arXiv subjects

Yanfeng Wang

Publications and source records attributed to Yanfeng Wang.

At least 55 records · Page 3Linked to original sources

arXiv2026

Predicting Neuromodulation Outcome for Parkinson's Disease with Generative Virtual Brain Model

Parkinson's disease (PD) affects over ten million people worldwide. Although temporal interference (TI) and deep brain stimulation (DBS) are promising therapies, inter-individual variability limits empirical treatment selection, increasing non-negligible surgical risk and cost. Previous explorations either resort to limited statistical biomarkers that are insufficient to characterize variability, or employ AI-driven methods which is prone to overfitting and opacity. We bridge this gap with a pretraining-finetuning framework to predict outcomes directly from resting-state fMRI. Critically, a generative virtual brain foundation model, pretrained on a collective dataset (2707 subjects, 5621 sessions) to capture universal disorder patterns, was finetuned on PD cohorts receiving TI (n=51) or DBS (n=55) to yield individualized virtual brains with high fidelity to empirical functional connectivity (r=0.935). By constructing counterfactual estimations between pathological and healthy neural states within these personalized models, we predicted clinical responses (TI: AUPR=0.853; DBS: AUPR=0.915), substantially outperforming baselines. External and prospective validations (n=14, n=11) highlight the feasibility of clinical translation. Moreover, our framework provides state-dependent regional patterns linked to response, offering hypothesis-generating mechanistic insights.

q-bio.NC↗

arXiv2026

GenMask: Adapting DiT for Segmentation via Direct Mask Generation

Recent approaches for segmentation have leveraged pretrained generative models as feature extractors, treating segmentation as a downstream adaptation task via indirect feature retrieval. This implicit use suffers from a fundamental misalignment in representation. It also depends heavily on indirect feature extraction pipelines, which complicate the workflow and limit adaptation. In this paper, we argue that instead of indirect adaptation, segmentation tasks should be trained directly in a generative manner. We identify a key obstacle to this unified formulation: VAE latents of binary masks are sharply distributed, noise robust, and linearly separable, distinct from natural image latents. To bridge this gap, we introduce timesteps sampling strategy for binary masks that emphasizes extreme noise levels for segmentation and moderate noise for image generation, enabling harmonious joint training. We present GenMask, a DiT trains to generate black-and-white segmentation masks as well as colorful images in RGB space under the original generative objective. GenMask preserves the original DiT architecture while removing the need of feature extraction pipelines tailored for segmentation tasks. Empirically, GenMask attains state-of-the-art performance on referring and reasoning segmentation benchmarks and ablations quantify the contribution of each component.

cs.CV↗

arXiv2026

Toward Ultra-Long-Horizon Agentic Science: Cognitive Accumulation for Machine Learning Engineering

The advancement of artificial intelligence toward agentic science is currently bottlenecked by the challenge of ultra-long-horizon autonomy, the ability to sustain strategic coherence and iterative correction over experimental cycles spanning days or weeks. While Large Language Models (LLMs) have demonstrated prowess in short-horizon reasoning, they are easily overwhelmed by execution details in the high-dimensional, delayed-feedback environments of real-world research, failing to consolidate sparse feedback into coherent long-term guidance. Here, we present ML-Master 2.0, an autonomous agent that masters ultra-long-horizon machine learning engineering (MLE) which is a representative microcosm of scientific discovery. By reframing context management as a process of cognitive accumulation, our approach introduces Hierarchical Cognitive Caching (HCC), a multi-tiered architecture inspired by computer systems that enables the structural differentiation of experience over time. By dynamically distilling transient execution traces into stable knowledge and cross-task wisdom, HCC allows agents to decouple immediate execution from long-term experimental strategy, effectively overcoming the scaling limits of static context windows. In evaluations on OpenAI's MLE-Bench under 24-hour budgets, ML-Master 2.0 achieves a state-of-the-art medal rate of 56.44%. Our findings demonstrate that ultra-long-horizon autonomy provides a scalable blueprint for AI capable of autonomous exploration beyond human-precedent complexities.

