Xiaosong Wang

Yunkun Zhang, Jin Gao, Mu Zhou et al.

The recent surge of foundation models in computer vision and natural language processing opens up perspectives in utilizing multi-modal clinical data to train large models with strong generalizability. Yet pathological image datasets often lack biomedical text annotation and enrichment. Guiding data-efficient image diagnosis from the use of biomedical text knowledge becomes a substantial interest. In this paper, we propose to Connect Image and Text Embeddings (CITE) to enhance pathological image classification. CITE injects text insights gained from language models pre-trained with a broad range of biomedical texts, leading to adapt foundation models towards pathological image understanding. Through extensive experiments on the PatchGastric stomach tumor pathological image dataset, we demonstrate that CITE achieves leading performance compared with various baselines especially when training data is scarce. CITE offers insights into leveraging in-domain text knowledge to reinforce data-efficient pathological image classification. Code is available at https://github.com/Yunkun-Zhang/CITE.

Dequan Wang, Xiaosong Wang, Lilong Wang et al. · berkeley

Foundation models, often pre-trained with large-scale data, have achieved paramount success in jump-starting various vision and language applications. Recent advances further enable adapting foundation models in downstream tasks efficiently using only a few training samples, e.g., in-context learning. Yet, the application of such learning paradigms in medical image analysis remains scarce due to the shortage of publicly accessible data and benchmarks. In this paper, we aim at approaches adapting the foundation models for medical image classification and present a novel dataset and benchmark for the evaluation, i.e., examining the overall performance of accommodating the large-scale foundation models downstream on a set of diverse real-world clinical tasks. We collect five sets of medical imaging data from multiple institutes targeting a variety of real-world clinical tasks (22,349 images in total), i.e., thoracic diseases screening in X-rays, pathological lesion tissue screening, lesion detection in endoscopy images, neonatal jaundice evaluation, and diabetic retinopathy grading. Results of multiple baseline methods are demonstrated using the proposed dataset from both accuracy and cost-effective perspectives.

Lijian Xu, Ziyu Ni, Xinglong Liu et al.

While multimodal deep learning has advanced medical imaging analysis, existing black-box systems \textcolor{black}{may remain confined to isolated tasks, often overlooking} the trust-sensitive nature of clinical diagnosis as a multi-task process. We propose IMT-CXR (Interpretable Multi-task Transformer for Chest X-ray Analysis), a framework that emulates radiologists' diagnostic workflow through three evidence-driven stages: 1) Disease recognition; 2) Attribute characterization (e.g., size, location, severity quantification); 3) Evidence-integrated report generation with traceable decision pathways. The framework employs a unified transformer architecture optimized via medical-domain instruction tuning, sequentially executing four clinical tasks: multi-label disease classification, lesion localization, anatomical segmentation, and radiology report generation. Experimental validation demonstrates competitive performance on ten CXR benchmarks under direct inference and fine-tuning settings. In a blinded evaluation of 160 historical reports from four medical centers, three radiologists rated 66\% of AI-generated reports as comparable to or surpassing original clinical reports in diagnostic clarity, highlighting the framework's translational potential. By establishing traceable diagnostic pathways from anatomical findings to conclusions, this work bridges the gap between AI technical metrics and clinical utility, advancing trustworthy AI systems in medical imaging.

Zhenyu Tang, Shaoting Zhang, Xiaosong Wang

Deep learning models often require large amounts of data for training, leading to increased costs. It is particularly challenging in medical imaging, i.e., gathering distributed data for centralized training, and meanwhile, obtaining quality labels remains a tedious job. Many methods have been proposed to address this issue in various training paradigms, e.g., continual learning, active learning, and federated learning, which indeed demonstrate certain forms of the data valuation process. However, existing methods are either overly intuitive or limited to common clean/toy datasets in the experiments. In this work, we present two data valuation metrics based on Synaptic Intelligence and gradient norms, respectively, to study the redundancy in real-world image data. Novel online and offline data selection algorithms are then proposed via clustering and grouping based on the examined data values. Our online approach effectively evaluates data utilizing layerwise model parameter updates and gradients in each epoch and can accelerate model training with fewer epochs and a subset (e.g., 19%-59%) of data while maintaining equivalent levels of accuracy in a variety of datasets. It also extends to the offline coreset construction, producing subsets of only 18%-30% of the original. The codes for the proposed adaptive data selection and coreset computation are available (https://github.com/ZhenyuTANG2023/data_selection).

Zhongying Deng, Cheng Tang, Ziyan Huang et al. · pku

Foundation models have demonstrated remarkable success across diverse domains and tasks, primarily due to the thrive of large-scale, diverse, and high-quality datasets. However, in the field of medical imaging, the curation and assembling of such medical datasets are highly challenging due to the reliance on clinical expertise and strict ethical and privacy constraints, resulting in a scarcity of large-scale unified medical datasets and hindering the development of powerful medical foundation models. In this work, we present the largest survey to date of medical image datasets, covering over 1,000 open-access datasets with a systematic catalog of their modalities, tasks, anatomies, annotations, limitations, and potential for integration. Our analysis exposes a landscape that is modest in scale, fragmented across narrowly scoped tasks, and unevenly distributed across organs and modalities, which in turn limits the utility of existing medical image datasets for developing versatile and robust medical foundation models. To turn fragmentation into scale, we propose a metadata-driven fusion paradigm (MDFP) that integrates public datasets with shared modalities or tasks, thereby transforming multiple small data silos into larger, more coherent resources. Building on MDFP, we release an interactive discovery portal that enables end-to-end, automated medical image dataset integration, and compile all surveyed datasets into a unified, structured table that clearly summarizes their key characteristics and provides reference links, offering the community an accessible and comprehensive repository. By charting the current terrain and offering a principled path to dataset consolidation, our survey provides a practical roadmap for scaling medical imaging corpora, supporting faster data discovery, more principled dataset creation, and more capable medical foundation models.

Yankai Jiang, Wenjie Lou, Lilong Wang et al.

We introduce SCP: the Science Context Protocol, an open-source standard designed to accelerate discovery by enabling a global network of autonomous scientific agents. SCP is built on two foundational pillars: (1) Unified Resource Integration: At its core, SCP provides a universal specification for describing and invoking scientific resources, spanning software tools, models, datasets, and physical instruments. This protocol-level standardization enables AI agents and applications to discover, call, and compose capabilities seamlessly across disparate platforms and institutional boundaries. (2) Orchestrated Experiment Lifecycle Management: SCP complements the protocol with a secure service architecture, which comprises a centralized SCP Hub and federated SCP Servers. This architecture manages the complete experiment lifecycle (registration, planning, execution, monitoring, and archival), enforces fine-grained authentication and authorization, and orchestrates traceable, end-to-end workflows that bridge computational and physical laboratories. Based on SCP, we have constructed a scientific discovery platform that offers researchers and agents a large-scale ecosystem of more than 1,600 tool resources. Across diverse use cases, SCP facilitates secure, large-scale collaboration between heterogeneous AI systems and human researchers while significantly reducing integration overhead and enhancing reproducibility. By standardizing scientific context and tool orchestration at the protocol level, SCP establishes essential infrastructure for scalable, multi-institution, agent-driven science.

