arXiv subjects

Yi Lin

Publications and source records attributed to Yi Lin.

At least 19 recordsLinked to original sources

arXiv2026

A Source-Grounded Framework for Constructing and Evaluating Progressive Multimodal Diagnostic Dialogues from Clinical Case Reports

Clinical diagnosis requires progressive integration of patient history, physical examination, laboratory findings, medical images, and diagnostic-informative tests. However, most multimodal medical benchmarks evaluate fixed inputs or endpoint answers, while fully interactive diagnostic agents conflate evidence selection with evidence interpretation. We present a source-grounded framework to construct progressive multimodal diagnostic dialogues from case reports and an evaluation strategy for assessing MLLMs on final diagnosis, diagnostic reasoning, and image-finding interpretation. Evaluation on 24 internal medicine case reports showed that our framework can accurately convert case reports into reference dialogues, achieving a diagnosis F1 of 0.99 and a reasoning-quality score of 4.79 out of 5. Evaluation on two frontier MLLMs (o4-mini and Claude Haiku 4.5) achieved reasoning-quality scores of 2.75 and 2.50, respectively, with substantially lower diagnosis, reasoning, and image-finding F1 scores. The results demonstrate that fluent responses do not necessarily reflect evidence-grounded clinical reasoning and highlight the utility of the proposed framework for evaluating multimodal diagnostic reasoning.

cs.CL↗

arXiv2026

LLM assisted writing deserves empirical evaluation

LLM-assisted writing is often treated as a detection problem, as it raises questions about clarity, integrity, equity, and evaluation. An analysis of 69,209 Health Informatics papers links it to more focused presentation, broader citation practices, and more globally distributed authorship. These patterns do not prove better science, but they support evaluating manuscripts by scholarly quality and accountability rather than by tool use.

cs.CL↗

arXiv2026

Evaluating Multi-Turn Multimodal Diagnostic Reasoning on Challenging Real-World Clinical Cases

Clinical diagnostic evaluation should not only assess whether models can provide correct diagnoses, but also reflect the realities of clinical practice, including progressive disclosure of multimodal information, dynamic updating of diagnostic hypotheses, and continuous refinement of clinical reasoning. However, existing evaluations of multimodal large language models (MLLMs) typically rely on single-turn or isolated tasks, making it difficult to fully capture the complexity of real-world clinical diagnosis. To bridge this gap, we developed ClinMM-Bench, the largest multi-turn multimodal clinical diagnostic evaluation benchmark to date. ClinMM-Bench contains 1,089 challenging real-world clinical cases and 3,760 medical images across eight specialties. We systematically evaluated 15 representative MLLMs using a two-level evaluation framework that assessed both diagnostic accuracy and diagnostic reasoning quality. Results showed that proprietary models achieved the highest overall diagnostic accuracy, but the proportion of completely correct diagnoses remained limited across all models. In terms of diagnostic reasoning quality, current models can identify plausible diagnostic directions but still have considerable limitations in generating reliable diagnostic reasoning. Error analysis further identified five representative failure modes: information synthesis failure, knowledge mapping error, perception error, premature closure, and visual hallucination.

cs.CL↗

arXiv2026

MonteRET: AI Agent Enhancing Multimodal LLMs with Multi-granularity Knowledge Retrieval for Chest CT Report Generation

Automated chest CT report generation remains challenging because clinically faithful reporting requires both whole-volume understanding and accurate description of localized anatomical findings. Here we developed and retrospectively evaluated MonteRET, a region-aware retrieval-enhanced framework for generating chest CT findings sections. MonteRET integrates global CT features with region-level anatomical representations, retrieves clinically relevant knowledge using predicted medical conditions and region-level vision-language alignment, and refines initial reports through a knowledge-guided report rewriting agent. We trained our model on a public cohort with 24,128 CT scans from RadGenome-ChestCT. We evaluated MonteRET on the public RadGenome-ChestCT test set of 1,564 CT scans and an external cohort of 82 CT scans from NewYork-Presbyterian/Weill Cornell Medical Center. MonteRET improved report quality, semantic similarity, and clinical efficacy compared with a matched baseline and several state-of-the-art methods. Gains were most pronounced for recall, suggesting fewer omitted findings. Human expert evaluation by radiology residents also favored MonteRET.

