the first-of-its-kind general guidance on micro-architecture design principles for heterogeneous FL. Intriguingly, our findings indicate that with strategic architectural modifications, pure CNNs can achieve a level of robustness that either matches or even exceeds that of ViTs when handling heterogeneous data clients in FL. Additionally, our approach is compatible with existing FL techniques and delivers state-of-the-art solutions across a broad spectrum of FL benchmarks. The code is publicly available at https://github.com/UCSC-VLAA/FedConv

Jieneng Chen, Jieru Mei, Xianhang Li et al.

Medical image segmentation plays a crucial role in advancing healthcare systems for disease diagnosis and treatment planning. The u-shaped architecture, popularly known as U-Net, has proven highly successful for various medical image segmentation tasks. However, U-Net's convolution-based operations inherently limit its ability to model long-range dependencies effectively. To address these limitations, researchers have turned to Transformers, renowned for their global self-attention mechanisms, as alternative architectures. One popular network is our previous TransUNet, which leverages Transformers' self-attention to complement U-Net's localized information with the global context. In this paper, we extend the 2D TransUNet architecture to a 3D network by building upon the state-of-the-art nnU-Net architecture, and fully exploring Transformers' potential in both the encoder and decoder design. We introduce two key components: 1) A Transformer encoder that tokenizes image patches from a convolution neural network (CNN) feature map, enabling the extraction of global contexts, and 2) A Transformer decoder that adaptively refines candidate regions by utilizing cross-attention between candidate proposals and U-Net features. Our investigations reveal that different medical tasks benefit from distinct architectural designs. The Transformer encoder excels in multi-organ segmentation, where the relationship among organs is crucial. On the other hand, the Transformer decoder proves more beneficial for dealing with small and challenging segmented targets such as tumor segmentation. Extensive experiments showcase the significant potential of integrating a Transformer-based encoder and decoder into the u-shaped medical image segmentation architecture. TransUNet outperforms competitors in various medical applications.

Yunfei Xie, Ce Zhou, Lang Gao et al.

This paper introduces MedTrinity-25M, a comprehensive, large-scale multimodal dataset for medicine, covering over 25 million images across 10 modalities with multigranular annotations for more than 65 diseases. These multigranular annotations encompass both global information, such as modality and organ detection, and local information like ROI analysis, lesion texture, and region-wise correlations. Unlike the existing multimodal datasets, which are limited by the availability of image-text pairs, we have developed the first automated pipeline that scales up multimodal data by generating multigranular visual and textual annotations in the form of image-ROI-description triplets without the need for any paired text descriptions. Specifically, data from over 30 different sources have been collected, preprocessed, and grounded using domain-specific expert models to identify ROIs related to abnormal regions. We then build a comprehensive knowledge base and prompt multimodal large language models to perform retrieval-augmented generation with the identified ROIs as guidance, resulting in multigranular textual descriptions. Compared to existing datasets, MedTrinity-25M provides the most enriched annotations, supporting a comprehensive range of multimodal tasks such as captioning and report generation, as well as vision-centric tasks like classification and segmentation. We propose LLaVA-Tri by pretraining LLaVA on MedTrinity-25M, achieving state-of-the-art performance on VQA-RAD, SLAKE, and PathVQA, surpassing representative SOTA multimodal large language models. Furthermore, MedTrinity-25M can also be utilized to support large-scale pre-training of multimodal medical AI models, contributing to the development of future foundation models in the medical domain. We will make our dataset available.

Shuang Zeng, Pengxin Guo, Shuai Wang et al.

Federated Learning (FL) is a rising approach towards collaborative and privacy-preserving machine learning where large-scale medical datasets remain localized to each client. However, the issue of data heterogeneity among clients often compels local models to diverge, leading to suboptimal global models. To mitigate the impact of data heterogeneity on FL performance, we start with analyzing how FL training influence FL performance by decomposing the global loss into three terms: local loss, distribution shift loss and aggregation loss. Remarkably, our loss decomposition reveals that existing local training-based FL methods attempt to reduce the distribution shift loss, while the global aggregation-based FL methods propose better aggregation strategies to reduce the aggregation loss. Nevertheless, a comprehensive joint effort to minimize all three terms is currently limited in the literature, leading to subpar performance when dealing with data heterogeneity challenges. To fill this gap, we propose a novel FL method based on global loss decomposition, called FedLD, to jointly reduce these three loss terms. Our FedLD involves a margin control regularization in local training to reduce the distribution shift loss, and a principal gradient-based server aggregation strategy to reduce the aggregation loss. Notably, under different levels of data heterogeneity, our strategies achieve better and more robust performance on retinal and chest X-ray classification compared to other FL algorithms. Our code is available at https://github.com/Zeng-Shuang/FedLD.

Yiqing Shen, Yuyin Zhou, Lequan Yu

Federated learning (FL) is a distributed learning paradigm that enables multiple clients to collaboratively learn a shared global model. Despite the recent progress, it remains challenging to deal with heterogeneous data clients, as the discrepant data distributions usually prevent the global model from delivering good generalization ability on each participating client. In this paper, we propose CD^2-pFed, a novel Cyclic Distillation-guided Channel Decoupling framework, to personalize the global model in FL, under various settings of data heterogeneity. Different from previous works which establish layer-wise personalization to overcome the non-IID data across different clients, we make the first attempt at channel-wise assignment for model personalization, referred to as channel decoupling. To further facilitate the collaboration between private and shared weights, we propose a novel cyclic distillation scheme to impose a consistent regularization between the local and global model representations during the federation. Guided by the cyclical distillation, our channel decoupling framework can deliver more accurate and generalized results for different kinds of heterogeneity, such as feature skew, label distribution skew, and concept shift. Comprehensive experiments on four benchmarks, including natural image and medical image analysis tasks, demonstrate the consistent effectiveness of our method on both local and external validations.