Linhao Qu, Dingkang Yang, Dan Huang et al.

Current multi-instance learning algorithms for pathology image analysis often require a substantial number of Whole Slide Images for effective training but exhibit suboptimal performance in scenarios with limited learning data. In clinical settings, restricted access to pathology slides is inevitable due to patient privacy concerns and the prevalence of rare or emerging diseases. The emergence of the Few-shot Weakly Supervised WSI Classification accommodates the significant challenge of the limited slide data and sparse slide-level labels for diagnosis. Prompt learning based on the pre-trained models (\eg, CLIP) appears to be a promising scheme for this setting; however, current research in this area is limited, and existing algorithms often focus solely on patch-level prompts or confine themselves to language prompts. This paper proposes a multi-instance prompt learning framework enhanced with pathology knowledge, \ie, integrating visual and textual prior knowledge into prompts at both patch and slide levels. The training process employs a combination of static and learnable prompts, effectively guiding the activation of pre-trained models and further facilitating the diagnosis of key pathology patterns. Lightweight Messenger (self-attention) and Summary (attention-pooling) layers are introduced to model relationships between patches and slides within the same patient data. Additionally, alignment-wise contrastive losses ensure the feature-level alignment between visual and textual learnable prompts for both patches and slides. Our method demonstrates superior performance in three challenging clinical tasks, significantly outperforming comparative few-shot methods.

Yiheng Wang, Yixin Chen, Shuo Li et al.

We introduce SciEvalKit, a unified benchmarking toolkit designed to evaluate AI models for science across a broad range of scientific disciplines and task capabilities. Unlike general-purpose evaluation platforms, SciEvalKit focuses on the core competencies of scientific intelligence, including Scientific Multimodal Perception, Scientific Multimodal Reasoning, Scientific Multimodal Understanding, Scientific Symbolic Reasoning, Scientific Code Generation, Science Hypothesis Generation and Scientific Knowledge Understanding. It supports six major scientific domains, spanning from physics and chemistry to astronomy and materials science. SciEvalKit builds a foundation of expert-grade scientific benchmarks, curated from real-world, domain-specific datasets, ensuring that tasks reflect authentic scientific challenges. The toolkit features a flexible, extensible evaluation pipeline that enables batch evaluation across models and datasets, supports custom model and dataset integration, and provides transparent, reproducible, and comparable results. By bridging capability-based evaluation and disciplinary diversity, SciEvalKit offers a standardized yet customizable infrastructure to benchmark the next generation of scientific foundation models and intelligent agents. The toolkit is open-sourced and actively maintained to foster community-driven development and progress in AI4Science.

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.

Jiaxuan Lu, Ziyu Kong, Yemin Wang et al.

The central challenge of AI for Science is not reasoning alone, but the ability to create computational methods in an open-ended scientific world. Existing LLM-based agents rely on static, pre-defined tool libraries, a paradigm that fundamentally fails in scientific domains where tools are sparse, heterogeneous, and intrinsically incomplete. In this paper, we propose Test-Time Tool Evolution (TTE), a new paradigm that enables agents to synthesize, verify, and evolve executable tools during inference. By transforming tools from fixed resources into problem-driven artifacts, TTE overcomes the rigidity and long-tail limitations of static tool libraries. To facilitate rigorous evaluation, we introduce SciEvo, a benchmark comprising 1,590 scientific reasoning tasks supported by 925 automatically evolved tools. Extensive experiments show that TTE achieves state-of-the-art performance in both accuracy and tool efficiency, while enabling effective cross-domain adaptation of computational tools. The code and benchmark have been released at https://github.com/lujiaxuan0520/Test-Time-Tool-Evol.

Xiaosong Wang, Xiaofan Zhang, Guotai Wang et al.

The emerging trend of advancing generalist artificial intelligence, such as GPTv4 and Gemini, has reshaped the landscape of research (academia and industry) in machine learning and many other research areas. However, domain-specific applications of such foundation models (e.g., in medicine) remain untouched or often at their very early stages. It will require an individual set of transfer learning and model adaptation techniques by further expanding and injecting these models with domain knowledge and data. The development of such technologies could be largely accelerated if the bundle of data, algorithms, and pre-trained foundation models were gathered together and open-sourced in an organized manner. In this work, we present OpenMEDLab, an open-source platform for multi-modality foundation models. It encapsulates not only solutions of pioneering attempts in prompting and fine-tuning large language and vision models for frontline clinical and bioinformatic applications but also building domain-specific foundation models with large-scale multi-modal medical data. Importantly, it opens access to a group of pre-trained foundation models for various medical image modalities, clinical text, protein engineering, etc. Inspiring and competitive results are also demonstrated for each collected approach and model in a variety of benchmarks for downstream tasks. We welcome researchers in the field of medical artificial intelligence to continuously contribute cutting-edge methods and models to OpenMEDLab, which can be accessed via https://github.com/openmedlab.

Kaitao Chen, Mianxin Liu, Fang Yan et al.

The advent of vision-language models fosters the interactive conversations between AI-enabled models and humans. Yet applying these models into clinics must deal with daunting challenges around large-scale training data, financial, and computational resources. Here we propose a cost-effective instruction learning framework for conversational pathology named as CLOVER. CLOVER only trains a lightweight module and uses instruction tuning while freezing the parameters of the large language model. Instead of using costly GPT-4, we propose well-designed prompts on GPT-3.5 for building generation-based instructions, emphasizing the utility of pathological knowledge derived from the Internet source. To augment the use of instructions, we construct a high-quality set of template-based instructions in the context of digital pathology. From two benchmark datasets, our findings reveal the strength of hybrid-form instructions in the visual question-answer in pathology. Extensive results show the cost-effectiveness of CLOVER in answering both open-ended and closed-ended questions, where CLOVER outperforms strong baselines that possess 37 times more training parameters and use instruction data generated from GPT-4. Through the instruction tuning, CLOVER exhibits robustness of few-shot learning in the external clinical dataset. These findings demonstrate that cost-effective modeling of CLOVER could accelerate the adoption of rapid conversational applications in the landscape of digital pathology.

Linhao Qu, Dan Huang, Shaoting Zhang et al.

Survival analysis stands as a pivotal process in cancer treatment research, crucial for predicting patient survival rates accurately. Recent advancements in data collection techniques have paved the way for enhancing survival predictions by integrating information from multiple modalities. However, real-world scenarios often present challenges with incomplete data, particularly when dealing with censored survival labels. Prior works have addressed missing modalities but have overlooked incomplete labels, which can introduce bias and limit model efficacy. To bridge this gap, we introduce a novel framework that simultaneously handles incomplete data across modalities and censored survival labels. Our approach employs advanced foundation models to encode individual modalities and align them into a universal representation space for seamless fusion. By generating pseudo labels and incorporating uncertainty, we significantly enhance predictive accuracy. The proposed method demonstrates outstanding prediction accuracy in two survival analysis tasks on both employed datasets. This innovative approach overcomes limitations associated with disparate modalities and improves the feasibility of comprehensive survival analysis using multiple large foundation models.

