arXiv subjects

Guanchen Wu

Publications and source records attributed to Guanchen Wu.

9 recordsLinked to original sources

arXiv2026

What the Reranker Sees: Multi-Aspect Page Annotation for Long-Document Multimodal Question Answering

Long-document visual question answering (VQA) over documents of tens to hundreds of pages mixing text, tables, charts, and figures typically follows retrieve-then-read pipelines. In our setting, the bottleneck shifts from retrieval recall to reranker-side evidence selection: on MMLongBench-Doc, BGE-M3 reaches Recall@20 = 0.86 but only F1@5 = 0.254, and even the visual retriever ColPali reaches only F1@5 = 0.332; a text-only rerank LLM seeing only raw snippets misses table, chart, and layout evidence even when the upstream retriever encoded images. We propose Trident, with two complementary components: Trident-R, a retriever-agnostic LLM reranker that converts each candidate into an LLM-readable semantic record, including a visual caption, section path, entity tags, multi-axis concept hits, and a text snippet, then performs a single adaptive-K rerank call; and Trident-S, a generation-side module that prompts the VLM under topical, entity, and structural lenses before synthesis. On two long-document datasets, the annotation+rerank protocol substantially improves retrieval F1 across five heterogeneous pools, with every reranked pool exceeding the strongest adaptive-K baseline PageIndex. An LLM rerank without the annotation barely changes first-hit ranking, indicating the lift comes from the structured annotation. Trident-S targets open-ended synthesis questions by design, adding up to 6.6 points in generation accuracy on these questions. The best Trident configuration is the strongest downstream QA pipeline in our evaluation, with rankings consistent across two LLM judges (kappa = 0.913).

cs.AI↗

arXiv2026

EHRBench: An Automated and Reliable EHR-based Benchmark for Clinical Decision Making with LLMs

Clinical decision-making (CDM) is central to real-world clinical workflows, where clinicians infer diagnoses, select treatments, or anticipate future health outcomes under incomplete evidence. LLMs are increasingly used to support these decisions due to strong language capabilities, broad biomedical knowledge, and efficiency, yet the reliability of LLMs on real-world clinical decision tasks remains insufficiently understood. To evaluate CDM models, especially LLM-based models, an ideal and practical medical decision benchmark should be constructed via an automated yet reliable pipeline to ensure both scale and quality. Moreover, the grounding of a CDM benchmark in real patient EHRs can better support evaluation on practical CDM tasks that require substantive biomedical knowledge and clinical inference. To fill the gaps, we introduce EHRBench, an automated and reliable EHR-grounded benchmark for evaluating LLM-based clinical decision-making at scale. To ensure scalability and reliability, EHRBench is constructed through an EHR-LLM-KB(knowledge-base) interaction pipeline. For efficiency, we use a specialized LLM to automatically convert encounter-level EHR trajectories into structured templates and deterministically instantiate the templates into QA items. In parallel, we apply systematic KB-based verification and enrichment to filter hallucinated or ambiguous relations and to improve reliability. Using this pipeline, we construct nearly 1M (960,067) QA items spanning three core inference-required clinical decision tasks: diagnosis, treatment, and prognosis. We benchmark more than 30 representative LLMs on EHRBench and provide detailed analyses of performance and robustness. The results show consistent capability trends across settings, further validating the reliability of EHRBench and highlighting actionable gaps toward clinically reliable LLM systems.

cs.AI↗

arXiv2026

Machine-Learned Leftmost Hessian Eigenvectors for Robust Transition State Finding