cs.CV↗

arXiv2026

UP: Unbounded Positive Asymmetric Optimization for Breaking the Exploration-Stability Dilemma

Reinforcement learning (RL) has become the standard paradigm for enhancing the complex reasoning capabilities of large language models (LLMs). To achieve sample efficiency, modern RL frameworks rely on importance sampling (IS). However, these algorithms suffer from an exploration-stability dilemma. Pure IS often leads to catastrophic training instability, while standard clipping mechanisms used to mitigate this instability strictly constrain the policy update budget. By formalizing the concept of Probability Capacity (Cap), we reveal that conservative clipping structurally stifles exploration by prematurely truncating the update budget for correct but low-confidence reasoning paths. To break free from these constraints, we propose Unbounded Positive Asymmetric Optimization (UP), a universal and plug-and-play objective. UP theoretically restructures the optimization process by anchoring the policy to its current state via the stop-gradient operator. This asymmetric design unleashes unclipped, stable gradients for positive advantages to maximize exploration, while maintaining standard clipping safeguards for negative advantages to prevent training instability. Furthermore, our formulation readily extends across different optimization granularities, including token-level (GRPO, DAPO) and sequence-level (GSPO) frameworks. Extensive experiments demonstrate that UP enhances exploration capacity and achieves superior reasoning accuracy across diverse RL algorithms (DAPO, GSPO, and GRPO), model architectures (Dense, MoE, and vision-language), and training modalities (language and multimodal), validating UP as a truly universal plug-and-play enhancement for RL-based training.

cs.LG↗

arXiv2026

BrainFIBRE: A Foundation Model via Information Decomposition for Brain Microstructure

Diffusion MRI probes brain microstructure with particular sensitivity to early cerebrovascular and neurodegenerative changes. Neurite Orientation Dispersion and Density Imaging (NODDI) decomposes the diffusion signal into three biophysically interpretable maps: neurite density index (NDI), orientation dispersion index (ODI), and free water fraction (FWF), capturing neurite packing, fiber coherence, and extracellular fluid. These 3D maps offer a rich substrate for transferable microstructural representations, yet integrating them is challenging: standard representation learning struggles to disentangle the unique information in each map from their shared and synergistic interactions. We present BrainFIBRE, the first foundation model for brain microstructure, pretrained on NODDI-derived maps from 55,592 UK Biobank participants. We propose Self-supervised Partial Information Decomposition (SPID), which extends PID-guided multimodal learning to the self-supervised regime for the first time. A novel Counterfactual Candidate Construction (CCC) paradigm perturbs inter-modality alignment through modality dropping and swapping, providing the contrastive signal for a Mixture-of-Experts architecture to disentangle unique, synergistic, and redundant information without any downstream label. On both Caucasian and Asian cohorts, BrainFIBRE achieves state-of-the-art performance across diverse tasks predicting age, sex, cerebrovascular and neurodegenerative markers, and cognition, while yielding neurobiologically interpretable representations that reveal task- and cohort-specific interaction patterns. BrainFIBRE establishes a versatile foundation for neuroimaging analysis at the microstructural level.

cs.CV↗

arXiv2026

Towards end-to-end LLM-based censoring-aware survival analysis

Objective: Survival analysis is central to medical prediction, yet large language models (LLMs) are rarely used as end-to-end survival models because censoring prevents straightforward supervised fine-tuning. Here we present LLMSurvival, a framework that enables censoring-aware survival analysis with unmodified LLMs operating directly on tabular clinical data. Materials and Methods: LLMSurvival reformulates time-to-event prediction as pairwise ranking among comparable subjects, and derives test-time risk by aggregating comparisons against anchor individuals from the training cohort. Results: Across two clinical tasks (ICU mortality prediction in MIMIC-IV and fragility fracture prediction in a NewYork-Presbyterian/Weill Cornell Medicine cohort), LLMSurvival improves overall concordance over Cox proportional hazards modeling by 3.1% for ICU mortality and 0.5% for fracture risk, 2.1% on average for ICU mortality and 2.8% for fracture risk over three established deep learning survival models. Discussion: The results show that survival modeling with censoring can be made compatible with LLM fine-tuning through comparison-based reformulation. The framework demonstrates high portability and superior performance over expert curated scores like SAPS-II and FRAX scores across diverse clinical context. Furthermore, the framework supports local deployment, as compact, publicly available base models provide sufficient performance. Conclusion: The LLMSurvival framework serves as a proof of concept for an integrated, censoring-conscious approach to survival analysis via LLMs.