Lijian Xu, Ziyu Ni, Xinglong Liu et al.

The emergence of multi-modal deep learning models has made significant impacts on clinical applications in the last decade. However, the majority of models are limited to single-tasking, without considering disease diagnosis is indeed a multi-task procedure. Here, we demonstrate a unified transformer model specifically designed for multi-modal clinical tasks by incorporating customized instruction tuning. We first compose a multi-task training dataset comprising 13.4 million instruction and ground-truth pairs (with approximately one million radiographs) for the customized tuning, involving both image- and pixel-level tasks. Thus, we can unify the various vision-intensive tasks in a single training framework with homogeneous model inputs and outputs to increase clinical interpretability in one reading. Finally, we demonstrate the overall superior performance of our model compared to prior arts on various chest X-ray benchmarks across multi-tasks in both direct inference and finetuning settings. Three radiologists further evaluate the generated reports against the recorded ones, which also exhibit the enhanced explainability of our multi-task model.

Shiyang Feng, Runmin Ma, Xiangchao Yan et al.

We introduce InternAgent-1.5, a unified system designed for end-to-end scientific discovery across computational and empirical domains. The system is built on a structured architecture composed of three coordinated subsystems for generation, verification, and evolution. These subsystems are supported by foundational capabilities for deep research, solution optimization, and long horizon memory. The architecture allows InternAgent-1.5 to operate continuously across extended discovery cycles while maintaining coherent and improving behavior. It also enables the system to coordinate computational modeling and laboratory experimentation within a single unified system. We evaluate InternAgent-1.5 on scientific reasoning benchmarks such as GAIA, HLE, GPQA, and FrontierScience, and the system achieves leading performance that demonstrates strong foundational capabilities. Beyond these benchmarks, we further assess two categories of discovery tasks. In algorithm discovery tasks, InternAgent-1.5 autonomously designs competitive methods for core machine learning problems. In empirical discovery tasks, it executes complete computational or wet lab experiments and produces scientific findings in earth, life, biological, and physical domains. Overall, these results show that InternAgent-1.5 provides a general and scalable framework for autonomous scientific discovery.

Lisheng Zhang, Lilong Wang, Xiangyu Sun et al.

Computational drug discovery, particularly the complex workflows of drug molecule screening and optimization, requires orchestrating dozens of specialized tools in multi-step workflows, yet current AI agents struggle to maintain robust performance and consistently underperform in these high-complexity scenarios. Here we present MolClaw, an autonomous agent that leads drug molecule evaluation, screening, and optimization. It unifies over 30 specialized domain resources through a three-tier hierarchical skill architecture (70 skills in total) that facilitates agent long-term interaction at runtime: tool-level skills standardize atomic operations, workflow-level skills compose them into validated pipelines with quality check and reflection, and a discipline-level skill supplies scientific principles governing planning and verification across all scenarios in the field. Additionally, we introduce MolBench, a benchmark comprising molecular screening, optimization, and end-to-end discovery challenges spanning 8 to 50+ sequential tool calls. MolClaw achieves state-of-the-art performance across all metrics, and ablation studies confirm that gains concentrate on tasks that demand structured workflows while vanishing on those solvable with ad hoc scripting, establishing workflow orchestration competence as the primary capability bottleneck for AI-driven drug discovery.

Yifan Gao, Haoyue Li, Feng Yuan et al.

Foundation models pre-trained on large-scale natural image datasets offer a powerful paradigm for medical image segmentation. However, effectively transferring their learned representations for precise clinical applications remains a challenge. In this work, we propose Dino U-Net, a novel encoder-decoder architecture designed to exploit the high-fidelity dense features of the DINOv3 vision foundation model. Our architecture introduces an encoder built upon a frozen DINOv3 backbone, which employs a specialized adapter to fuse the model's rich semantic features with low-level spatial details. To preserve the quality of these representations during dimensionality reduction, we design a new fidelity-aware projection module (FAPM) that effectively refines and projects the features for the decoder. We conducted extensive experiments on seven diverse public medical image segmentation datasets. Our results show that Dino U-Net achieves state-of-the-art performance, consistently outperforming previous methods across various imaging modalities. Our framework proves to be highly scalable, with segmentation accuracy consistently improving as the backbone model size increases up to the 7-billion-parameter variant. The findings demonstrate that leveraging the superior, dense-pretrained features from a general-purpose foundation model provides a highly effective and parameter-efficient approach to advance the accuracy of medical image segmentation. The code is available at https://github.com/yifangao112/DinoUNet.

Haoran Sun, Yankai Jiang, Wenjie Lou et al.

Multimodal large language models (MLLMs) have begun to demonstrate robust reasoning capabilities on general tasks, yet their application in the medical domain remains in its early stages. Constructing chain-of-thought (CoT) training data is essential for bolstering the reasoning abilities of medical MLLMs. However, existing approaches exhibit a deficiency in offering a comprehensive framework for searching and evaluating effective reasoning paths towards critical diagnosis. To address this challenge, we propose Mentor-Intern Collaborative Search (MICS), a novel reasoning-path searching scheme to generate rigorous and effective medical CoT data. MICS first leverages mentor models to initialize the reasoning, one step at a time, then prompts each intern model to continue the thinking along those initiated paths, and finally selects the optimal reasoning path according to the overall reasoning performance of multiple intern models. The reasoning performance is determined by an MICS-Score, which assesses the quality of generated reasoning paths. Eventually, we construct MMRP, a multi-task medical reasoning dataset with ranked difficulty, and Chiron-o1, a new medical MLLM devised via a curriculum learning strategy, with robust visual question-answering and generalizable reasoning capabilities. Extensive experiments demonstrate that Chiron-o1, trained on our CoT dataset constructed using MICS, achieves state-of-the-art performance across a list of medical visual question answering and reasoning benchmarks. Codes are available at https://github.com/manglu097/Chiron-o1

Yuan Tian, Kaiyuan Ji, Rongzhao Zhang et al.

Medical image re-identification (MedReID) is under-explored so far, despite its critical applications in personalized healthcare and privacy protection. In this paper, we introduce a thorough benchmark and a unified model for this problem. First, to handle various medical modalities, we propose a novel Continuous Modality-based Parameter Adapter (ComPA). ComPA condenses medical content into a continuous modality representation and dynamically adjusts the modality-agnostic model with modality-specific parameters at runtime. This allows a single model to adaptively learn and process diverse modality data. Furthermore, we integrate medical priors into our model by aligning it with a bag of pre-trained medical foundation models, in terms of the differential features. Compared to single-image feature, modeling the inter-image difference better fits the re-identification problem, which involves discriminating multiple images. We evaluate the proposed model against 25 foundation models and 8 large multi-modal language models across 11 image datasets, demonstrating consistently superior performance. Additionally, we deploy the proposed MedReID technique to two real-world applications, i.e., history-augmented personalized diagnosis and medical privacy protection. Codes and model is available at \href{https://github.com/tianyuan168326/All-in-One-MedReID-Pytorch}{https://github.com/tianyuan168326/All-in-One-MedReID-Pytorch}.