The reliable determination of transition states (TSs) benefits from second-order information for robust convergence and validation, but the computational expense of Hessians prohibits their routine use in TS optimization. Here, we present a machine-learning-driven TS optimizer that directly predicts the leftmost Hessian eigenvector (LMHE), the critical mode that locally approximates the reaction coordinate encompassing the TS. We demonstrate that our LMHE optimizer recovers TS solutions at the same rate as full Hessian optimizers, and more robustly from degraded initial guess geometries, thereby eliminating the excessively long wall times characteristic of full-Hessian approaches and reducing total gradient evaluations compared to standard quasi-Newton methods. We further improve accuracy and robustness using uncertainty quantification for identifying occasional LMHE prediction failures, that then falls back to a full Hessian update from the machine learned potential at that optimization step, avoiding expensive active learning. Overall our methodology and semi-automated workflow delivers second-order stability at first-order computational expense to provide a highly efficient engine for high-throughput reaction discovery.

physics.chem-ph↗

arXiv2026

MIRAGE: Knowledge Graph-Guided Cross-Cohort MRI Synthesis for Alzheimer's Disease Prediction

Reliable Alzheimer's disease (AD) diagnosis increasingly relies on multimodal assessments combining structural Magnetic Resonance Imaging (MRI) and Electronic Health Records (EHR). However, deploying these models is bottlenecked by modality missingness, as MRI scans are expensive and frequently unavailable in many patient cohorts. Furthermore, synthesizing de novo 3D anatomical scans from sparse, high-dimensional tabular records is technically challenging and poses severe clinical risks. To address this, we introduce MIRAGE, a novel framework that reframes the missing-MRI problem as an anatomy-guided cross-modal latent distillation task. First, MIRAGE leverages a Biomedical Knowledge Graph (KG) and Graph Attention Networks to map heterogeneous EHR variables into a unified embedding space that can be propagated from cohorts with real MRIs to cohorts without them. To bridge the semantic gap and enforce physical spatial awareness, we employ a frozen pre-trained 3D U-Net decoder strictly as an auxiliary regularization engine. Supported by a novel cohort-aggregated skip feature compensation strategy, this decoder acts as a rigorous structural penalty, forcing 1D latent representations to encode biologically plausible, macro-level pathological semantics. By exclusively utilizing this distilled "diagnostic-surrogate" representation during inference, MIRAGE completely bypasses computationally expensive 3D voxel reconstruction. Experiments demonstrate that our framework successfully bridges the missing-modality gap, improving the AD classification rate by 13% compared to unimodal baselines in cohorts without real MRIs.

cs.CV↗

arXiv2026

EpiQAL: Benchmarking Large Language Models in Epidemiological Question Answering and Reasoning

Reliable epidemiological reasoning requires synthesizing study evidence to infer disease burden, transmission dynamics, and intervention effects at the population level. Existing medical question answering benchmarks primarily emphasize clinical knowledge or patient-level reasoning, yet few systematically evaluate evidence-grounded epidemiological inference. We present EpiQAL, to our knowledge the first diagnostic benchmark for epidemiological question answering over research literature, comprising three subsets built from open-access articles across diverse diseases. The three subsets progressively test factual recall, multi-step inference, and conclusion reconstruction under incomplete information, and are constructed through a quality-controlled pipeline combining taxonomy guidance, multi-model verification, and difficulty screening. Experiments on fifteen models spanning open-source and proprietary systems reveal that current LLMs show limited performance on epidemiological reasoning, with multi-step inference posing the greatest challenge. Model rankings shift across subsets, and scale alone does not predict success. Chain-of-Thought prompting benefits multi-step inference but yields mixed results elsewhere. EpiQAL provides fine-grained diagnostic signals for evidence-grounding, inferential reasoning, and conclusion reconstruction.

cs.CL↗

arXiv2025

Utilizing Large Language Models for Zero-Shot Medical Ontology Extension from Clinical Notes