Shiyi Du, Xiaosong Wang, Yongyi Lu et al.

Image synthesis approaches, e.g., generative adversarial networks, have been popular as a form of data augmentation in medical image analysis tasks. It is primarily beneficial to overcome the shortage of publicly accessible data and associated quality annotations. However, the current techniques often lack control over the detailed contents in generated images, e.g., the type of disease patterns, the location of lesions, and attributes of the diagnosis. In this work, we adapt the latest advance in the generative model, i.e., the diffusion model, with the added control flow using lesion-specific visual and textual prompts for generating dermatoscopic images. We further demonstrate the advantage of our diffusion model-based framework over the classical generation models in both the image quality and boosting the segmentation performance on skin lesions. It can achieve a 9% increase in the SSIM image quality measure and an over 5% increase in Dice coefficients over the prior arts.

Haipeng Zhou, Lei Zhu, Yuyin Zhou

The Diffusion Probabilistic Model (DPM) has emerged as a highly effective generative model in the field of computer vision. Its intermediate latent vectors offer rich semantic information, making it an attractive option for various downstream tasks such as segmentation and detection. In order to explore its potential further, we have taken a step forward and considered a more complex scenario in the medical image domain, specifically, under an unsupervised adaptation condition. To this end, we propose a Diffusion-based and Prototype-guided network (DP-Net) for unsupervised domain adaptive segmentation. Concretely, our DP-Net consists of two stages: 1) Distribution Aligned Diffusion (DADiff), which involves training a domain discriminator to minimize the difference between the intermediate features generated by the DPM, thereby aligning the inter-domain distribution; and 2) Prototype-guided Consistency Learning (PCL), which utilizes feature centroids as prototypes and applies a prototype-guided loss to ensure that the segmentor learns consistent content from both source and target domains. Our approach is evaluated on fundus datasets through a series of experiments, which demonstrate that the performance of the proposed method is reliable and outperforms state-of-the-art methods. Our work presents a promising direction for using DPM in complex medical image scenarios, opening up new possibilities for further research in medical imaging.

Hardy Chen, Haoqin Tu, Fali Wang et al.

This work revisits the dominant supervised fine-tuning (SFT) then reinforcement learning (RL) paradigm for training Large Vision-Language Models (LVLMs), and reveals a key finding: SFT can significantly undermine subsequent RL by inducing ``pseudo reasoning paths'' imitated from expert models. While these paths may resemble the native reasoning paths of RL models, they often involve prolonged, hesitant, less informative steps, and incorrect reasoning. To systematically study this effect, we introduce VLAA-Thinking, a new multimodal dataset designed to support reasoning in LVLMs. Constructed via a six-step pipeline involving captioning, reasoning distillation, answer rewrite and verification, VLAA-Thinking comprises high-quality, step-by-step visual reasoning traces for SFT, along with a more challenging RL split from the same data source. Using this dataset, we conduct extensive experiments comparing SFT, RL and their combinations. Results show that while SFT helps models learn reasoning formats, it often locks aligned models into imitative, rigid reasoning modes that impede further learning. In contrast, building on the Group Relative Policy Optimization (GRPO) with a novel mixed reward module integrating both perception and cognition signals, our RL approach fosters more genuine, adaptive reasoning behavior. Notably, our model VLAA-Thinker, based on Qwen2.5VL 3B, achieves top-1 performance on Open LMM Reasoning Leaderboard (https://huggingface.co/spaces/opencompass/Open_LMM_Reasoning_Leaderboard) among 4B scale LVLMs, surpassing the previous state-of-the-art by 1.8%. We hope our findings provide valuable insights in developing reasoning-capable LVLMs and can inform future research in this area.

Zhiheng Cheng, Qingyue Wei, Hongru Zhu et al.

The Segment Anything Model (SAM) has garnered significant attention for its versatile segmentation abilities and intuitive prompt-based interface. However, its application in medical imaging presents challenges, requiring either substantial training costs and extensive medical datasets for full model fine-tuning or high-quality prompts for optimal performance. This paper introduces H-SAM: a prompt-free adaptation of SAM tailored for efficient fine-tuning of medical images via a two-stage hierarchical decoding procedure. In the initial stage, H-SAM employs SAM's original decoder to generate a prior probabilistic mask, guiding a more intricate decoding process in the second stage. Specifically, we propose two key designs: 1) A class-balanced, mask-guided self-attention mechanism addressing the unbalanced label distribution, enhancing image embedding; 2) A learnable mask cross-attention mechanism spatially modulating the interplay among different image regions based on the prior mask. Moreover, the inclusion of a hierarchical pixel decoder in H-SAM enhances its proficiency in capturing fine-grained and localized details. This approach enables SAM to effectively integrate learned medical priors, facilitating enhanced adaptation for medical image segmentation with limited samples. Our H-SAM demonstrates a 4.78% improvement in average Dice compared to existing prompt-free SAM variants for multi-organ segmentation using only 10% of 2D slices. Notably, without using any unlabeled data, H-SAM even outperforms state-of-the-art semi-supervised models relying on extensive unlabeled training data across various medical datasets. Our code is available at https://github.com/Cccccczh404/H-SAM.

Juncheng Wu, Wenlong Deng, Xingxuan Li et al.