cs.AI↗

arXiv2026

Demographic-Aware Self-Supervised Anomaly Detection Pretraining for Equitable Rare Cardiac Diagnosis

Rare cardiac anomalies are difficult to detect from electrocardiograms (ECGs) due to their long-tailed distribution with extremely limited case counts and demographic disparities in diagnostic performance. These limitations contribute to delayed recognition and uneven quality of care, creating an urgent need for a generalizable framework that enhances sensitivity while ensuring equity across diverse populations. In this study, we developed an AI-assisted two-stage ECG framework integrating self-supervised anomaly detection with demographic-aware representation learning. The first stage performs self-supervised anomaly detection pretraining by reconstructing masked global and local ECG signals, modeling signal trends, and predicting patient attributes to learn robust ECG representations without diagnostic labels. The pretrained model is then fine-tuned for multi-label ECG classification using asymmetric loss to better handle long-tail cardiac abnormalities, and additionally produces anomaly score maps for localization, with CPU-based optimization enabling practical deployment. Evaluated on a longitudinal cohort of over one million clinical ECGs, our method achieves an AUROC of 94.7% for rare anomalies and reduces the common-rare performance gap by 73%, while maintaining consistent diagnostic accuracy across age and sex groups. In conclusion, the proposed equity-aware AI framework demonstrates strong clinical utility, interpretable anomaly localization, and scalable performance across multiple cohorts, highlighting its potential to mitigate diagnostic disparities and advance equitable anomaly detection in biomedical signals and digital health. Source code is available at https://github.com/MediaBrain-SJTU/Rare-ECG.

cs.CV↗

arXiv2026

Overthinking Reduction with Decoupled Rewards and Curriculum Data Scheduling

While large reasoning models trained with critic-free reinforcement learning and verifiable rewards (RLVR) represent the state-of-the-art, their practical utility is hampered by ``overthinking'', a critical issue where models generate excessively long reasoning paths without any performance benefit. Existing solutions that penalize length often fail, inducing performance degradation due to a fundamental misalignment between trajectory-level rewards and token-level optimization. In this work, we introduce a novel framework, DECS, built on our theoretical discovery of two previously unaddressed flaws in current length rewards: (1) the erroneous penalization of essential exploratory tokens and (2) the inadvertent rewarding of partial redundancy. Our framework's innovations include (i) a first-of-its-kind decoupled token-level reward mechanism that surgically distinguishes and penalizes redundant tokens, and (ii) a novel curriculum batch scheduling strategy to master the efficiency-efficacy equilibrium. Experimental results show DECS can achieve a dramatic reduction in reasoning tokens by over 50\% across seven benchmarks while simultaneously maintaining or even improving performance. It demonstrates conclusively that substantial gains in reasoning efficiency can be achieved without compromising a model's underlying reasoning power. Code is available at https://github.com/pixas/DECS.

cs.CL↗

arXiv2026

GLM-OCR Technical Report

GLM-OCR is an efficient 0.9B-parameter compact multimodal model designed for real-world document understanding. It combines a 0.4B-parameter CogViT visual encoder with a 0.5B-parameter GLM language decoder, achieving a strong balance between computational efficiency and recognition performance. To address the inefficiency of standard autoregressive decoding in deterministic OCR tasks, GLM-OCR introduces a Multi-Token Prediction (MTP) mechanism that predicts multiple tokens per step, significantly improving decoding throughput while keeping memory overhead low through shared parameters. At the system level, a two-stage pipeline is adopted: PP-DocLayout-V3 first performs layout analysis, followed by parallel region-level recognition. Extensive evaluations on public benchmarks and industrial scenarios show that GLM-OCR achieves competitive or state-of-the-art performance in document parsing, text and formula transcription, table structure recovery, and key information extraction. Its compact architecture and structured generation make it suitable for both resource-constrained edge deployment and large-scale production systems.