Kaitao Chen, Mianxin Liu, Daoming Zong et al.

Complex medical decision-making involves cooperative workflows operated by different clinicians. Designing AI multi-agent systems can expedite and augment human-level clinical decision-making. Existing multi-agent researches primarily focus on language-only tasks, yet their extension to multimodal scenarios remains challenging. A blind combination of diverse vision-language models (VLMs) can amplify an erroneous outcome interpretation. VLMs in general are less capable in instruction following and importantly self-reflection, compared to large language models (LLMs) of comparable sizes. This disparity largely constrains VLMs' ability in cooperative workflows. In this study, we propose MedOrch, a mediator-guided multi-agent collaboration framework for medical multimodal decision-making. MedOrch employs an LLM-based mediator agent that enables multiple VLM-based expert agents to exchange and reflect on their outputs towards collaboration. We utilize multiple open-source general-purpose and domain-specific VLMs instead of costly GPT-series models, revealing the strength of heterogeneous models. We show that the collaboration within distinct VLM-based agents can surpass the capabilities of any individual agent. We validate our approach on five medical vision question answering benchmarks, demonstrating superior collaboration performance without model training. Our findings underscore the value of mediator-guided multi-agent collaboration in advancing medical multimodal intelligence.

Jie Yang, Ziqi Ye, Aihua Ke et al.

Data heterogeneity hinders clinical deployment of medical image analysis models, and generative data augmentation helps mitigate this issue. However, recent diffusion-based methods that synthesize image-mask pairs often ignore distribution shifts between generated and real images across scenarios, and such mismatches can markedly degrade downstream performance. To address this issue, we propose AlignFlow, a flow matching model that aligns with the target reference image distribution via differentiable reward fine-tuning, and remains effective even when only a small number of reference images are provided. Specifically, we divide the training of the flow matching model into two stages: in the first stage, the model fits the training data to generate plausible images; Then, we introduce a distribution alignment mechanism and employ differentiable reward to steer the generated images toward the distribution of the given samples from the target domain. In addition, to enhance the diversity of generated masks, we also design a flow matching based mask generation to complement the diversity in regions of interest. Extensive experiments demonstrate the effectiveness of our approach, i.e., performance improvement by 3.5-4.0% in mDice and 3.5-5.6% in mIoU across a variety of datasets and scenarios.

Haoran Sun, Yankai Jiang, Zhenyu Tang et al.

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.

Yifan Gao, Haoyue Li, Feng Yuan et al.

We present Camyla, a system for fully autonomous research within the scientific domain of medical image segmentation. Camyla transforms raw datasets into literature-grounded research proposals, executable experiments, and complete manuscripts without human intervention. Autonomous experimentation over long horizons poses three interrelated challenges: search effort drifts toward unpromising directions, knowledge from earlier trials degrades as context accumulates, and recovery from failures collapses into repetitive incremental fixes. To address these challenges, the system combines three coupled mechanisms: Quality-Weighted Branch Exploration for allocating effort across competing proposals, Layered Reflective Memory for retaining and compressing cross-trial knowledge at multiple granularities, and Divergent Diagnostic Feedback for diversifying recovery after underperforming trials. The system is evaluated on CamylaBench, a contamination-free benchmark of 31 datasets constructed exclusively from 2025 publications, under a strict zero-intervention protocol across two independent runs within a total of 28 days on an 8-GPU cluster. Across the two runs, Camyla generates more than 2,700 novel model implementations and 40 complete manuscripts, and surpasses the strongest per-dataset baseline selected from 14 established architectures, including nnU-Net, on 22 and 18 of 31 datasets under identical training budgets, respectively (union: 24/31). Senior human reviewers score the generated manuscripts at the T1/T2 boundary of contemporary medical imaging journals. Relative to automated baselines, Camyla outperforms AutoML and NAS systems on aggregate segmentation performance and exceeds six open-ended research agents on both task completion and baseline-surpassing frequency. These results suggest that domain-scale autonomous research is achievable in medical image segmentation.

Yankai Jiang, Peng Zhang, Donglin Yang et al.

We explore Generalizable Tumor Segmentation, aiming to train a single model for zero-shot tumor segmentation across diverse anatomical regions. Existing methods face limitations related to segmentation quality, scalability, and the range of applicable imaging modalities. In this paper, we uncover the potential of the internal representations within frozen medical foundation diffusion models as highly efficient zero-shot learners for tumor segmentation by introducing a novel framework named DiffuGTS. DiffuGTS creates anomaly-aware open-vocabulary attention maps based on text prompts to enable generalizable anomaly segmentation without being restricted by a predefined training category list. To further improve and refine anomaly segmentation masks, DiffuGTS leverages the diffusion model, transforming pathological regions into high-quality pseudo-healthy counterparts through latent space inpainting, and applies a novel pixel-level and feature-level residual learning approach, resulting in segmentation masks with significantly enhanced quality and generalization. Comprehensive experiments on four datasets and seven tumor categories demonstrate the superior performance of our method, surpassing current state-of-the-art models across multiple zero-shot settings. Codes are available at https://github.com/Yankai96/DiffuGTS.

Zihao Luo, Shaohao Rui, Zhenyu Tang et al.

Continual self-supervised learning (CSSL) in medical imaging trains a foundation model sequentially, alleviating the need for collecting multi-modal images for joint training and offering promising improvements in downstream performance while preserving data privacy. However, most existing methods still rely on replaying data from previous stages to prevent catastrophic forgetting, which compromises privacy and limits their applicability in real-world scenarios where data transfer across sites is often restricted. In this work, we propose InvCoSS, an inversion-driven continual self-supervised learning framework for medical multi-modal image pre-training. Specifically, after training on a previous task, InvCoSS inverts the pre-trained self-supervised model to generate synthetic images that approximate the original training distribution. These synthetic images are then combined with data from the new task for joint optimization, which effectively mitigates catastrophic forgetting while strictly adhering to the constraint of no access to previous real data. Furthermore, to improve the fidelity of synthetic images, we introduce a novel InvUNet with a multi-scale fusion architecture to restore both high- and low-frequency components of the inverted images. To enhance diversity and prevent mode collapse, we design a repulsive representation-learning mechanism that encourages a diverse feature space for synthetic images without class guidance. Extensive experiments across nine downstream tasks validate the effectiveness of InvCoSS, achieving performance comparable to or even superior to prior data-replay methods while significantly reducing storage requirements and eliminating data privacy constraints.

Yihao Liu, Xu Cao, Tingting Chen et al.