Medical tasks such as diagnosis and treatment planning require precise and complex reasoning, particularly in life-critical domains. Unlike mathematical reasoning, medical reasoning demands meticulous, verifiable thought processes to ensure reliability and accuracy. However, there is a notable lack of datasets that provide transparent, step-by-step reasoning to validate and enhance the medical reasoning ability of AI models. To bridge this gap, we introduce MedReason, a large-scale high-quality medical reasoning dataset designed to enable faithful and explainable medical problem-solving in large language models (LLMs). We utilize a structured medical knowledge graph (KG) to convert clinical QA pairs into logical chains of reasoning, or ``thinking paths'', which trace connections from question elements to answers via relevant KG entities. Each path is validated for consistency with clinical logic and evidence-based medicine. Our pipeline generates detailed reasoning for various medical questions from 7 medical datasets, resulting in a dataset of 32,682 question-answer pairs, each with detailed, step-by-step explanations. Experiments demonstrate that fine-tuning with our dataset consistently boosts medical problem-solving capabilities, achieving significant gains of up to 7.7% for DeepSeek-Ditill-8B. Our top-performing model, MedReason-8B, outperforms the Huatuo-o1-8B, a state-of-the-art medical reasoning model, by up to 4.2% on the clinical benchmark MedBullets. We also engage medical professionals from diverse specialties to assess our dataset's quality, ensuring MedReason offers accurate and coherent medical reasoning. Our data, models, and code is available at https://github.com/UCSC-VLAA/MedReason.

Hongxu Jiang, Muhammad Imran, Teng Zhang et al.

Denoising diffusion probabilistic models (DDPMs) have achieved unprecedented success in computer vision. However, they remain underutilized in medical imaging, a field crucial for disease diagnosis and treatment planning. This is primarily due to the high computational cost associated with (1) the use of large number of time steps (e.g., 1,000) in diffusion processes and (2) the increased dimensionality of medical images, which are often 3D or 4D. Training a diffusion model on medical images typically takes days to weeks, while sampling each image volume takes minutes to hours. To address this challenge, we introduce Fast-DDPM, a simple yet effective approach capable of improving training speed, sampling speed, and generation quality simultaneously. Unlike DDPM, which trains the image denoiser across 1,000 time steps, Fast-DDPM trains and samples using only 10 time steps. The key to our method lies in aligning the training and sampling procedures to optimize time-step utilization. Specifically, we introduced two efficient noise schedulers with 10 time steps: one with uniform time step sampling and another with non-uniform sampling. We evaluated Fast-DDPM across three medical image-to-image generation tasks: multi-image super-resolution, image denoising, and image-to-image translation. Fast-DDPM outperformed DDPM and current state-of-the-art methods based on convolutional networks and generative adversarial networks in all tasks. Additionally, Fast-DDPM reduced the training time to 0.2x and the sampling time to 0.01x compared to DDPM. Our code is publicly available at: https://github.com/mirthAI/Fast-DDPM.

Feng Wang, Jiahao Wang, Sucheng Ren et al.

Similar to Vision Transformers, this paper identifies artifacts also present within the feature maps of Vision Mamba. These artifacts, corresponding to high-norm tokens emerging in low-information background areas of images, appear much more severe in Vision Mamba -- they exist prevalently even with the tiny-sized model and activate extensively across background regions. To mitigate this issue, we follow the prior solution of introducing register tokens into Vision Mamba. To better cope with Mamba blocks' uni-directional inference paradigm, two key modifications are introduced: 1) evenly inserting registers throughout the input token sequence, and 2) recycling registers for final decision predictions. We term this new architecture Mamba-R. Qualitative observations suggest, compared to vanilla Vision Mamba, Mamba-R's feature maps appear cleaner and more focused on semantically meaningful regions. Quantitatively, Mamba-R attains stronger performance and scales better. For example, on the ImageNet benchmark, our base-size Mamba-R attains 83.0% accuracy, significantly outperforming Vim-B's 81.8%; furthermore, we provide the first successful scaling to the large model size (i.e., with 341M parameters), attaining a competitive accuracy of 83.6% (84.5% if finetuned with 384x384 inputs). Additional validation on the downstream semantic segmentation task also supports Mamba-R's efficacy. Code is available at https://github.com/wangf3014/Mamba-Reg.

Amarjeet Kumar, Hongxu Jiang, Muhammad Imran et al.

Deep learning has become the de facto method for medical image segmentation, with 3D segmentation models excelling in capturing complex 3D structures and 2D models offering high computational efficiency. However, segmenting 2.5D images, which have high in-plane but low through-plane resolution, is a relatively unexplored challenge. While applying 2D models to individual slices of a 2.5D image is feasible, it fails to capture the spatial relationships between slices. On the other hand, 3D models face challenges such as resolution inconsistencies in 2.5D images, along with computational complexity and susceptibility to overfitting when trained with limited data. In this context, 2.5D models, which capture inter-slice correlations using only 2D neural networks, emerge as a promising solution due to their reduced computational demand and simplicity in implementation. In this paper, we introduce CSA-Net, a flexible 2.5D segmentation model capable of processing 2.5D images with an arbitrary number of slices through an innovative Cross-Slice Attention (CSA) module. This module uses the cross-slice attention mechanism to effectively capture 3D spatial information by learning long-range dependencies between the center slice (for segmentation) and its neighboring slices. Moreover, CSA-Net utilizes the self-attention mechanism to understand correlations among pixels within the center slice. We evaluated CSA-Net on three 2.5D segmentation tasks: (1) multi-class brain MRI segmentation, (2) binary prostate MRI segmentation, and (3) multi-class prostate MRI segmentation. CSA-Net outperformed leading 2D and 2.5D segmentation methods across all three tasks, demonstrating its efficacy and superiority. Our code is publicly available at https://github.com/mirthAI/CSA-Net.

Yuhan Wang, Siwei Yang, Bingchen Zhao et al.