cs.CL↗

arXiv2026

Stepping VLMs onto the Court: Benchmarking Spatial Intelligence in Sports

Sports have long attracted broad attention as they push the limits of human physical and cognitive capabilities. Amid growing interest in spatial intelligence for vision-language models (VLMs), sports provide a natural testbed for understanding high-intensity human motion and dynamic object interactions. To this end, we present CourtSI, the first large-scale spatial intelligence dataset tailored to sports scenarios. CourtSI contains over 1M QA pairs, organized under a holistic taxonomy that systematically covers spatial counting, distance measurement, localization, and relational reasoning, across representative net sports including badminton, tennis, and table tennis. Leveraging well-defined court geometry as metric anchors, we develop a semi-automatic data engine to reconstruct sports scenes, enabling scalable curation of CourtSI. In addition, we introduce CourtSI-Bench, a high-quality evaluation benchmark comprising 3,686 QA pairs with rigorous human verification. We evaluate 25 proprietary and open-source VLMs on CourtSI-Bench, revealing a remaining human-AI performance gap and limited generalization from existing spatial intelligence benchmarks. These findings indicate that sports scenarios expose limitations in spatial intelligence capabilities captured by existing benchmarks. Further, fine-tuning Qwen3-VL-8B on CourtSI improves accuracy on CourtSI-Bench by 23.5 percentage points. The adapted model also generalizes effectively to CourtSI-Ext, an evaluation set built on a similar but unseen sport, and demonstrates enhanced spatial-aware commentary generation. Together, these findings demonstrate that CourtSI provides a scalable pathway toward advancing spatial intelligence of VLMs in sports.

cs.CV↗

arXiv2026

Rejection Mixing: Fast Semantic Propagation of Mask Tokens for Efficient DLLM Inference

Diffusion Large Language Models (DLLMs) promise fast non-autoregressive inference but suffer a severe quality-speed trade-off in parallel decoding. This stems from the ''combinatorial contradiction'' phenomenon, where parallel tokens form semantically inconsistent combinations. We address this by integrating continuous representations into the discrete decoding process, as they preserve rich inter-position dependency. We propose ReMix (Rejection Mixing), a framework that introduces a novel Continuous Mixing State as an intermediate between the initial masked state and the final decoded token state. This intermediate state allows a token's representation to be iteratively refined in a continuous space, resolving mutual conflicts with other tokens before collapsing into a final discrete sample. Furthermore, a rejection rule reverts uncertain representations from the continuous state back to the masked state for reprocessing, ensuring stability and preventing error propagation. ReMix thus mitigates combinatorial contradictions by enabling continuous-space refinement during discrete diffusion decoding. Extensive experiments demonstrate that ReMix, as a training-free method, achieves a $2-8 \times$ inference speedup without any quality degradation.

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arXiv2026

An Agentic System for Rare Disease Diagnosis with Traceable Reasoning

Rare diseases affect over 300 million individuals worldwide, yet timely and accurate diagnosis remains an urgent challenge. Patients often endure a prolonged diagnostic odyssey exceeding five years, marked by repeated referrals, misdiagnoses, and unnecessary interventions, leading to delayed treatment and substantial emotional and economic burdens. Here we present DeepRare, a multi-agent system for rare disease differential diagnosis decision support powered by large language models, integrating over 40 specialized tools and up-to-date knowledge sources. DeepRare processes heterogeneous clinical inputs, including free-text descriptions, structured Human Phenotype Ontology terms, and genetic testing results, to generate ranked diagnostic hypotheses with transparent reasoning linked to verifiable medical evidence. Evaluated across nine datasets from literature, case reports and clinical centres across Asia, North America and Europe spanning 14 medical specialties, DeepRare demonstrates exceptional performance on 3,134 diseases. In human-phenotype-ontology-based tasks, it achieves an average Recall@1 of 57.18%, outperforming the next-best method by 23.79%; in multi-modal tests, it reaches 69.1% compared with Exomiser's 55.9% on 168 cases. Expert review achieved 95.4% agreement on its reasoning chains, confirming their validity and traceability. Our work not only advances rare disease diagnosis but also demonstrates how the latest powerful large-language-model-driven agentic systems can reshape current clinical workflows.