Integrating novel medical concepts and relationships into existing ontologies can significantly enhance their coverage and utility for both biomedical research and clinical applications. Clinical notes, as unstructured documents rich with detailed patient observations, offer valuable context-specific insights and represent a promising yet underutilized source for ontology extension. Despite this potential, directly leveraging clinical notes for ontology extension remains largely unexplored. To address this gap, we propose CLOZE, a novel framework that uses large language models (LLMs) to automatically extract medical entities from clinical notes and integrate them into hierarchical medical ontologies. By capitalizing on the strong language understanding and extensive biomedical knowledge of pre-trained LLMs, CLOZE effectively identifies disease-related concepts and captures complex hierarchical relationships. The zero-shot framework requires no additional training or labeled data, making it a cost-efficient solution. Furthermore, CLOZE ensures patient privacy through automated removal of protected health information (PHI). Experimental results demonstrate that CLOZE provides an accurate, scalable, and privacy-preserving ontology extension framework, with strong potential to support a wide range of downstream applications in biomedical research and clinical informatics.

cs.AI↗

arXiv2025

Towards Automatic Evaluation and Selection of PHI De-identification Models via Multi-Agent Collaboration

Protected health information (PHI) de-identification is critical for enabling the safe reuse of clinical notes, yet evaluating and comparing PHI de-identification models typically depends on costly, small-scale expert annotations. We present TEAM-PHI, a multi-agent evaluation and selection framework that uses large language models (LLMs) to automatically measure de-identification quality and select the best-performing model without heavy reliance on gold labels. TEAM-PHI deploys multiple Evaluation Agents, each independently judging the correctness of PHI extractions and outputting structured metrics. Their results are then consolidated through an LLM-based majority voting mechanism that integrates diverse evaluator perspectives into a single, stable, and reproducible ranking. Experiments on a real-world clinical note corpus demonstrate that TEAM-PHI produces consistent and accurate rankings: despite variation across individual evaluators, LLM-based voting reliably converges on the same top-performing systems. Further comparison with ground-truth annotations and human evaluation confirms that the framework's automated rankings closely match supervised evaluation. By combining independent evaluation agents with LLM majority voting, TEAM-PHI offers a practical, secure, and cost-effective solution for automatic evaluation and best-model selection in PHI de-identification, even when ground-truth labels are limited.

cs.AI↗

arXiv2025

Large Language Model Empowered Privacy-Protected Framework for PHI Annotation in Clinical Notes

The de-identification of private information in medical data is a crucial process to mitigate the risk of confidentiality breaches, particularly when patient personal details are not adequately removed before the release of medical records. Although rule-based and learning-based methods have been proposed, they often struggle with limited generalizability and require substantial amounts of annotated data for effective performance. Recent advancements in large language models (LLMs) have shown significant promise in addressing these issues due to their superior language comprehension capabilities. However, LLMs present challenges, including potential privacy risks when using commercial LLM APIs and high computational costs for deploying open-source LLMs locally. In this work, we introduce LPPA, an LLM-empowered Privacy-Protected PHI Annotation framework for clinical notes, targeting the English language. By fine-tuning LLMs locally with synthetic notes, LPPA ensures strong privacy protection and high PHI annotation accuracy. Extensive experiments demonstrate LPPA's effectiveness in accurately de-identifying private information, offering a scalable and efficient solution for enhancing patient privacy protection.

cs.CR↗

arXiv2024

GraphNarrator: Generating Textual Explanations for Graph Neural Networks

Graph representation learning has garnered significant attention due to its broad applications in various domains, such as recommendation systems and social network analysis. Despite advancements in graph learning methods, challenges still remain in explainability when graphs are associated with semantic features. In this paper, we present GraphNarrator, the first method designed to generate natural language explanations for Graph Neural Networks. GraphNarrator employs a generative language model that maps input-output pairs to explanations reflecting the model's decision-making process. To address the lack of ground truth explanations to train the model, we propose first generating pseudo-labels that capture the model's decisions from saliency-based explanations, then using Expert Iteration to iteratively train the pseudo-label generator based on training objectives on explanation quality. The high-quality pseudo-labels are finally utilized to train an end-to-end explanation generator model. Extensive experiments are conducted to demonstrate the effectiveness of GraphNarrator in producing faithful, concise, and human-preferred natural language explanations.

cs.LG↗