Healthcare systems worldwide face persistent challenges in efficiency, accessibility, and personalization. Powered by modern AI technologies such as multimodal large language models and world models, Embodied AI (EmAI) represents a transformative frontier, offering enhanced autonomy and the ability to interact with the physical world to address these challenges. As an interdisciplinary and rapidly evolving research domain, "EmAI in healthcare" spans diverse fields such as algorithms, robotics, and biomedicine. This complexity underscores the importance of timely reviews and analyses to track advancements, address challenges, and foster cross-disciplinary collaboration. In this paper, we provide a comprehensive overview of the "brain" of EmAI for healthcare, wherein we introduce foundational AI algorithms for perception, actuation, planning, and memory, and focus on presenting the healthcare applications spanning clinical interventions, daily care & companionship, infrastructure support, and biomedical research. Despite its promise, the development of EmAI for healthcare is hindered by critical challenges such as safety concerns, gaps between simulation platforms and real-world applications, the absence of standardized benchmarks, and uneven progress across interdisciplinary domains. We discuss the technical barriers and explore ethical considerations, offering a forward-looking perspective on the future of EmAI in healthcare. A hierarchical framework of intelligent levels for EmAI systems is also introduced to guide further development. By providing systematic insights, this work aims to inspire innovation and practical applications, paving the way for a new era of intelligent, patient-centered healthcare.

InternAgent Team, Bo Zhang, Shiyang Feng et al.

Artificial Intelligence (AI) is accelerating the transformation of scientific research paradigms, not only enhancing research efficiency but also driving innovation. We introduce InternAgent, a unified closed-loop multi-agent framework to conduct Autonomous Scientific Research (ASR) across various scientific research fields, enabling researchers to tackle complicated problems in these fields with unprecedented speed and precision. InternAgent highlights three key advantages: 1) Scalability: InternAgent has demonstrated its versatility across 12 scientific research tasks, capable of generating innovative ideas to enhance the performance of baseline code. 2) Interactivity: InternAgent provides an interface for human expert feedback and multi-agent interaction in automated end-to-end processes, allowing for the seamless integration of domain expert knowledge. 3) Efficiency: InternAgent has achieved promising performance gains in several scientific fields with significantly less time cost compared to human efforts. For instance, in reaction yield prediction, it increased from 27.6% to 35.4% in just 12 hours; in enhancer activity prediction, accuracy rose from 0.65 to 0.79 with only 4 hours of processing; and in 2D semantic segmentation, precision advanced from 78.8% to 81.0% in a mere 30 hours.

Shaohao Rui, Kaitao Chen, Weijie Ma et al.

Recent advances in reinforcement learning with verifiable, rule-based rewards have greatly enhanced the reasoning capabilities and out-of-distribution generalization of VLMs/LLMs, obviating the need for manually crafted reasoning chains. Despite these promising developments in the general domain, their translation to medical imaging remains limited. Current medical reinforcement fine-tuning (RFT) methods predominantly focus on close-ended VQA, thereby restricting the model's ability to engage in world knowledge retrieval and flexible task adaptation. More critically, these methods fall short of addressing the critical clinical demand for open-ended, reasoning-intensive decision-making. To bridge this gap, we introduce \textbf{MedCCO}, the first multimodal reinforcement learning framework tailored for medical VQA that unifies close-ended and open-ended data within a curriculum-driven RFT paradigm. Specifically, MedCCO is initially fine-tuned on a diverse set of close-ended medical VQA tasks to establish domain-grounded reasoning capabilities, and is then progressively adapted to open-ended tasks to foster deeper knowledge enhancement and clinical interpretability. We validate MedCCO across eight challenging medical VQA benchmarks, spanning both close-ended and open-ended settings. Experimental results show that MedCCO consistently enhances performance and generalization, achieving a 11.4\% accuracy gain across three in-domain tasks, and a 5.7\% improvement on five out-of-domain benchmarks. These findings highlight the promise of curriculum-guided RL in advancing robust, clinically-relevant reasoning in medical multimodal language models.

Shaohao Rui, Lingzhi Chen, Zhenyu Tang et al.

Self-supervised learning has greatly facilitated medical image analysis by suppressing the training data requirement for real-world applications. Current paradigms predominantly rely on self-supervision within uni-modal image data, thereby neglecting the inter-modal correlations essential for effective learning of cross-modal image representations. This limitation is particularly significant for naturally grouped multi-modal data, e.g., multi-parametric MRI scans for a patient undergoing various functional imaging protocols in the same study. To bridge this gap, we conduct a novel multi-modal image pre-training with three proxy tasks to facilitate the learning of cross-modality representations and correlations using multi-modal brain MRI scans (over 2.4 million images in 16,022 scans of 3,755 patients), i.e., cross-modal image reconstruction, modality-aware contrastive learning, and modality template distillation. To demonstrate the generalizability of our pre-trained model, we conduct extensive experiments on various benchmarks with ten downstream tasks. The superior performance of our method is reported in comparison to state-of-the-art pre-training methods, with Dice Score improvement of 0.28\%-14.47\% across six segmentation benchmarks and a consistent accuracy boost of 0.65\%-18.07\% in four individual image classification tasks.

Shaohao Rui, Haoyang Su, Jinyi Xiang et al.

Accurate prediction of major adverse cardiovascular events recurrence risk in acute myocardial infarction patients based on postoperative cardiac MRI and associated clinical notes is crucial for precision treatment and personalized intervention. Existing methods primarily focus on risk stratification capability while overlooking the need for intermediate robust reasoning and model interpretability in clinical practice. Moreover, end-to-end risk prediction using LLM/VLM faces significant challenges due to data limitations and modeling complexity. To bridge this gap, we propose CardioCoT, a novel two-stage hierarchical reasoning-enhanced survival analysis framework designed to enhance both model interpretability and predictive performance. In the first stage, we employ an evidence-augmented self-refinement mechanism to guide LLM/VLMs in generating robust hierarchical reasoning trajectories based on associated radiological findings. In the second stage, we integrate the reasoning trajectories with imaging data for risk model training and prediction. CardioCoT demonstrates superior performance in MACE recurrence risk prediction while providing interpretable reasoning processes, offering valuable insights for clinical decision-making.

Kaitao Chen, Shaohao Rui, Yankai Jiang et al.

Medical vision-language models (VLMs) excel at image-text understanding but typically rely on a single-pass reasoning that neglects localized visual cues. In clinical practice, however, human experts iteratively scan, focus, and refine the regions of interest before reaching a final diagnosis. To narrow this machine-human perception gap, we introduce ViTAR, a novel VLM framework that emulates the iterative reasoning process of human experts through a cognitive chain of "think-act-rethink-answer". ViTAR treats medical images as interactive objects, enabling models to engage multi-step visual reasoning. To support this approach, we curate a high-quality instruction dataset comprising 1K interactive examples that encode expert-like diagnostic behaviors. In addition, a 16K visual question answering training data has been curated towards fine-grained visual diagnosis. We introduce a two-stage training strategy that begins with supervised fine-tuning to guide cognitive trajectories, followed by the reinforcement learning to optimize decision-making. Extensive evaluations demonstrate that ViTAR outperforms strong state-of-the-art models. Visual attention analysis reveals that from the "think" to "rethink" rounds, ViTAR increasingly anchors visual grounding to clinically critical regions and maintains high attention allocation to visual tokens during reasoning, providing mechanistic insight into its improved performance. These findings demonstrate that embedding expert-style iterative thinking chains into VLMs enhances both performance and trustworthiness of medical AI.

