Rongshan Yu

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.

Wenxian Yang, Hanzheng Qiu, Bangqun Zhang et al.

Large language model (LLM) agents extend conventional generative models by integrating reasoning, tool invocation, and persistent memory. Recent studies suggest that such agents may significantly improve clinical workflows by automating documentation, coordinating care processes, and assisting medical decision making. However, despite rapid progress, deploying autonomous agents in healthcare environments remains difficult due to reliability limitations, security risks, and insufficient long-term memory mechanisms. This work proposes an architecture that adapts LLM agents for hospital environments. The design introduces four core components: a restricted execution environment inspired by Linux multi-user systems, a document-centric interaction paradigm connecting patient and clinician agents, a page-indexed memory architecture designed for long-term clinical context management, and a curated medical skills library enabling ad-hoc composition of clinical task sequences. Rather than granting agents unrestricted system access, the architecture constrains actions through predefined skill interfaces and resource isolation. We argue that such a system forms the basis of an Agentic Operating System for Hospital, a computing layer capable of coordinating clinical workflows while maintaining safety, transparency, and auditability. This work grounds the design in OpenClaw, an open-source autonomous agent framework that structures agent capabilities as a curated library of discrete skills, and extends it with the infrastructure-level constraints required for safe clinical deployment.

Hao Li, Ying Chen, Yifei Chen et al.

Whole Slide Image (WSI) classification is often formulated as a Multiple Instance Learning (MIL) problem. Recently, Vision-Language Models (VLMs) have demonstrated remarkable performance in WSI classification. However, existing methods leverage coarse-grained pathogenetic descriptions for visual representation supervision, which are insufficient to capture the complex visual appearance of pathogenetic images, hindering the generalizability of models on diverse downstream tasks. Additionally, processing high-resolution WSIs can be computationally expensive. In this paper, we propose a novel "Fine-grained Visual-Semantic Interaction" (FiVE) framework for WSI classification. It is designed to enhance the model's generalizability by leveraging the interaction between localized visual patterns and fine-grained pathological semantics. Specifically, with meticulously designed queries, we start by utilizing a large language model to extract fine-grained pathological descriptions from various non-standardized raw reports. The output descriptions are then reconstructed into fine-grained labels used for training. By introducing a Task-specific Fine-grained Semantics (TFS) module, we enable prompts to capture crucial visual information in WSIs, which enhances representation learning and augments generalization capabilities significantly. Furthermore, given that pathological visual patterns are redundantly distributed across tissue slices, we sample a subset of visual instances during training. Our method demonstrates robust generalizability and strong transferability, dominantly outperforming the counterparts on the TCGA Lung Cancer dataset with at least 9.19% higher accuracy in few-shot experiments. The code is available at: https://github.com/ls1rius/WSI_FiVE.

Ying Chen, Guoan Wang, Yuanfeng Ji et al.

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

Zheng Wang, Xiaoliang Fan, Jianzhong Qi et al.

Fairness has emerged as a critical problem in federated learning (FL). In this work, we identify a cause of unfairness in FL -- conflicting gradients with large differences in the magnitudes. To address this issue, we propose the federated fair averaging (FedFV) algorithm to mitigate potential conflicts among clients before averaging their gradients. We first use the cosine similarity to detect gradient conflicts, and then iteratively eliminate such conflicts by modifying both the direction and the magnitude of the gradients. We further show the theoretical foundation of FedFV to mitigate the issue conflicting gradients and converge to Pareto stationary solutions. Extensive experiments on a suite of federated datasets confirm that FedFV compares favorably against state-of-the-art methods in terms of fairness, accuracy and efficiency. The source code is available at https://github.com/WwZzz/easyFL.

Yuxiang Lin, Ling Luo, Ying Chen et al.