Recent advancements in large multimodal models like GPT-4o have set a new standard for high-fidelity, instruction-guided image editing. However, the proprietary nature of these models and their training data creates a significant barrier for open-source research. To bridge this gap, we introduce GPT-IMAGE-EDIT-1.5M, a publicly available, large-scale image-editing corpus containing more than 1.5 million high-quality triplets (instruction, source image, edited image). We systematically construct this dataset by leveraging the versatile capabilities of GPT-4o to unify and refine three popular image-editing datasets: OmniEdit, HQ-Edit, and UltraEdit. Specifically, our methodology involves 1) regenerating output images to enhance visual quality and instruction alignment, and 2) selectively rewriting prompts to improve semantic clarity. To validate the efficacy of our dataset, we fine-tune advanced open-source models on GPT-IMAGE-EDIT-1.5M. The empirical results are exciting, e.g., the fine-tuned FluxKontext achieves highly competitive performance across a comprehensive suite of benchmarks, including 7.24 on GEdit-EN, 3.80 on ImgEdit-Full, and 8.78 on Complex-Edit, showing stronger instruction following and higher perceptual quality while maintaining identity. These scores markedly exceed all previously published open-source methods and substantially narrow the gap to leading proprietary models. We hope the full release of GPT-IMAGE-EDIT-1.5M can help to catalyze further open research in instruction-guided image editing.

Feng Wang, Yaodong Yu, Guoyizhe Wei et al.

Since the introduction of Vision Transformer (ViT), patchification has long been regarded as a de facto image tokenization approach for plain visual architectures. By compressing the spatial size of images, this approach can effectively shorten the token sequence and reduce the computational cost of ViT-like plain architectures. In this work, we aim to thoroughly examine the information loss caused by this patchification-based compressive encoding paradigm and how it affects visual understanding. We conduct extensive patch size scaling experiments and excitedly observe an intriguing scaling law in patchification: the models can consistently benefit from decreased patch sizes and attain improved predictive performance, until it reaches the minimum patch size of 1x1, i.e., pixel tokenization. This conclusion is broadly applicable across different vision tasks, various input scales, and diverse architectures such as ViT and the recent Mamba models. Moreover, as a by-product, we discover that with smaller patches, task-specific decoder heads become less critical for dense prediction. In the experiments, we successfully scale up the visual sequence to an exceptional length of 50,176 tokens, achieving a competitive test accuracy of 84.6% with a base-sized model on the ImageNet-1k benchmark. We hope this study can provide insights and theoretical foundations for future works of building non-compressive vision models. Code is available at https://github.com/wangf3014/Patch_Scaling.

Mude Hui, Zihao Wei, Hongru Zhu et al.

Volumetric optical microscopy using non-diffracting beams enables rapid imaging of 3D volumes by projecting them axially to 2D images but lacks crucial depth information. Addressing this, we introduce MicroDiffusion, a pioneering tool facilitating high-quality, depth-resolved 3D volume reconstruction from limited 2D projections. While existing Implicit Neural Representation (INR) models often yield incomplete outputs and Denoising Diffusion Probabilistic Models (DDPM) excel at capturing details, our method integrates INR's structural coherence with DDPM's fine-detail enhancement capabilities. We pretrain an INR model to transform 2D axially-projected images into a preliminary 3D volume. This pretrained INR acts as a global prior guiding DDPM's generative process through a linear interpolation between INR outputs and noise inputs. This strategy enriches the diffusion process with structured 3D information, enhancing detail and reducing noise in localized 2D images. By conditioning the diffusion model on the closest 2D projection, MicroDiffusion substantially enhances fidelity in resulting 3D reconstructions, surpassing INR and standard DDPM outputs with unparalleled image quality and structural fidelity. Our code and dataset are available at https://github.com/UCSC-VLAA/MicroDiffusion.

Siwei Yang, Mude Hui, Bingchen Zhao et al.

We introduce $\texttt{Complex-Edit}$, a comprehensive benchmark designed to systematically evaluate instruction-based image editing models across instructions of varying complexity. To develop this benchmark, we harness GPT-4o to automatically collect a diverse set of editing instructions at scale. Our approach follows a well-structured ``Chain-of-Edit'' pipeline: we first generate individual atomic editing tasks independently and then integrate them to form cohesive, complex instructions. Additionally, we introduce a suite of metrics to assess various aspects of editing performance, along with a VLM-based auto-evaluation pipeline that supports large-scale assessments. Our benchmark yields several notable insights: 1) Open-source models significantly underperform relative to proprietary, closed-source models, with the performance gap widening as instruction complexity increases; 2) Increased instructional complexity primarily impairs the models' ability to retain key elements from the input images and to preserve the overall aesthetic quality; 3) Decomposing a complex instruction into a sequence of atomic steps, executed in a step-by-step manner, substantially degrades performance across multiple metrics; 4) A straightforward Best-of-N selection strategy improves results for both direct editing and the step-by-step sequential approach; and 5) We observe a ``curse of synthetic data'': when synthetic data is involved in model training, the edited images from such models tend to appear increasingly synthetic as the complexity of the editing instructions rises -- a phenomenon that intriguingly also manifests in the latest GPT-4o outputs.

Vishal Balaji Sivaraman, Muhammad Imran, Qingyue Wei et al.