Yuan Tian, Shuo Wang, Rongzhao Zhang et al.

Medical imaging has significantly advanced computer-aided diagnosis, yet its re-identification (ReID) risks raise critical privacy concerns, calling for de-identification (DeID) techniques. Unfortunately, existing DeID methods neither particularly preserve medical semantics, nor are flexibly adjustable towards different privacy levels. To address these issues, we propose a divide-and-conquer framework comprising two steps: (1) Identity-Blocking, which blocks varying proportions of identity-related regions, to achieve different privacy levels; and (2) Medical-Semantics-Compensation, which leverages pre-trained Medical Foundation Models (MFMs) to extract medical semantic features to compensate the blocked regions. Moreover, recognizing that features from MFMs may still contain residual identity information, we introduce a Minimum Description Length principle-based feature decoupling strategy, to effectively decouple and discard such identity components. Extensive evaluations against existing approaches across seven datasets and three downstream tasks, demonstrates our state-of-the-art performance.

Haoyang Su, Shaohao Rui, Jinyi Xiang et al.

Accurate and contrast-free Major Adverse Cardiac Events (MACE) prediction from Cine MRI sequences remains a critical challenge. Existing methods typically necessitate supervised learning based on human-refined masks in the ventricular myocardium, which become impractical without contrast agents. We introduce a self-supervised framework, namely Codebook-based Temporal-Spatial Learning (CTSL), that learns dynamic, spatiotemporal representations from raw Cine data without requiring segmentation masks. CTSL decouples temporal and spatial features through a multi-view distillation strategy, where the teacher model processes multiple Cine views, and the student model learns from reduced-dimensional Cine-SA sequences. By leveraging codebook-based feature representations and dynamic lesion self-detection through motion cues, CTSL captures intricate temporal dependencies and motion patterns. High-confidence MACE risk predictions are achieved through our model, providing a rapid, non-invasive solution for cardiac risk assessment that outperforms traditional contrast-dependent methods, thereby enabling timely and accessible heart disease diagnosis in clinical settings.

Jiaxuan Lu, Yuhui Lin, Junyan Shi et al.

Whole Slide Images (WSIs) in histopathology pose a significant challenge for extensive medical image analysis due to their ultra-high resolution, massive scale, and intricate spatial relationships. Although existing Multiple Instance Learning (MIL) approaches like Graph Neural Networks (GNNs) and Transformers demonstrate strong instance-level modeling capabilities, they encounter constraints regarding scalability and computational expenses. To overcome these limitations, we introduce the WSI-HGMamba, a novel framework that unifies the high-order relational modeling capabilities of the Hypergraph Neural Networks (HGNNs) with the linear-time sequential modeling efficiency of the State Space Models. At the core of our design is the HGMamba block, which integrates message passing, hypergraph scanning & flattening, and bidirectional state space modeling (Bi-SSM), enabling the model to retain both relational and contextual cues while remaining computationally efficient. Compared to Transformer and Graph Transformer counterparts, WSI-HGMamba achieves superior performance with up to 7* reduction in FLOPs. Extensive experiments on multiple public and private WSI benchmarks demonstrate that our method provides a scalable, accurate, and efficient solution for slide-level understanding, making it a promising backbone for next-generation pathology AI systems.

Haoyang Su, Shaoting Zhang, Xiaosong Wang

The emergence of tool-calling-based agent systems introduces a more evidence-driven paradigm for pathology image analysis in contrast to the coarse-grained text-image diagnostic approaches. With the recent large-scale experimental adoption of spatial transcriptomics technologies, molecularly validated pathological diagnosis is becoming increasingly open and accessible. In this work, we propose LAMMI-Pathology (LVLM-Agent System for Molecularly Informed Medical Intelligence in Pathology), a scalable agent framework for domain-specific agent tool-calling. LAMMI-Pathology adopts a tool-centric, bottom-up architecture in which customized domain-adaptive tools serve as the foundation. These tools are clustered by domain style to form component agents, which are then coordinated through a top-level planner hierarchically, avoiding excessively long context lengths that could induce task drift. Based on that, we introduce a novel trajectory construction mechanism based on Atomic Execution Nodes (AENs), which serve as reliable and composable units for building semi-simulated reasoning trajectories that capture credible agent-tool interactions. Building on this foundation, we develop a trajectory-aware fine-tuning strategy that aligns the planner's decision-making process with these multi-step reasoning trajectories, thereby enhancing inference robustness in pathology understanding and its adaptive use of the customized toolset.

Shaohao Rui, Kaitao Chen, Weijie Ma et al.

Recent advances in inference time scaling with extended long chain-of thought have significantly improved the reasoning capabilities of both general and medical large language models (LLMs). However, these models tend to engage in lengthy reasoning processes regardless of the difficulty of the input question, leading to increased inference costs in real-world applications. Therefore, enabling adaptive thinking where models think less for simpler questions and think more for complex ones is critical for the effective use of medical LLMs in practice. Despite its importance, there is a lack of end-to-end approaches designed to enhance the adaptive thinking capabilities of medical LLMs while providing a comprehensive examination of the trade-off between performance and computational cost. To bridge this gap, we propose AdaThink-Med, the first end-to-end framework designed to enhance adaptive thinking ability in medical reasoning models with uncertainty-guided length calibration. AdaThink-Med first generates multiple candidate outputs for each question, evaluates the correctness and uncertainty of each candidate, and then estimates problem difficulty via an uncertainty-guided length calibration module. For outputs with low difficulty and correct answers, the framework penalizes longer reasoning paths; whereas for those with high difficulty and incorrect answers, it encourages extending the chain of thought to explore alternative solutions. On six public medical QA benchmarks, AdaThink-Med achieves up to 6.4x length reduction on average while retaining performance with only minimal degradation. Intriguingly, we observe that AdaThink-Med spontaneously develops two distinct reasoning modes, which we characterize as "non-thinking" and "thinking", demonstrating the model's ability to suppress redundant reasoning processes dynamically.

Haoyang Su, Jin-Yi Xiang, Shaohao Rui et al.

Accurate prediction of major adverse cardiac events (MACE) remains a central challenge in cardiovascular prognosis. We present PRISM (Prompt-guided Representation Integration for Survival Modeling), a self-supervised framework that integrates visual representations from non-contrast cardiac cine magnetic resonance imaging with structured electronic health records (EHRs) for survival analysis. PRISM extracts temporally synchronized imaging features through motion-aware multi-view distillation and modulates them using medically informed textual prompts to enable fine-grained risk prediction. Across four independent clinical cohorts, PRISM consistently surpasses classical survival prediction models and state-of-the-art (SOTA) deep learning baselines under internal and external validation. Further clinical findings demonstrate that the combined imaging and EHR representations derived from PRISM provide valuable insights into cardiac risk across diverse cohorts. Three distinct imaging signatures associated with elevated MACE risk are uncovered, including lateral wall dyssynchrony, inferior wall hypersensitivity, and anterior elevated focus during diastole. Prompt-guided attribution further identifies hypertension, diabetes, and smoking as dominant contributors among clinical and physiological EHR factors.