cs.CL↗

arXiv2026

Evolving Interactive Diagnostic Agents in a Virtual Clinical Environment

We present a framework for training large language models (LLMs) as diagnostic agents with reinforcement learning, enabling them to manage multi-turn interactive diagnostic processes, adaptively select examinations, and commit to final diagnoses. Unlike instruction-tuned models trained on static data, our method acquires diagnostic strategies through dynamic exploration and outcome-based feedback, mapping evolving patient states to the next optimal examination and subsequent diagnosis. Our contributions include: (i) DiagGym, a diagnostics world model trained with electronic health records, serving as a virtual clinical environment to support closed-loop in-silico training and evaluation for interactive diagnosis; (ii) DiagAgent, trained via end-to-end multi-turn RL to learn dynamic diagnostic policies that optimize both interactive effectiveness and final accuracy; (iii) DiagBench, a multi-center diagnostic benchmark designed to evaluate multi-turn diagnostic interaction trajectories. The benchmark comprises 2.2K physician-validated cases sourced from 4 distinct distributions, alongside 3.3K physician-written rubrics for granular process-oriented evaluation. (iv) Extensive evaluations demonstrate DiagAgent's superior performance across both in-domain and out-of-domain (OOD) settings. DiagAgent significantly outperforms 11 SOTA LLMs and 2 prompt-engineered agents. In the end-to-end setting, it delivers a 11.20% increase in diagnostic accuracy and a 17.58% boost in examination recommendation F1 score, while consistently maintaining SOTA performance across all three external centers. Furthermore, in rubric-based evaluations, it surpasses the next-best model by 7.1% in weighted rubric score. These findings indicate that learning policies in interactive clinical environments confers long-term diagnostic management abilities unattainable through passive training.

cs.CL↗

arXiv2026

VersaViT: Enhancing MLLM Vision Backbones via Task-Guided Optimization

Multimodal Large Language Models (MLLMs) have recently achieved remarkable success in visual-language understanding, demonstrating superior high-level semantic alignment within their vision encoders. An important question thus arises: Can these encoders serve as versatile vision backbones, capable of reliably performing classic vision-centric tasks as well? To address the question, we make the following contributions: (i) we identify that the vision encoders within MLLMs exhibit deficiencies in their dense feature representations, as evidenced by their suboptimal performance on dense prediction tasks (e.g., semantic segmentation, depth estimation); (ii) we propose VersaViT, a well-rounded vision transformer that instantiates a novel multi-task framework for collaborative post-training. This framework facilitates the optimization of the vision backbone via lightweight task heads with multi-granularity supervision; (iii) extensive experiments across various downstream tasks demonstrate the effectiveness of our method, yielding a versatile vision backbone suited for both language-mediated reasoning and pixel-level understanding.

cs.CV↗

arXiv2026

VocalNet-MDM: Accelerating Streaming Speech LLM via Self-Distilled Masked Diffusion Modeling

Recent Speech Large Language Models~(LLMs) have achieved impressive capabilities in end-to-end speech interaction. However, the prevailing autoregressive paradigm imposes strict serial constraints, limiting generation efficiency and introducing exposure bias. In this paper, we investigate Masked Diffusion Modeling~(MDM) as a non-autoregressive paradigm for speech LLMs and introduce VocalNet-MDM. To adapt MDM for streaming speech interaction, we address two critical challenges: training-inference mismatch and iterative overhead. We propose Hierarchical Block-wise Masking to align training objectives with the progressive masked states encountered during block diffusion decoding, and Iterative Self-Distillation to compress multi-step refinement into fewer steps for low-latency inference. Trained on a limited scale of only 6K hours of speech data, VocalNet-MDM achieves a 3.7$\times$--10$\times$ decoding speedup and reduces first-chunk latency by 34\% compared to AR baselines. It maintains competitive recognition accuracy while achieving state-of-the-art text quality and speech naturalness, demonstrating that MDM is a promising and scalable alternative for low-latency, efficient speech LLMs.