We introduce RetinaRegNet, a zero-shot image registration model designed to register retinal images with minimal overlap, large deformations, and varying image quality. RetinaRegNet addresses these challenges and achieves robust and accurate registration through the following steps. First, we extract features from the moving and fixed images using latent diffusion models. We then sample feature points from the fixed image using a combination of the SIFT algorithm and random point sampling. For each sampled point, we identify its corresponding point in the moving image using a 2D correlation map, which computes the cosine similarity between the diffusion feature vectors of the point in the fixed image and all pixels in the moving image. Second, we eliminate most incorrectly detected point correspondences (outliers) by enforcing an inverse consistency constraint, ensuring that correspondences are consistent in both forward and backward directions. We further remove outliers with large distances between corresponding points using a global transformation based outlier detector. Finally, we implement a two-stage registration framework to handle large deformations. The first stage estimates a homography transformation to achieve global alignment between the images, while the second stage uses a third-order polynomial transformation to estimate local deformations. We evaluated RetinaRegNet on three retinal image registration datasets: color fundus images, fluorescein angiography images, and laser speckle flowgraphy images. Our model consistently outperformed state-of-the-art methods across all datasets. The accurate registration achieved by RetinaRegNet enables the tracking of eye disease progression, enhances surgical planning, and facilitates the evaluation of treatment efficacy. Our code is publicly available at: https://github.com/mirthAI/RetinaRegNet.

Muhammad Imran, Jonathan R. Krebs, Vishal Balaji Sivaraman et al.

Multi-class segmentation of the aorta in computed tomography angiography (CTA) scans is essential for diagnosing and planning complex endovascular treatments for patients with aortic dissections. However, existing methods reduce aortic segmentation to a binary problem, limiting their ability to measure diameters across different branches and zones. Furthermore, no open-source dataset is currently available to support the development of multi-class aortic segmentation methods. To address this gap, we organized the AortaSeg24 MICCAI Challenge, introducing the first dataset of 100 CTA volumes annotated for 23 clinically relevant aortic branches and zones. This dataset was designed to facilitate both model development and validation. The challenge attracted 121 teams worldwide, with participants leveraging state-of-the-art frameworks such as nnU-Net and exploring novel techniques, including cascaded models, data augmentation strategies, and custom loss functions. We evaluated the submitted algorithms using the Dice Similarity Coefficient (DSC) and Normalized Surface Distance (NSD), highlighting the approaches adopted by the top five performing teams. This paper presents the challenge design, dataset details, evaluation metrics, and an in-depth analysis of the top-performing algorithms. The annotated dataset, evaluation code, and implementations of the leading methods are publicly available to support further research. All resources can be accessed at https://aortaseg24.grand-challenge.org.

Xiaoke Huang, Juncheng Wu, Hui Liu et al.

Large Reasoning Models (LRMs) have introduced a new paradigm in AI by enabling models to ``think before responding" via chain-of-thought reasoning. However, the absence of open and reproducible recipes for building reasoning-centric medical LMMs hinders community-wide research, analysis, and comparison. In this paper, we present MedVLThinker, a suite of simple yet strong baselines. Our fully open recipe consists of: (1) systematic data curation for both text-only and image-text medical data, filtered according to varying levels of reasoning difficulty, and (2) two training paradigms: Supervised Fine-Tuning (SFT) on distilled reasoning traces and Reinforcement Learning with Verifiable Rewards (RLVR) based on final answer correctness. Across extensive experiments on the Qwen2.5-VL model family (3B, 7B) and six medical QA benchmarks, we find that RLVR consistently and significantly outperforms SFT. Additionally, under the RLVR framework, a key, counter-intuitive finding is that training on our curated text-only reasoning data provides a more substantial performance boost than training on multimodal image-text data. Our best open 7B model, trained using the RLVR recipe on text-only data, establishes a new state-of-the-art on existing public VQA benchmarks, surpassing all previous open-source medical LMMs. Furthermore, scaling our model to 32B achieves performance on par with the proprietary GPT-4o. We release all curated data, models, and code to provide the community with a strong, open foundation for future research in multimodal medical reasoning.

Ruiyu Wang, Tuan Vinh, Ran Xu et al.

Electronic health records (EHRs) support powerful clinical prediction models, but existing methods typically provide coarse, post hoc explanations that offer limited value for patient-level decision making. We introduce a knowledge graph (KG)-guided chain-of-thought (CoT) framework that generates clinically grounded and temporally consistent reasoning for visit-level disease prediction in MIMIC-III. ICD-9 codes are mapped to PrimeKG, from which disease-relevant nodes and multi-hop reasoning paths are extracted and used as scaffolds for CoT generation; only explanations whose conclusions match observed outcomes are retained. Lightweight LLaMA-3.1-Instruct-8B and Gemma-7B models are then fine-tuned on this supervision corpus. Across ten PrimeKG-mapped diseases and limited training cohorts (400 and 1000 cases), KG-guided models outperform strong classical baselines, achieving AUROC values of 0.66 to 0.70 and macro-AUPR values of 0.40 to 0.47. The models also transfer zero-shot to the CRADLE cohort, improving accuracy from approximately 0.40 to 0.51 up to 0.72 to 0.77. A blinded clinician evaluation shows consistent preference for KG-guided CoT explanations in clarity, relevance, and clinical correctness.

Junfei Xiao, Ziqi Zhou, Wenxuan Li et al.

This paper introduces ProLab, a novel approach using property-level label space for creating strong interpretable segmentation models. Instead of relying solely on category-specific annotations, ProLab uses descriptive properties grounded in common sense knowledge for supervising segmentation models. It is based on two core designs. First, we employ Large Language Models (LLMs) and carefully crafted prompts to generate descriptions of all involved categories that carry meaningful common sense knowledge and follow a structured format. Second, we introduce a description embedding model preserving semantic correlation across descriptions and then cluster them into a set of descriptive properties (e.g., 256) using K-Means. These properties are based on interpretable common sense knowledge consistent with theories of human recognition. We empirically show that our approach makes segmentation models perform stronger on five classic benchmarks (e.g., ADE20K, COCO-Stuff, Pascal Context, Cityscapes, and BDD). Our method also shows better scalability with extended training steps than category-level supervision. Our interpretable segmentation framework also emerges with the generalization ability to segment out-of-domain or unknown categories using only in-domain descriptive properties. Code is available at https://github.com/lambert-x/ProLab.