Dong Yang, Andriy Myronenko, Xiaosong Wang et al.

Lesion segmentation in medical imaging has been an important topic in clinical research. Researchers have proposed various detection and segmentation algorithms to address this task. Recently, deep learning-based approaches have significantly improved the performance over conventional methods. However, most state-of-the-art deep learning methods require the manual design of multiple network components and training strategies. In this paper, we propose a new automated machine learning algorithm, T-AutoML, which not only searches for the best neural architecture, but also finds the best combination of hyper-parameters and data augmentation strategies simultaneously. The proposed method utilizes the modern transformer model, which is introduced to adapt to the dynamic length of the search space embedding and can significantly improve the ability of the search. We validate T-AutoML on several large-scale public lesion segmentation data-sets and achieve state-of-the-art performance.

Riddhish Bhalodia, Ali Hatamizadeh, Leo Tam et al.

Localization and characterization of diseases like pneumonia are primary steps in a clinical pipeline, facilitating detailed clinical diagnosis and subsequent treatment planning. Additionally, such location annotated datasets can provide a pathway for deep learning models to be used for downstream tasks. However, acquiring quality annotations is expensive on human resources and usually requires domain expertise. On the other hand, medical reports contain a plethora of information both about pneumonia characteristics and its location. In this paper, we propose a novel weakly-supervised attention-driven deep learning model that leverages encoded information in medical reports during training to facilitate better localization. Our model also performs classification of attributes that are associated to pneumonia and extracted from medical reports for supervision. Both the classification and localization are trained in conjunction and once trained, the model can be utilized for both the localization and characterization of pneumonia using only the input image. In this paper, we explore and analyze the model using chest X-ray datasets and demonstrate qualitatively and quantitatively that the introduction of textual information improves pneumonia localization. We showcase quantitative results on two datasets, MIMIC-CXR and Chest X-ray-8, and we also showcase severity characterization on the COVID-19 dataset.

Holger R. Roth, Dong Yang, Wenqi Li et al.

Building robust deep learning-based models requires diverse training data, ideally from several sources. However, these datasets cannot be combined easily because of patient privacy concerns or regulatory hurdles, especially if medical data is involved. Federated learning (FL) is a way to train machine learning models without the need for centralized datasets. Each FL client trains on their local data while only sharing model parameters with a global server that aggregates the parameters from all clients. At the same time, each client's data can exhibit differences and inconsistencies due to the local variation in the patient population, imaging equipment, and acquisition protocols. Hence, the federated learned models should be able to adapt to the local particularities of a client's data. In this work, we combine FL with an AutoML technique based on local neural architecture search by training a "supernet". Furthermore, we propose an adaptation scheme to allow for personalized model architectures at each FL client's site. The proposed method is evaluated on four different datasets from 3D prostate MRI and shown to improve the local models' performance after adaptation through selecting an optimal path through the AutoML supernet.

Xiaosong Wang, Ziyue Xu, Leo Tam et al.

Pre-trained models, e.g., from ImageNet, have proven to be effective in boosting the performance of many downstream applications. It is too demanding to acquire large-scale annotations to build such models for medical imaging. Meanwhile, there are numerous clinical data (in the form of images and text reports) stored in the hospital information systems. The paired image-text data from the same patient study could be utilized for the pre-training task in a weakly supervised manner. However, the integrity, accessibility, and amount of such raw data vary across different institutes, e.g., paired vs. unpaired (image-only or text-only). In this work, we introduce an image-text pre-training framework that can learn from these raw data with mixed data inputs, i.e., paired image-text data, a mixture of paired and unpaired data. The unpaired data can be sourced from one or multiple institutes (e.g., images from one institute coupled with texts from another). Specifically, we propose a transformer-based training framework for jointly learning the representation of both the image and text data. In addition to the existing masked language modeling, multi-scale masked vision modeling is introduced as a self-supervised training task for image patch regeneration. We not only demonstrate the feasibility of pre-training across mixed data inputs but also illustrate the benefits of adopting such pre-trained models in 3 chest X-ray applications, i.e., classification, retrieval, and image regeneration. Superior results are reported in comparison to prior art using MIMIC-CXR, NIH14-CXR, and OpenI-CXR datasets.

Leo K. Tam, Xiaosong Wang, Daguang Xu

Previous work established skip-gram word2vec models could be used to mine knowledge in the materials science literature for the discovery of thermoelectrics. Recent transformer architectures have shown great progress in language modeling and associated fine-tuned tasks, but they have yet to be adapted for drug discovery. We present a RoBERTa transformer-based method that extends the masked language token prediction using query-target conditioning to treat the specificity challenge. The transformer discovery method entails several benefits over the word2vec method including domain-specific (antiviral) analogy performance, negation handling, and flexible query analysis (specific) and is demonstrated on influenza drug discovery. To stimulate COVID-19 research, we release an influenza clinical trials and antiviral analogies dataset used in conjunction with the COVID-19 Open Research Dataset Challenge (CORD-19) literature dataset in the study. We examine k-shot fine-tuning to improve the downstream analogies performance as well as to mine analogies for model explainability. Further, the query-target analysis is verified in a forward chaining analysis against the influenza drug clinical trials dataset, before adapted for COVID-19 drugs (combinations and side-effects) and on-going clinical trials. In consideration of the present topic, we release the model, dataset, and code.

Dong Yang, Ziyue Xu, Wenqi Li et al.

The recent outbreak of COVID-19 has led to urgent needs for reliable diagnosis and management of SARS-CoV-2 infection. As a complimentary tool, chest CT has been shown to be able to reveal visual patterns characteristic for COVID-19, which has definite value at several stages during the disease course. To facilitate CT analysis, recent efforts have focused on computer-aided characterization and diagnosis, which has shown promising results. However, domain shift of data across clinical data centers poses a serious challenge when deploying learning-based models. In this work, we attempt to find a solution for this challenge via federated and semi-supervised learning. A multi-national database consisting of 1704 scans from three countries is adopted to study the performance gap, when training a model with one dataset and applying it to another. Expert radiologists manually delineated 945 scans for COVID-19 findings. In handling the variability in both the data and annotations, a novel federated semi-supervised learning technique is proposed to fully utilize all available data (with or without annotations). Federated learning avoids the need for sensitive data-sharing, which makes it favorable for institutions and nations with strict regulatory policy on data privacy. Moreover, semi-supervision potentially reduces the annotation burden under a distributed setting. The proposed framework is shown to be effective compared to fully supervised scenarios with conventional data sharing instead of model weight sharing.

Holger R Roth, Dong Yang, Ziyue Xu et al.

