Jiashi Lin

Jiyao Liu, Jianghan Shen, Sida Song et al.

Recent advances in deep research systems enable large language models to retrieve, synthesize, and reason over large-scale external knowledge. In medicine, developing clinical guidelines critically depends on such deep evidence integration. However, existing benchmarks fail to evaluate this capability in realistic workflows requiring multi-step evidence integration and expert-level judgment. To address this gap, we introduce MedProbeBench, the first benchmark leveraging high-quality clinical guidelines as expert-level references. Medical guidelines, with their rigorous standards in neutrality and verifiability, represent the pinnacle of medical expertise and pose substantial challenges for deep research agents. For evaluation, we propose MedProbe-Eval, a comprehensive evaluation framework featuring: (1) Holistic Rubrics with 1,200+ task-adaptive rubric criteria for comprehensive quality assessment, and (2) Fine-grained Evidence Verification for rigorous validation of evidence precision, grounded in 5,130+ atomic claims. Evaluation of 17 LLMs and deep research agents reveals critical gaps in evidence integration and guideline generation, underscoring the substantial distance between current capabilities and expert-level clinical guideline development. Project: https://github.com/uni-medical/MedProbeBench

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.

Jianghan Shen, Siqi Luo, Xinyu Cheng et al.

Reinforcement Learning with Verifiable Rewards (RLVR) has emerged as a promising paradigm for training agentic retrieval-augmented generation (RAG) systems from outcome-only supervision. Most existing methods optimize policies from uniformly sampled rollouts, implicitly treating all trajectories as equally informative. However, trajectories differ substantially in search depth and are therefore not equally informative: deeper-search trajectories contain more retrieval decision points and provide denser direct supervision for the retrieval sub-policy. Moreover, this heterogeneity grows over training as the within-batch depth distribution shifts toward higher values, yet uniform rollout sampling remains blind to this shift. To address this, we propose CuSearch, a curriculum rollout sampling framework built on Search-Depth Greedy Allocation (SDGA), a batch-level operator that reallocates a fixed update budget toward deeper-search trajectories. SDGA-Auto always targets the deepest available trajectories in the current batch, yielding an implicit training-aligned curriculum as the depth distribution shifts upward. SDGA-Phase explicitly advances the curriculum threshold as deeper trajectories become sufficiently abundant. Experiments across model types and retrieval frameworks show that CuSearch consistently improves performance, achieving up to 11.8 exact-match points over standard GRPO on ZeroSearch. These results establish per-trajectory search depth as a reliable, annotation-free proxy for retrieval supervision density in RLVR-based agentic RAG training. The code is available at https://github.com/MrToser/CuSearch.

Junzhi Ning, Jiashi Lin, Yingying Fang et al.

Multimodal large language models (MLLMs) have advanced clinical tasks for common conditions, but their performance on rare diseases remains largely untested. In rare-disease scenarios, clinicians often lack prior clinical knowledge, forcing them to rely strictly on case-level evidence for clinical judgments. Existing benchmarks predominantly evaluate common-condition, single-image settings, leaving multimodal and multi-image evidence integration under rare-disease data scarcity systematically unevaluated. We introduce MMRareBench, to our knowledge the first rare-disease benchmark jointly evaluating multimodal and multi-image clinical capability across four workflow-aligned tracks: diagnosis, treatment planning, cross-image evidence alignment, and examination suggestion. The benchmark comprises 1,756 question-answer pairs with 7,958 associated medical images curated from PMC case reports, with Orphanet-anchored ontology alignment, track-specific leakage control, evidence-grounded annotations, and a two-level evaluation protocol. A systematic evaluation of 23 MLLMs reveals fragmented capability profiles and universally low treatment-planning performance, with medical-domain models trailing general-purpose MLLMs substantially on multi-image tracks despite competitive diagnostic scores. These patterns are consistent with a capacity dilution effect: medical fine-tuning can narrow the diagnostic gap but may erode the compositional multi-image capability that rare-disease evidence integration demands.

Junzhi Ning, Wei Li, Cheng Tang et al.

Medical diagnostic applications require models that can process multimodal medical inputs (images, patient histories, lab results) and generate diverse outputs including both textual reports and visual content (annotations, segmentation masks, and images). Despite this need, existing medical AI systems disrupt this unified process: medical image understanding models interpret images but cannot generate visual outputs, while medical image generation models synthesize images but cannot provide textual explanations. This leads to gaps in data representation, feature integration, and task-level multimodal capabilities. To this end, we propose a multi-level framework that draws inspiration from diagnostic workflows through the Observation-Knowledge-Analysis (OKA) paradigm. Specifically, at the observation level, we construct UniMed-5M, a dataset comprising over 5.6M samples that reformat diverse unimodal data into multimodal pairs for foundational observation. At the knowledge level, we propose Progressive Curriculum Learning that systematically introduces medical multimodal knowledge. At the analysis level, we introduce UniMedVL, the first medical unified multimodal model for the simultaneous analysis of image understanding and generation tasks within a single architecture. UniMedVL achieves superior performance on five medical image understanding benchmarks, while matching specialized models in generation quality across eight medical imaging modalities. Crucially, our unified architecture enables bidirectional knowledge sharing: generation tasks enhance visual understanding features, demonstrating that integrating traditionally separate capabilities within a single medical framework unlocks improvements across diverse medical vision-language tasks. Code is available at https://github.com/uni-medical/UniMedVL.