cs.CL↗

arXiv2026

Rethinking Explainable Disease Prediction: Synergizing Accuracy and Reliability via Reflective Cognitive Architecture

In clinical decision-making, predictive models face a persistent trade-off: accurate models are often opaque "black boxes," while interpretable methods frequently lack predictive precision or statistical grounding. In this paper, we challenge this dichotomy, positing that high predictive accuracy and high-quality descriptive explanations are not competing goals but synergistic outcomes of a deep, first-hand understanding of data. We propose the Reflective Cognitive Architecture (RCA), a novel framework designed to enable Large Language Models (LLMs) to learn directly from tabular data through experience and reflection. RCA integrates two core mechanisms: an iterative rules optimization process that refines logical argumentation by learning from prediction errors, and a distribution-aware rules check that grounds this logic in global statistical evidence to ensure robustness. We evaluated RCA against over 20 baselines - ranging from traditional machine learning to advanced reasoning LLMs and agents - across diverse medical datasets, including a proprietary real-world Catheter-Related Thrombosis (CRT) cohort. Crucially, to demonstrate real-world scalability, we extended our evaluation to two large-scale datasets. The results confirm that RCA achieves state-of-the-art predictive performance and superior robustness to data noise while simultaneously generating clear, logical, and evidence-based explanatory statements, maintaining its efficacy even at scale. The code is available at https://github.com/ssssszj/RCA.

cs.AI↗

arXiv2026

PhenoLIP: Integrating Phenotype Ontology Knowledge into Medical Vision-Language Pretraining

Recent progress in large-scale CLIP-like vision-language models(VLMs) has greatly advanced medical image analysis. However, most existing medical VLMs still rely on coarse image-text contrastive objectives and fail to capture the systematic visual knowledge encoded in well-defined medical phenotype ontologies. To address this gap, we construct PhenoKG, the first large-scale, phenotype-centric multimodal knowledge graph that encompasses over 520K high-quality image-text pairs linked to more than 3,000 phenotypes. Building upon PhenoKG, we propose PhenoLIP, a novel pretraining framework that explicitly incorporates structured phenotype knowledge into medical VLMs through a two-stage process. We first learn a knowledge-enhanced phenotype embedding space from textual ontology data and then distill this structured knowledge into multimodal pretraining via a teacher-guided knowledge distillation objective. To support evaluation, we further introduce PhenoBench, an expert-verified benchmark designed for phenotype recognition, comprising over 7,800 image--caption pairs covering more than 1,000 phenotypes. Extensive experiments demonstrate that PhenoLIP outperforms previous state-of-the-art baselines, improving upon BiomedCLIP in phenotype classification accuracy by 8.85\% and BIOMEDICA in cross-modal retrieval by 15.03%, underscoring the value of integrating phenotype-centric priors into medical VLMs for structured and interpretable medical image understanding.

cs.CV↗

arXiv2026

End-to-End Agentic RAG System Training for Traceable Diagnostic Reasoning

The integration of Large Language Models (LLMs) into healthcare is constrained by knowledge limitations, hallucinations, and a disconnect from Evidence-Based Medicine (EBM). While Retrieval-Augmented Generation (RAG) offers a solution, current systems often rely on static workflows that miss the iterative, hypothetico-deductive reasoning of clinicians. To address this, we introduce Deep-DxSearch, an agentic RAG system trained end-to-end via reinforcement learning (RL) for traceable diagnostic reasoning. Deep-DxSearch acts as an active investigator, treating the LLM as an agent within an environment of 16,000+ guideline-derived disease profiles, 150,000+ patient records for case-based reasoning, and over 27 million biomedical documents. Using soft verifiable rewards that co-optimize retrieval and reasoning, the model learns to formulate queries, evaluate evidence, and refine searches to close diagnostic gaps. Experiments show our end-to-end RL framework consistently outperforms prompt-engineering and training-free RAG methods. On in-distribution (ID) and out-of-distribution (OOD) benchmarks for common and rare diseases, Deep-DxSearch surpasses strong baselines-including GPT-4o, DeepSeek-R1, and medical-specific frameworks-achieving an average accuracy gain of 22.7% over the second-best model. In validation with 150 real-world cases, Deep-DxSearch boosts physicians' average diagnostic accuracy from 45.6% to 69.1%. These results indicate that evolving agentic systems to leverage statistical regularities in large-scale healthcare data is key for trustworthy diagnostic assistants. All data, code, and checkpoints are available at https://qiaoyu-zheng.github.io/Deep-DxSearch.