cs.AI↗

arXiv2026

Training Long-Context Vision-Language Models Effectively with Generalization Beyond 128K Context

Long-context modeling is becoming a core capability of modern large vision-language models (LVLMs), enabling sustained context management across long-document understanding, video analysis, and multi-turn tool use in agentic workflows. Yet practical training recipes remain insufficiently explored, particularly for designing and balancing long-context data mixtures. In this work, we present a systematic study of long-context continued pre-training for LVLMs, extending a 7B model from 32K to 128K context with extensive ablations on long-document data. We first show that long-document VQA is substantially more effective than OCR transcription. Building on this observation, our ablations further yield three key findings: i) for sequence-length distribution, balanced data outperforms target-length-focused data (e.g., 128K), suggesting that long-context ability requires generalizable key-information retrieval across various lengths and positions; ii) retrieval remains the primary bottleneck, favoring retrieval-heavy mixtures with modest reasoning data for task diversity; and iii) pure long-document VQA largely preserves short-context capabilities, suggesting that instruction-formatted long data reduces the need for short-data mixing. Based on these findings, we introduce MMProLong, obtained by long-context continued pre-training from Qwen2.5-VL-7B with only a 5B-token budget. MMProLong improves long-document VQA scores by 7.1% and maintains strong performance at 256K and 512K contexts beyond its 128K training window, without additional training. It further generalizes to webpage-based multimodal needle retrieval, long-context vision-text compression, and long-video understanding without task-specific supervision. Overall, our study establishes a practical LongPT recipe and an empirical foundation for advancing long-context vision-language models.

cs.CV↗

arXiv2026

Value-Decomposed Reinforcement Learning Framework for Taxiway Routing with Hierarchical Conflict-Aware Observations

Taxiway routing and on-surface conflict avoidance are coupled safety-critical decision problems in airport surface operations. Existing planning and optimization methods are often limited by online computational cost, while reinforcement learning methods may struggle to represent downstream traffic conflicts and balance multiple objectives. This paper presents Conflict-aware Taxiway Routing (CaTR), a reinforcement learning framework for real-time multi-aircraft taxiway routing. CaTR constructs a grid-based airport surface environment with action masking, introduces a hierarchical foresight traffic representation to encode current and downstream conflict-related traffic conditions, and adopts a value-decomposed reinforcement learning strategy to prioritize sparse but safety-critical objectives. Experiments are conducted on a realistic environment based on Changsha Huanghua International Airport under multiple traffic density levels. Results show that CaTR achieves better safety--efficiency trade-offs than representative planning, optimization, and reinforcement learning baselines while maintaining practical runtime.

cs.AI↗

arXiv2026

MegaScale-Omni: A Hyper-Scale, Workload-Resilient System for MultiModal LLM Training in Production

As the foundational component of versatile AI applications, training an multimodal large language model (MLLM) relies on multimodal datasets with dynamic modality mixture proportions and sample length distributions. However, existing MLLM systems remain inefficient under dynamic workloads, due to statically coupled decisions of resource allocation and model parallelization between encoders and the LLM backbone. This paper presents MegaScale-Omni, an industrial-grade MLLM training system tailored for dynamic workload adaption and hyper-scale deployment. MegaScale-Omni is built upon the training scheme of encoder-LLM multiplexing with three key innovations: (1) Decoupled parallelism strategies with long-short sequence parallelism for encoders to process variable-length samples, and full-fledged 5D parallelism for the LLM backbone, both organized under a communication-efficient parallelization layout. (2) Unified encoder-LLM representations for flexible, extensible colocation, and a new paradigm of encoder-LLM joint pipeline with workload resilience. (3) Workload balancing techniques via decentralized grouped reordering in data loaders and adaptive resharding from encoder to LLM ranks. MegaScale-Omni is deployed as the foundation of our in-house large-scale MLLM training tasks with thousands of GPUs. Our experimental results demonstrate $1.27\times$-$7.57\times$ throughput improvement under production-grade dynamic workloads, as compared to four state-of-the-art systems.