Spatial transcriptomics (ST) provides high-resolution pathological images and whole-transcriptomic expression profiles at individual spots across whole-slide scales. This setting makes it an ideal data source to develop multimodal foundation models. Although recent studies attempted to fine-tune visual encoders with trainable gene encoders based on spot-level, the absence of a wider slide perspective and spatial intrinsic relationships limits their ability to capture ST-specific insights effectively. Here, we introduce ST-Align, the first foundation model designed for ST that deeply aligns image-gene pairs by incorporating spatial context, effectively bridging pathological imaging with genomic features. We design a novel pretraining framework with a three-target alignment strategy for ST-Align, enabling (1) multi-scale alignment across image-gene pairs, capturing both spot- and niche-level contexts for a comprehensive perspective, and (2) cross-level alignment of multimodal insights, connecting localized cellular characteristics and broader tissue architecture. Additionally, ST-Align employs specialized encoders tailored to distinct ST contexts, followed by an Attention-Based Fusion Network (ABFN) for enhanced multimodal fusion, effectively merging domain-shared knowledge with ST-specific insights from both pathological and genomic data. We pre-trained ST-Align on 1.3 million spot-niche pairs and evaluated its performance through two downstream tasks across six datasets, demonstrating superior zero-shot and few-shot capabilities. ST-Align highlights the potential for reducing the cost of ST and providing valuable insights into the distinction of critical compositions within human tissue.

Ying Chen, Jiajing Xie, Yuxiang Lin et al.

Multi-modal learning that combines pathological images with genomic data has significantly enhanced the accuracy of survival prediction. Nevertheless, existing methods have not fully utilized the inherent hierarchical structure within both whole slide images (WSIs) and transcriptomic data, from which better intra-modal representations and inter-modal integration could be derived. Moreover, many existing studies attempt to improve multi-modal representations through attention mechanisms, which inevitably lead to high complexity when processing high-dimensional WSIs and transcriptomic data. Recently, a structured state space model named Mamba emerged as a promising approach for its superior performance in modeling long sequences with low complexity. In this study, we propose Mamba with multi-grained multi-modal interaction (SurvMamba) for survival prediction. SurvMamba is implemented with a Hierarchical Interaction Mamba (HIM) module that facilitates efficient intra-modal interactions at different granularities, thereby capturing more detailed local features as well as rich global representations. In addition, an Interaction Fusion Mamba (IFM) module is used for cascaded inter-modal interactive fusion, yielding more comprehensive features for survival prediction. Comprehensive evaluations on five TCGA datasets demonstrate that SurvMamba outperforms other existing methods in terms of performance and computational cost.

Ling Luo, Wenbin Jiang, Xushi Zhang et al.

Large language models (LLMs) have significantly advanced protein representation learning. However, their capacity to interpret and design antibodies through natural language remains limited. To address this challenge, we present AFD-Instruction, the first large-scale instruction dataset with functional annotations tailored to antibodies. This dataset encompasses two key components: antibody understanding, which infers functional attributes directly from sequences, and antibody design, which enables de novo sequence generation under functional constraints. These components provide explicit sequence-function alignment and support antibody design guided by natural language instructions. Extensive instruction-tuning experiments on general-purpose LLMs demonstrate that AFD-Instruction consistently improves performance across diverse antibody-related tasks. By linking antibody sequences with textual descriptions of function, AFD-Instruction establishes a new foundation for advancing antibody modeling and accelerating therapeutic discovery.

Chen Zhang, Yilu An, Ying Chen et al.

Spatial Transcriptomics (ST) merges the benefits of pathology images and gene expression, linking molecular profiles with tissue structure to analyze spot-level function comprehensively. Predicting gene expression from histology images is a cost-effective alternative to expensive ST technologies. However, existing methods mainly focus on spot-level image-to-gene matching but fail to leverage the full hierarchical structure of ST data, especially on the gene expression side, leading to incomplete image-gene alignment. Moreover, a challenge arises from the inherent information asymmetry: gene expression profiles contain more molecular details that may lack salient visual correlates in histological images, demanding a sophisticated representation learning approach to bridge this modality gap. We propose HyperST, a framework for ST prediction that learns multi-level image-gene representations by modeling the data's inherent hierarchy within hyperbolic space, a natural geometric setting for such structures. First, we design a Multi-Level Representation Extractors to capture both spot-level and niche-level representations from each modality, providing context-aware information beyond individual spot-level image-gene pairs. Second, a Hierarchical Hyperbolic Alignment module is introduced to unify these representations, performing spatial alignment while hierarchically structuring image and gene embeddings. This alignment strategy enriches the image representations with molecular semantics, significantly improving cross-modal prediction. HyperST achieves state-of-the-art performance on four public datasets from different tissues, paving the way for more scalable and accurate spatial transcriptomics prediction.