Medical image annotation is a major hurdle for developing precise and robust machine learning models. Annotation is expensive, time-consuming, and often requires expert knowledge, particularly in the medical field. Here, we suggest using minimal user interaction in the form of extreme point clicks to train a segmentation model which, in effect, can be used to speed up medical image annotation. An initial segmentation is generated based on the extreme points utilizing the random walker algorithm. This initial segmentation is then used as a noisy supervision signal to train a fully convolutional network that can segment the organ of interest, based on the provided user clicks. Through experimentation on several medical imaging datasets, we show that the predictions of the network can be refined using several rounds of training with the prediction from the same weakly annotated data. Further improvements are shown utilizing the clicked points within a custom-designed loss and attention mechanism. Our approach has the potential to speed up the process of generating new training datasets for the development of new machine learning and deep learning-based models for, but not exclusively, medical image analysis.

Xiaosong Wang, Ziyue Xu, Dong Yang et al.

Current deep learning paradigms largely benefit from the tremendous amount of annotated data. However, the quality of the annotations often varies among labelers. Multi-observer studies have been conducted to study these annotation variances (by labeling the same data for multiple times) and its effects on critical applications like medical image analysis. This process indeed adds an extra burden to the already tedious annotation work that usually requires professional training and expertise in the specific domains. On the other hand, automated annotation methods based on NLP algorithms have recently shown promise as a reasonable alternative, relying on the existing diagnostic reports of those images that are widely available in the clinical system. Compared to human labelers, different algorithms provide labels with varying qualities that are even noisier. In this paper, we show how noisy annotations (e.g., from different algorithm-based labelers) can be utilized together and mutually benefit the learning of classification tasks. Specifically, the concept of attention-on-label is introduced to sample better label sets on-the-fly as the training data. A meta-training based label-sampling module is designed to attend the labels that benefit the model learning the most through additional back-propagation processes. We apply the attention-on-label scheme on the classification task of a synthetic noisy CIFAR-10 dataset to prove the concept, and then demonstrate superior results (3-5% increase on average in multiple disease classification AUCs) on the chest x-ray images from a hospital-scale dataset (MIMIC-CXR) and hand-labeled dataset (OpenI) in comparison to regular training paradigms.

Leo K. Tam, Xiaosong Wang, Evrim Turkbey et al.

Detecting clinically relevant objects in medical images is a challenge despite large datasets due to the lack of detailed labels. To address the label issue, we utilize the scene-level labels with a detection architecture that incorporates natural language information. We present a challenging new set of radiologist paired bounding box and natural language annotations on the publicly available MIMIC-CXR dataset especially focussed on pneumonia and pneumothorax. Along with the dataset, we present a joint vision language weakly supervised transformer layer-selected one-stage dual head detection architecture (LITERATI) alongside strong baseline comparisons with class activation mapping (CAM), gradient CAM, and relevant implementations on the NIH ChestXray-14 and MIMIC-CXR dataset. Borrowing from advances in vision language architectures, the LITERATI method demonstrates joint image and referring expression (objects localized in the image using natural language) input for detection that scales in a purely weakly supervised fashion. The architectural modifications address three obstacles -- implementing a supervised vision and language detection method in a weakly supervised fashion, incorporating clinical referring expression natural language information, and generating high fidelity detections with map probabilities. Nevertheless, the challenging clinical nature of the radiologist annotations including subtle references, multi-instance specifications, and relatively verbose underlying medical reports, ensures the vision language detection task at scale remains stimulating for future investigation.

Liyue Shen, Wentao Zhu, Xiaosong Wang et al.

Multi-domain data are widely leveraged in vision applications taking advantage of complementary information from different modalities, e.g., brain tumor segmentation from multi-parametric magnetic resonance imaging (MRI). However, due to possible data corruption and different imaging protocols, the availability of images for each domain could vary amongst multiple data sources in practice, which makes it challenging to build a universal model with a varied set of input data. To tackle this problem, we propose a general approach to complete the random missing domain(s) data in real applications. Specifically, we develop a novel multi-domain image completion method that utilizes a generative adversarial network (GAN) with a representational disentanglement scheme to extract shared skeleton encoding and separate flesh encoding across multiple domains. We further illustrate that the learned representation in multi-domain image completion could be leveraged for high-level tasks, e.g., segmentation, by introducing a unified framework consisting of image completion and segmentation with a shared content encoder. The experiments demonstrate consistent performance improvement on three datasets for brain tumor segmentation, prostate segmentation, and facial expression image completion respectively.

Dong Yang, Holger Roth, Xiaosong Wang et al.

Object segmentation plays an important role in the modern medical image analysis, which benefits clinical study, disease diagnosis, and surgery planning. Given the various modalities of medical images, the automated or semi-automated segmentation approaches have been used to identify and parse organs, bones, tumors, and other regions-of-interest (ROI). However, these contemporary segmentation approaches tend to fail to predict the boundary areas of ROI, because of the fuzzy appearance contrast caused during the imaging procedure. To further improve the segmentation quality of boundary areas, we propose a boundary enhancement loss to enforce additional constraints on optimizing machine learning models. The proposed loss function is light-weighted and easy to implement without any pre- or post-processing. Our experimental results validate that our loss function are better than, or at least comparable to, other state-of-the-art loss functions in terms of segmentation accuracy.

Yixiao Zhang, Xiaosong Wang, Ziyue Xu et al.

Automatic radiology report generation has been an attracting research problem towards computer-aided diagnosis to alleviate the workload of doctors in recent years. Deep learning techniques for natural image captioning are successfully adapted to generating radiology reports. However, radiology image reporting is different from the natural image captioning task in two aspects: 1) the accuracy of positive disease keyword mentions is critical in radiology image reporting in comparison to the equivalent importance of every single word in a natural image caption; 2) the evaluation of reporting quality should focus more on matching the disease keywords and their associated attributes instead of counting the occurrence of N-gram. Based on these concerns, we propose to utilize a pre-constructed graph embedding module (modeled with a graph convolutional neural network) on multiple disease findings to assist the generation of reports in this work. The incorporation of knowledge graph allows for dedicated feature learning for each disease finding and the relationship modeling between them. In addition, we proposed a new evaluation metric for radiology image reporting with the assistance of the same composed graph. Experimental results demonstrate the superior performance of the methods integrated with the proposed graph embedding module on a publicly accessible dataset (IU-RR) of chest radiographs compared with previous approaches using both the conventional evaluation metrics commonly adopted for image captioning and our proposed ones.

Holger Roth, Ling Zhang, Dong Yang et al.

Annotation of medical images has been a major bottleneck for the development of accurate and robust machine learning models. Annotation is costly and time-consuming and typically requires expert knowledge, especially in the medical domain. Here, we propose to use minimal user interaction in the form of extreme point clicks in order to train a segmentation model that can, in turn, be used to speed up the annotation of medical images. We use extreme points in each dimension of a 3D medical image to constrain an initial segmentation based on the random walker algorithm. This segmentation is then used as a weak supervisory signal to train a fully convolutional network that can segment the organ of interest based on the provided user clicks. We show that the network's predictions can be refined through several iterations of training and prediction using the same weakly annotated data. Ultimately, our method has the potential to speed up the generation process of new training datasets for the development of new machine learning and deep learning-based models for, but not exclusively, medical image analysis.