Huihui Xu, Jiashi Lin, Haoyu Chen et al.

Referring Video Object Segmentation (RVOS) aims to segment out the object in a video referred by an expression. Current RVOS methods view referring expressions as unstructured sequences, neglecting their crucial semantic structure essential for referent reasoning. Besides, in contrast to image-referring expressions whose semantics focus only on object attributes and object-object relations, video-referring expressions also encompass event attributes and event-event temporal relations. This complexity challenges traditional structured reasoning image approaches. In this paper, we propose the Event Referential Reasoning (EventRR) framework. EventRR decouples RVOS into object summarization part and referent reasoning part. The summarization phase begins by summarizing each frame into a set of bottleneck tokens, which are then efficiently aggregated in the video-level summarization step to exchange the global cross-modal temporal context. For reasoning part, EventRR extracts semantic eventful structure of a video-referring expression into highly expressive Referential Event Graph (REG), which is a single-rooted directed acyclic graph. Guided by topological traversal of REG, we propose Temporal Concept-Role Reasoning (TCRR) to accumulate the referring score of each temporal query from REG leaf nodes to root node. Each reasoning step can be interpreted as a question-answer pair derived from the concept-role relations in REG. Extensive experiments across four widely recognized benchmark datasets, show that EventRR quantitatively and qualitatively outperforms state-of-the-art RVOS methods. Code is available at https://github.com/bio-mlhui/EventRR

Huihui Xu, Jin Ye, Hongqiu Wang et al.

Recent self-supervised image segmentation models have achieved promising performance on semantic segmentation and class-agnostic instance segmentation. However, their pretraining schedule is multi-stage, requiring a time-consuming pseudo-masks generation process between each training epoch. This time-consuming offline process not only makes it difficult to scale with training dataset size, but also leads to sub-optimal solutions due to its discontinuous optimization routine. To solve these, we first present a novel pseudo-mask algorithm, Fast Universal Agglomerative Pooling (UniAP). Each layer of UniAP can identify groups of similar nodes in parallel, allowing to generate both semantic-level and instance-level and multi-granular pseudo-masks within ens of milliseconds for one image. Based on the fast UniAP, we propose the Scalable Self-Supervised Universal Segmentation (S2-UniSeg), which employs a student and a momentum teacher for continuous pretraining. A novel segmentation-oriented pretext task, Query-wise Self-Distillation (QuerySD), is proposed to pretrain S2-UniSeg to learn the local-to-global correspondences. Under the same setting, S2-UniSeg outperforms the SOTA UnSAM model, achieving notable improvements of AP+6.9 on COCO, AR+11.1 on UVO, PixelAcc+4.5 on COCOStuff-27, RQ+8.0 on Cityscapes. After scaling up to a larger 2M-image subset of SA-1B, S2-UniSeg further achieves performance gains on all four benchmarks. Our code and pretrained models are available at https://github.com/bio-mlhui/S2-UniSeg

Ming Hu, Chenglong Ma, Wei Li et al. · pku

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

Jiyao Liu, Junzhi Ning, Chenglong Ma et al.

Despite impressive performance on standard benchmarks, multimodal large language models (MLLMs) face critical challenges in real-world clinical environments where medical images inevitably suffer various quality degradations. Existing benchmarks exhibit two key limitations: (1) absence of large-scale, multidimensional assessment across medical image quality gradients and (2) no systematic confidence calibration analysis. To address these gaps, we present MedQ-Deg, a comprehensive benchmark for evaluating medical MLLMs under image quality degradations. MedQ-Deg provides multi-dimensional evaluation spanning 18 distinct degradation types, 30 fine-grained capability dimensions, and 7 imaging modalities, with 24,894 question-answer pairs. Each degradation is implemented at 3 severity degrees, calibrated by expert radiologists. We further introduce Calibration Shift metric, which quantifies the gap between a model's perceived confidence and actual performance to assess metacognitive reliability under degradation. Our comprehensive evaluation of 40 mainstream MLLMs reveals several critical findings: (1) overall model performance degrades systematically as degradation severity increases, (2) models universally exhibit the AI Dunning-Kruger Effect, maintaining inappropriately high confidence despite severe accuracy collapse, and (3) models display markedly differentiated behavioral patterns across capability dimensions, imaging modalities, and degradation types. We hope MedQ-Deg drives progress toward medical MLLMs that are robust and trustworthy in real clinical practice.