cs.CL↗

arXiv2026

Knowledge-enhanced Pretraining for Vision-language Pathology Foundation Model on Cancer Diagnosis

Vision-language foundation models have shown great promise in computational pathology but remain primarily data-driven, lacking explicit integration of medical knowledge. We introduce KEEP (KnowledgE-Enhanced Pathology), a foundation model that systematically incorporates disease knowledge into pretraining for cancer diagnosis. KEEP leverages a comprehensive disease knowledge graph encompassing 11,454 diseases and 139,143 attributes to reorganize millions of pathology image-text pairs into 143,000 semantically structured groups aligned with disease ontology hierarchies. This knowledge-enhanced pretraining aligns visual and textual representations within hierarchical semantic spaces, enabling deeper understanding of disease relationships and morphological patterns. Across 18 public benchmarks (over 14,000 whole-slide images) and 4 institutional rare cancer datasets (926 cases), KEEP consistently outperformed existing foundation models, showing substantial gains for rare subtypes. These results establish knowledge-enhanced vision-language modeling as a powerful paradigm for advancing computational pathology.

eess.IV↗

arXiv2026

Innovator-VL: A Multimodal Large Language Model for Scientific Discovery

We present Innovator-VL, a scientific multimodal large language model designed to advance understanding and reasoning across diverse scientific domains while maintaining excellent performance on general vision tasks. Contrary to the trend of relying on massive domain-specific pretraining and opaque pipelines, our work demonstrates that principled training design and transparent methodology can yield strong scientific intelligence with substantially reduced data requirements. (i) First, we provide a fully transparent, end-to-end reproducible training pipeline, covering data collection, cleaning, preprocessing, supervised fine-tuning, reinforcement learning, and evaluation, along with detailed optimization recipes. This facilitates systematic extension by the community. (ii) Second, Innovator-VL exhibits remarkable data efficiency, achieving competitive performance on various scientific tasks using fewer than five million curated samples without large-scale pretraining. These results highlight that effective reasoning can be achieved through principled data selection rather than indiscriminate scaling. (iii) Third, Innovator-VL demonstrates strong generalization, achieving competitive performance on general vision, multimodal reasoning, and scientific benchmarks. This indicates that scientific alignment can be integrated into a unified model without compromising general-purpose capabilities. Our practices suggest that efficient, reproducible, and high-performing scientific multimodal models can be built even without large-scale data, providing a practical foundation for future research.

cs.CV↗

arXiv2026

AgentEHR: Advancing Autonomous Clinical Decision-Making via Retrospective Summarization

Large Language Models have demonstrated profound utility in the medical domain. However, their application to autonomous Electronic Health Records~(EHRs) navigation remains constrained by a reliance on curated inputs and simplified retrieval tasks. To bridge the gap between idealized experimental settings and realistic clinical environments, we present AgentEHR. This benchmark challenges agents to execute complex decision-making tasks, such as diagnosis and treatment planning, requiring long-range interactive reasoning directly within raw and high-noise databases. In tackling these tasks, we identify that existing summarization methods inevitably suffer from critical information loss and fractured reasoning continuity. To address this, we propose RetroSum, a novel framework that unifies a retrospective summarization mechanism with an evolving experience strategy. By dynamically re-evaluating interaction history, the retrospective mechanism prevents long-context information loss and ensures unbroken logical coherence. Additionally, the evolving strategy bridges the domain gap by retrieving accumulated experience from a memory bank. Extensive empirical evaluations demonstrate that RetroSum achieves performance gains of up to 29.16% over competitive baselines, while significantly decreasing total interaction errors by up to 92.3%.

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