cs.DC↗

arXiv2026

Descent of Basic Forms to Quotients by Locally Free Lie Group Actions

We prove an equivariant version of the theorem of Hector, Mac\'{\i}as-Virg\'os, and Sanmart\'{\i}n-Carb\'on identifying diffeological forms on the leaf space of a foliation with basic forms. For any group $K$ acting by foliation-preserving diffeomorphisms, we show that this identification is an isomorphism of $K$-equivariant cochain complexes. We then establish a descent theorem for basic differential forms under locally free Lie group actions without assuming properness. Let a Lie group $H$, not necessarily connected or second countable, act smoothly and locally freely on a second countable manifold $M$, and let $\mathcal F$ be the foliation by $H_0$-orbits. We prove that pullback induces an isomorphism \[ \Omega^\bullet(M/H)\cong\Omega^\bullet(M,\mathcal F)^H \] provided that $H$ is second countable or that the induced action of $H/H_0$ on $M/H_0$ satisfies a natural subduction condition. We also give a smooth free action for which descent fails, showing that an additional hypothesis is genuinely necessary.

math.DG↗

arXiv2026

Reinforcement Learning Improves LLM Accuracy and Reasoning in Disease Classification from Radiology Reports

Accurate disease classification from radiology reports is essential for many applications. While supervised fine-tuning (SFT) of lightweight LLMs improves accuracy, it can degrade reasoning. We propose a two-stage approach: SFT on disease labels followed by Group Relative Policy Optimization (GRPO) to refine predictions by optimizing accuracy and format without reasoning supervision. Across three radiologist-annotated datasets, SFT outperformed baselines and GRPO further improved classification and enhanced reasoning recall and comprehensiveness.

cs.AI↗

arXiv2026

A Transverse Averaging Operator and Cohomology of Quotients by Homogeneous Non-closed Subgroups

In this article, we introduce a transverse averaging operator for basic forms on a complete Riemannian foliation with compact leaf closure space, equipped with an isometric transverse Lie algebra action. In contrast to the classical averaging operator in equivariant geometry, which is defined by integration over a compact Lie group, our operator is constructed purely from infinitesimal transverse data and does not require any global group action. We prove that every closed basic form is sent to an invariant basic form representing the same basic cohomology class. The main application is formulated independently of foliation theory. We compute the diffeological de Rham cohomology of the homogeneous quotient $G/H$, where $G$ is a connected Lie group, not necessarily compact, and $H$ is a connected Lie subgroup, not necessarily closed. Let $\mathfrak g$ and $\mathfrak h$ be the Lie algebras of $G$ and $H$, respectively. Assuming that $\mathfrak g$ is of compact type and that $G/\overline{H}$ is compact, we prove that $ H^\bullet_{\mathrm{dR}}(G/H) \cong H^\bullet(\mathfrak g,\mathfrak h)$. When $\mathfrak h$ is an ideal in $\mathfrak g$, the compact-type assumption on $\mathfrak g$ can be dropped, and under the sole assumption that $G/\overline{H}$ is compact we obtain $ H^\bullet_{\mathrm{dR}}(G/H) \cong H^\bullet(\mathfrak g/\mathfrak h)$. These results extend the classical Chevalley--Eilenberg computation from compact Lie groups and closed subgroups to homogeneous quotients $G/H$ by possibly non-closed subgroups $H$.

math.DG↗

arXiv2026

MARCH: Multi-Agent Radiology Clinical Hierarchy for CT Report Generation

Automated 3D radiology report generation often suffers from clinical hallucinations and a lack of the iterative verification found in human practice. While recent Vision-Language Models (VLMs) have advanced the field, they typically operate as monolithic "black-box" systems without the collaborative oversight characteristic of clinical workflows. To address these challenges, we propose MARCH (Multi-Agent Radiology Clinical Hierarchy), a multi-agent framework that emulates the professional hierarchy of radiology departments and assigns specialized roles to distinct agents. MARCH utilizes a Resident Agent for initial drafting with multi-scale CT feature extraction, multiple Fellow Agents for retrieval-augmented revision, and an Attending Agent that orchestrates an iterative, stance-based consensus discourse to resolve diagnostic discrepancies. On the RadGenome-ChestCT dataset, MARCH significantly outperforms state-of-the-art baselines in both clinical fidelity and linguistic accuracy. Our work demonstrates that modeling human-like organizational structures enhances the reliability of AI in high-stakes medical domains.