Mude Hui, Siwei Yang, Bingchen Zhao et al.

This study introduces HQ-Edit, a high-quality instruction-based image editing dataset with around 200,000 edits. Unlike prior approaches relying on attribute guidance or human feedback on building datasets, we devise a scalable data collection pipeline leveraging advanced foundation models, namely GPT-4V and DALL-E 3. To ensure its high quality, diverse examples are first collected online, expanded, and then used to create high-quality diptychs featuring input and output images with detailed text prompts, followed by precise alignment ensured through post-processing. In addition, we propose two evaluation metrics, Alignment and Coherence, to quantitatively assess the quality of image edit pairs using GPT-4V. HQ-Edits high-resolution images, rich in detail and accompanied by comprehensive editing prompts, substantially enhance the capabilities of existing image editing models. For example, an HQ-Edit finetuned InstructPix2Pix can attain state-of-the-art image editing performance, even surpassing those models fine-tuned with human-annotated data. The project page is https://thefllood.github.io/HQEdit_web.

Xianhang Li, Haoqin Tu, Mude Hui et al.

Web-crawled image-text pairs are inherently noisy. Prior studies demonstrate that semantically aligning and enriching textual descriptions of these pairs can significantly enhance model training across various vision-language tasks, particularly text-to-image generation. However, large-scale investigations in this area remain predominantly closed-source. Our paper aims to bridge this community effort, leveraging the powerful and \textit{open-sourced} LLaMA-3, a GPT-4 level LLM. Our recaptioning pipeline is simple: first, we fine-tune a LLaMA-3-8B powered LLaVA-1.5 and then employ it to recaption 1.3 billion images from the DataComp-1B dataset. Our empirical results confirm that this enhanced dataset, Recap-DataComp-1B, offers substantial benefits in training advanced vision-language models. For discriminative models like CLIP, we observe enhanced zero-shot performance in cross-modal retrieval tasks. For generative models like text-to-image Diffusion Transformers, the generated images exhibit a significant improvement in alignment with users' text instructions, especially in following complex queries. Our project page is https://www.haqtu.me/Recap-Datacomp-1B/

Juncheng Wu, Zhangkai Ni, Hanli Wang et al.

Image deep features extracted by pre-trained networks are known to contain rich and informative representations. In this paper, we present Deep Degradation Response (DDR), a method to quantify changes in image deep features under varying degradation conditions. Specifically, our approach facilitates flexible and adaptive degradation, enabling the controlled synthesis of image degradation through text-driven prompts. Extensive evaluations demonstrate the versatility of DDR as an image descriptor, with strong correlations observed with key image attributes such as complexity, colorfulness, sharpness, and overall quality. Moreover, we demonstrate the efficacy of DDR across a spectrum of applications. It excels as a blind image quality assessment metric, outperforming existing methodologies across multiple datasets. Additionally, DDR serves as an effective unsupervised learning objective in image restoration tasks, yielding notable advancements in image deblurring and single-image super-resolution. Our code is available at: https://github.com/eezkni/DDR

Sucheng Ren, Xiaoke Huang, Xianhang Li et al.

This study presents Medical Vision Generalist (MVG), the first foundation model capable of handling various medical imaging tasks -- such as cross-modal synthesis, image segmentation, denoising, and inpainting -- within a unified image-to-image generation framework. Specifically, MVG employs an in-context generation strategy that standardizes the handling of inputs and outputs as images. By treating these tasks as an image generation process conditioned on prompt image-label pairs and input images, this approach enables a flexible unification of various tasks, even those spanning different modalities and datasets. To capitalize on both local and global context, we design a hybrid method combining masked image modeling with autoregressive training for conditional image generation. This hybrid approach yields the most robust performance across all involved medical imaging tasks. To rigorously evaluate MVG's capabilities, we curated the first comprehensive generalist medical vision benchmark, comprising 13 datasets and spanning four imaging modalities (CT, MRI, X-ray, and micro-ultrasound). Our results consistently establish MVG's superior performance, outperforming existing vision generalists, such as Painter and LVM. Furthermore, MVG exhibits strong scalability, with its performance demonstrably improving when trained on a more diverse set of tasks, and can be effectively adapted to unseen datasets with only minimal task-specific samples. The code is available at \url{https://github.com/OliverRensu/MVG}.

Hongxu Jiang, Muhammad Imran, Preethika Muralidharan et al.

Micro-ultrasound (micro-US) is a novel 29-MHz ultrasound technique that provides 3-4 times higher resolution than traditional ultrasound, potentially enabling low-cost, accurate diagnosis of prostate cancer. Accurate prostate segmentation is crucial for prostate volume measurement, cancer diagnosis, prostate biopsy, and treatment planning. However, prostate segmentation on micro-US is challenging due to artifacts and indistinct borders between the prostate, bladder, and urethra in the midline. This paper presents MicroSegNet, a multi-scale annotation-guided transformer UNet model designed specifically to tackle these challenges. During the training process, MicroSegNet focuses more on regions that are hard to segment (hard regions), characterized by discrepancies between expert and non-expert annotations. We achieve this by proposing an annotation-guided binary cross entropy (AG-BCE) loss that assigns a larger weight to prediction errors in hard regions and a lower weight to prediction errors in easy regions. The AG-BCE loss was seamlessly integrated into the training process through the utilization of multi-scale deep supervision, enabling MicroSegNet to capture global contextual dependencies and local information at various scales. We trained our model using micro-US images from 55 patients, followed by evaluation on 20 patients. Our MicroSegNet model achieved a Dice coefficient of 0.939 and a Hausdorff distance of 2.02 mm, outperforming several state-of-the-art segmentation methods, as well as three human annotators with different experience levels. Our code is publicly available at https://github.com/mirthAI/MicroSegNet and our dataset is publicly available at https://zenodo.org/records/10475293.