cs.AI↗

arXiv2026

CXR-LT 2026 Challenge: Multi-Center Long-Tailed and Zero Shot Chest X-ray Classification

Chest X-ray (CXR) interpretation is hindered by the long-tailed distribution of pathologies and the open-world nature of clinical environments. Existing benchmarks often rely on closed-set classes from a single institution, failing to capture the prevalence of rare diseases or the appearance of novel findings. To address this, we present the CXR-LT challenge. The first event, CXR-LT 2023, established a large-scale benchmark for long-tailed multi-label CXR classification and identified key challenges in rare disease recognition. CXR-LT 2024 further expanded the label space and introduced a zero-shot task to study generalization to unseen findings. Building on the success of CXR-LT 2023 and 2024, this third iteration of the benchmark introduces a multi-center dataset comprising over 145,000 images from PadChest and NIH Chest X-ray datasets. Additionally, all development and test sets in CXR-LT 2026 are annotated by radiologists, providing a more reliable and clinically grounded evaluation than report-derived labels. The challenge defines two core tasks this year: (1) Robust Multi-Label Classification on 30 known classes and (2) Open-World Generalization to 6 unseen (out-of-distribution) rare disease classes. This paper summarizes the overview of the CXR-LT 2026 challenge. We describe the data collection and annotation procedures, analyze solution strategies adopted by participating teams, and evaluate head-versus-tail performance, calibration, and cross-center generalization gaps. Our results show that vision-language foundation models improve both in-distribution and zero-shot performance, but detecting rare findings under multi-center shift remains challenging. Our study provides a foundation for developing and evaluating AI systems in realistic long-tailed and open-world clinical conditions.

cs.CV↗

arXiv2026

Contract-Coding: Towards Repo-Level Generation via Structured Symbolic Paradigm

The shift toward intent-driven software engineering (often termed "Vibe Coding") exposes a critical Context-Fidelity Trade-off: vague user intents overwhelm linear reasoning chains, leading to architectural collapse in complex repo-level generation. We propose Contract-Coding, a structured symbolic paradigm that bridges unstructured intent and executable code via Autonomous Symbolic Grounding. By projecting ambiguous intents into a formal Language Contract, our framework serves as a Single Source of Truth (SSOT) that enforces topological independence, effectively isolating inter-module implementation details, decreasing topological execution depth and unlocking Architectural Parallelism. Empirically, while state-of-the-art agents suffer from different hallucinations on the Greenfield-5 benchmark, Contract-Coding achieves 47\% functional success while maintaining near-perfect structural integrity. Our work marks a critical step towards repository-scale autonomous engineering: transitioning from strict "specification-following" to robust, intent-driven architecture synthesis. Our code is available at https://github.com/imliinyi/Contract-Coding.

cs.SE↗

arXiv2026

Mixture-of-Depths Attention

Scaling depth is a key driver for large language models (LLMs). Yet, as LLMs become deeper, they often suffer from signal degradation: informative features formed in shallow layers are gradually diluted by repeated residual updates, making them harder to recover in deeper layers. We introduce mixture-of-depths attention (MoDA), a mechanism that allows each attention head to attend to sequence KV pairs at the current layer and depth KV pairs from preceding layers. We further describe a hardware-efficient algorithm for MoDA that resolves non-contiguous memory-access patterns, achieving 97.3% of FlashAttention-2's efficiency at a sequence length of 64K. Experiments on 1.5B-parameter models demonstrate that MoDA consistently outperforms strong baselines. Notably, it improves average perplexity by 0.2 across 10 validation benchmarks and increases average performance by 2.11% on 10 downstream tasks, with a negligible 3.7% FLOPs computational overhead. We also find that combining MoDA with post-norm yields better performance than using it with pre-norm. These results suggest that MoDA is a promising primitive for depth scaling. Code is released at https://github.com/hustvl/MoDA .

cs.CL↗

arXiv2026

Overview of the CXR-LT 2026 Challenge: Multi-Center Long-Tailed and Zero Shot Chest X-ray Classification

cs.CV↗