Kai Zhang, Rong Zhou, Eashan Adhikarla et al.

Traditional biomedical artificial intelligence (AI) models, designed for specific tasks or modalities, often exhibit limited flexibility in real-world deployment and struggle to utilize holistic information. Generalist AI holds the potential to address these limitations due to its versatility in interpreting different data types and generating tailored outputs for diverse needs. However, existing biomedical generalist AI solutions are typically heavyweight and closed source to researchers, practitioners, and patients. Here, we propose BiomedGPT, the first open-source and lightweight vision-language foundation model, designed as a generalist capable of performing various biomedical tasks. BiomedGPT achieved state-of-the-art results in 16 out of 25 experiments while maintaining a computing-friendly model scale. We also conducted human evaluations to assess the capabilities of BiomedGPT in radiology visual question answering, report generation, and summarization. BiomedGPT exhibits robust prediction ability with a low error rate of 3.8% in question answering, satisfactory performance with an error rate of 8.3% in writing complex radiology reports, and competitive summarization ability with a nearly equivalent preference score to human experts. Our method demonstrates that effective training with diverse data can lead to more practical biomedical AI for improving diagnosis and workflow efficiency.

Yuyin Zhou, Xianhang Li, Fengze Liu et al.

Deep neural networks have shown great success in representation learning. However, when learning with noisy labels (LNL), they can easily overfit and fail to generalize to new data. This paper introduces a simple and effective method, named Learning to Bootstrap (L2B), which enables models to bootstrap themselves using their own predictions without being adversely affected by erroneous pseudo-labels. It achieves this by dynamically adjusting the importance weight between real observed and generated labels, as well as between different samples through meta-learning. Unlike existing instance reweighting methods, the key to our method lies in a new, versatile objective that enables implicit relabeling concurrently, leading to significant improvements without incurring additional costs. L2B offers several benefits over the baseline methods. It yields more robust models that are less susceptible to the impact of noisy labels by guiding the bootstrapping procedure more effectively. It better exploits the valuable information contained in corrupted instances by adapting the weights of both instances and labels. Furthermore, L2B is compatible with existing LNL methods and delivers competitive results spanning natural and medical imaging tasks including classification and segmentation under both synthetic and real-world noise. Extensive experiments demonstrate that our method effectively mitigates the challenges of noisy labels, often necessitating few to no validation samples, and is well generalized to other tasks such as image segmentation. This not only positions it as a robust complement to existing LNL techniques but also underscores its practical applicability. The code and models are available at https://github.com/yuyinzhou/l2b.

Liangqiong Qu, Yuyin Zhou, Paul Pu Liang et al.

Federated learning is an emerging research paradigm enabling collaborative training of machine learning models among different organizations while keeping data private at each institution. Despite recent progress, there remain fundamental challenges such as the lack of convergence and the potential for catastrophic forgetting across real-world heterogeneous devices. In this paper, we demonstrate that self-attention-based architectures (e.g., Transformers) are more robust to distribution shifts and hence improve federated learning over heterogeneous data. Concretely, we conduct the first rigorous empirical investigation of different neural architectures across a range of federated algorithms, real-world benchmarks, and heterogeneous data splits. Our experiments show that simply replacing convolutional networks with Transformers can greatly reduce catastrophic forgetting of previous devices, accelerate convergence, and reach a better global model, especially when dealing with heterogeneous data. We release our code and pretrained models at https://github.com/Liangqiong/ViT-FL-main to encourage future exploration in robust architectures as an alternative to current research efforts on the optimization front.

Junfei Xiao, Lequan Yu, Zongwei Zhou et al.

Batch normalization (BN) uniformly shifts and scales the activations based on the statistics of a batch of images. However, the intensity distribution of the background pixels often dominates the BN statistics because the background accounts for a large proportion of the entire image. This paper focuses on enhancing BN with the intensity distribution of foreground pixels, the one that really matters for image segmentation. We propose a new normalization strategy, named categorical normalization (CateNorm), to normalize the activations according to categorical statistics. The categorical statistics are obtained by dynamically modulating specific regions in an image that belong to the foreground. CateNorm demonstrates both precise and robust segmentation results across five public datasets obtained from different domains, covering complex and variable data distributions. It is attributable to the ability of CateNorm to capture domain-invariant information from multiple domains (institutions) of medical data. Code is available at https://github.com/lambert-x/CateNorm.

Jieneng Chen, Yongyi Lu, Qihang Yu et al.

Medical image segmentation is an essential prerequisite for developing healthcare systems, especially for disease diagnosis and treatment planning. On various medical image segmentation tasks, the u-shaped architecture, also known as U-Net, has become the de-facto standard and achieved tremendous success. However, due to the intrinsic locality of convolution operations, U-Net generally demonstrates limitations in explicitly modeling long-range dependency. Transformers, designed for sequence-to-sequence prediction, have emerged as alternative architectures with innate global self-attention mechanisms, but can result in limited localization abilities due to insufficient low-level details. In this paper, we propose TransUNet, which merits both Transformers and U-Net, as a strong alternative for medical image segmentation. On one hand, the Transformer encodes tokenized image patches from a convolution neural network (CNN) feature map as the input sequence for extracting global contexts. On the other hand, the decoder upsamples the encoded features which are then combined with the high-resolution CNN feature maps to enable precise localization. We argue that Transformers can serve as strong encoders for medical image segmentation tasks, with the combination of U-Net to enhance finer details by recovering localized spatial information. TransUNet achieves superior performances to various competing methods on different medical applications including multi-organ segmentation and cardiac segmentation. Code and models are available at https://github.com/Beckschen/TransUNet.

Yingwei Li, Xiaojie Jin, Jieru Mei et al.

Non-Local (NL) blocks have been widely studied in various vision tasks. However, it has been rarely explored to embed the NL blocks in mobile neural networks, mainly due to the following challenges: 1) NL blocks generally have heavy computation cost which makes it difficult to be applied in applications where computational resources are limited, and 2) it is an open problem to discover an optimal configuration to embed NL blocks into mobile neural networks. We propose AutoNL to overcome the above two obstacles. Firstly, we propose a Lightweight Non-Local (LightNL) block by squeezing the transformation operations and incorporating compact features. With the novel design choices, the proposed LightNL block is 400x computationally cheaper} than its conventional counterpart without sacrificing the performance. Secondly, by relaxing the structure of the LightNL block to be differentiable during training, we propose an efficient neural architecture search algorithm to learn an optimal configuration of LightNL blocks in an end-to-end manner. Notably, using only 32 GPU hours, the searched AutoNL model achieves 77.7% top-1 accuracy on ImageNet under a typical mobile setting (350M FLOPs), significantly outperforming previous mobile models including MobileNetV2 (+5.7%), FBNet (+2.8%) and MnasNet (+2.1%). Code and models are available at https://github.com/LiYingwei/AutoNL.

Qihang Yu, Yingwei Li, Jieru Mei et al.

3D Convolution Neural Networks (CNNs) have been widely applied to 3D scene understanding, such as video analysis and volumetric image recognition. However, 3D networks can easily lead to over-parameterization which incurs expensive computation cost. In this paper, we propose Channel-wise Automatic KErnel Shrinking (CAKES), to enable efficient 3D learning by shrinking standard 3D convolutions into a set of economic operations e.g., 1D, 2D convolutions. Unlike previous methods, CAKES performs channel-wise kernel shrinkage, which enjoys the following benefits: 1) enabling operations deployed in every layer to be heterogeneous, so that they can extract diverse and complementary information to benefit the learning process; and 2) allowing for an efficient and flexible replacement design, which can be generalized to both spatial-temporal and volumetric data. Further, we propose a new search space based on CAKES, so that the replacement configuration can be determined automatically for simplifying 3D networks. CAKES shows superior performance to other methods with similar model size, and it also achieves comparable performance to state-of-the-art with much fewer parameters and computational costs on tasks including 3D medical imaging segmentation and video action recognition. Codes and models are available at https://github.com/yucornetto/CAKES

Yingwei Li, Song Bai, Yuyin Zhou et al.

Recent development of adversarial attacks has proven that ensemble-based methods outperform traditional, non-ensemble ones in black-box attack. However, as it is computationally prohibitive to acquire a family of diverse models, these methods achieve inferior performance constrained by the limited number of models to be ensembled. In this paper, we propose Ghost Networks to improve the transferability of adversarial examples. The critical principle of ghost networks is to apply feature-level perturbations to an existing model to potentially create a huge set of diverse models. After that, models are subsequently fused by longitudinal ensemble. Extensive experimental results suggest that the number of networks is essential for improving the transferability of adversarial examples, but it is less necessary to independently train different networks and ensemble them in an intensive aggregation way. Instead, our work can be used as a computationally cheap and easily applied plug-in to improve adversarial approaches both in single-model and multi-model attack, compatible with residual and non-residual networks. By reproducing the NeurIPS 2017 adversarial competition, our method outperforms the No.1 attack submission by a large margin, demonstrating its effectiveness and efficiency. Code is available at https://github.com/LiYingwei/ghost-network.

Cihang Xie, Zhishuai Zhang, Yuyin Zhou et al.

Though CNNs have achieved the state-of-the-art performance on various vision tasks, they are vulnerable to adversarial examples --- crafted by adding human-imperceptible perturbations to clean images. However, most of the existing adversarial attacks only achieve relatively low success rates under the challenging black-box setting, where the attackers have no knowledge of the model structure and parameters. To this end, we propose to improve the transferability of adversarial examples by creating diverse input patterns. Instead of only using the original images to generate adversarial examples, our method applies random transformations to the input images at each iteration. Extensive experiments on ImageNet show that the proposed attack method can generate adversarial examples that transfer much better to different networks than existing baselines. By evaluating our method against top defense solutions and official baselines from NIPS 2017 adversarial competition, the enhanced attack reaches an average success rate of 73.0%, which outperforms the top-1 attack submission in the NIPS competition by a large margin of 6.6%. We hope that our proposed attack strategy can serve as a strong benchmark baseline for evaluating the robustness of networks to adversaries and the effectiveness of different defense methods in the future. Code is available at https://github.com/cihangxie/DI-2-FGSM.

Chengzhi Liu, Zhongxing Xu, Qingyue Wei et al.

Test-time compute has empowered multimodal large language models to generate extended reasoning chains, yielding strong performance on tasks such as multimodal math reasoning. However, this improved reasoning ability often comes with increased hallucination: as generations become longer, models tend to drift away from image-grounded content and rely more heavily on language priors. Attention analysis shows that longer reasoning chains lead to reduced focus on visual inputs, which contributes to hallucination. To systematically study this phenomenon, we introduce RH-AUC, a metric that quantifies how a model's perception accuracy changes with reasoning length, allowing us to evaluate whether the model preserves visual grounding during reasoning. We also release RH-Bench, a diagnostic benchmark that spans a variety of multimodal tasks, designed to assess the trade-off between reasoning ability and hallucination. Our analysis reveals that (i) larger models typically achieve a better balance between reasoning and perception, and (ii) this balance is influenced more by the types and domains of training data than by its overall volume. These findings underscore the importance of evaluation frameworks that jointly consider both reasoning quality and perceptual fidelity.