Researcher profile

Weihao Xuan

Weihao Xuan contributes to research discovery and scholarly infrastructure.

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Computation and Language Artificial Intelligence Computational Engineering, Finance, and Science Genomics Human-Computer Interaction Machine Learning

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preprint2026arXiv

A Versatile AI Agent for Rare Disease Diagnosis and Risk Gene Prioritization

Accurate and timely diagnosis is essential for effective treatment, particularly in the context of rare diseases. However, current diagnostic workflows often lead to prolonged assessment times and low accuracy. To address these limitations, we introduce Hygieia, a multi-modal AI agent system designed to support precision disease diagnosis by integrating diverse data sources, including phenotypic features, genetic profiles, and clinical records. Hygieia features a router-based and knowledge-enhanced framework that mitigates hallucination and tailors diagnostic strategies to different disease categories. Notably, it prioritizes risk-related genomic factors for rare diseases and provides confidence scores to assist clinical decision-making. We conducted a comprehensive evaluation demonstrating that Hygieia achieves state-of-the-art performance across multiple diagnostic benchmarks. In collaboration with clinical experts from Yale School of Medicine and Duke-NUS Medical School, we further validated its practical utility by showing (1) Hygieia's superior diagnostic performance compared to physicians with an improvement from 12%-60% and (2) its effectiveness in assisting clinicians with medical records for handling real-world cases. Our findings indicate that Hygieia not only enhances diagnostic accuracy and interpretability but also significantly reduces clinician workload, highlighting its potential as a valuable tool in clinical decision support systems.

preprint2026arXiv

Can LLM Agents Respond to Disasters? Benchmarking Heterogeneous Geospatial Reasoning in Emergency Operations

Operational disaster response goes beyond damage assessment, requiring responders to integrate multi-sensor signals, reason over road networks, populations and key facilities, plan evacuations, and produce actionable reports. However, prior work largely isolates remote-sensing perception or evaluates generic tool use, leaving the end-to-end workflows of emergency operations underexplored. In this paper, we introduce Disaster Operational Response Agent benchmark (DORA), the first agentic benchmark for end-to-end disaster response: 515 expert-authored tasks across 45 real-world disaster events spanning 10 types, paired with expert-verified, replayable gold trajectories totaling 3,500 tool-call steps. Tasks span five dimensions that cover the operational disaster-response pipeline: disaster perception, spatial relational analysis, rescue and evacuation planning, temporal evolution reasoning, and multi-modal report synthesis. Agents compose calls from a 108-tool MCP library over heterogeneous geospatial data: optical, SAR, and multi-spectral imagery across single-, bi-, and multi-temporal sequences (0.015-10m GSD), complemented by elevation and social vector layers. We comprehensively evaluate 13 frontier LLMs on our benchmark, revealing three persistent challenges: 1) disaster-domain grounding exposes unique failure modes (damage-semantic grounding, sensor-modality mismatch, and disaster-pipeline composition); 2) agents are doubly bottlenecked by tool selection and argument grounding, where gold tool-order hints improve accuracy by only 1.08-4.40%, and alternative scaffolds yield at most a 3.24% gain; 3) compositional fragility scales with trajectory length, the agent-to-gold gap widening from 7% to 56% on long pipelines. DORA establishes a rigorous testbed for operationally reliable disaster-response agents.

preprint2026arXiv

MixSD: Mixed Contextual Self-Distillation for Knowledge Injection

Supervised fine-tuning (SFT) is widely used to inject new knowledge into language models, but it often degrades pretrained capabilities such as reasoning and general-domain performance. We argue this forgetting arises because fine-tuning targets from humans or external systems diverge from the model's autoregressive distribution, forcing the optimizer to imitate low-probability token sequences. To address this problem, we propose MixSD, a simple external-teacher-free method for distribution-aligned knowledge injection. Instead of training on fixed targets, MixSD constructs supervision dynamically by mixing tokens from two conditionals of the base model itself: an expert conditional that observes the injected fact in context, and a naive conditional that reflects the model's original prior. The resulting supervision sequences preserve the factual learning signal while remaining substantially closer to the base model's distribution. We evaluate MixSD on two synthetic corpora that we construct to study factual recall and arithmetic function acquisition in a controlled setting, together with established benchmarks for open-domain factual question answering and knowledge editing. Across multiple model scales and settings, MixSD consistently achieves a better memorization-retention trade-off compared to SFT and on-policy self distillation baselines, retaining up to 100% of the base model's held-out capability while maintaining near-perfect training accuracy, whereas standard SFT retains as little as 1%. We further show that MixSD produces substantially lower-NLL supervision targets under the base model and reduces harmful movement along Fisher-sensitive parameter directions. These results suggest that aligning supervision with the model's native generation distribution is a simple and effective principle for knowledge injection that mitigates catastrophic forgetting.

preprint2026arXiv

Proteo-R1: Reasoning Foundation Models for De Novo Protein Design

Deep learning in \emph{de novo} protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries without explicitly reasoning about which residues or interactions are functionally essential. As a result, design decisions are entangled with continuous sampling dynamics, limiting interpretability, controllability, and systematic reuse of biochemical knowledge. We introduce \textbf{Proteo-R1}, a reasoning-guided protein design framework that explicitly decouples \emph{molecular understanding} from \emph{geometric generation}. Proteo-R1 adopts a dual-expert architecture in which a multimodal large language model (MLLM) serves as an \emph{understanding expert}, analyzing protein sequences, structures, and textual context to identify key functional residues that govern binding and specificity. These residue-level decisions are then passed as hard constraints to a separate diffusion-based \emph{generation expert}, which performs conditional co-design while respecting the fixed interaction anchors. This factorization mirrors how human experts approach molecular engineering: first, reasoning about critical interactions, then optimizing geometry subject to those constraints. By operationalizing reasoning as explicit residue-level commitments rather than latent textual guidance, Proteo-R1 achieves stable, interpretable, and modular integration of LLM reasoning with state-of-the-art geometric generative models. Code, data, and demos are available at https://smiles724.github.io/r1/.

preprint2026arXiv

The Confidence Dichotomy: Analyzing and Mitigating Miscalibration in Tool-Use Agents

Autonomous agents based on large language models (LLMs) are rapidly evolving to handle multi-turn tasks, but ensuring their trustworthiness remains a critical challenge. A fundamental pillar of this trustworthiness is calibration, which refers to an agent's ability to express confidence that reliably reflects its actual performance. While calibration is well-established for static models, its dynamics in tool-integrated agentic workflows remain underexplored. In this work, we systematically investigate verbalized calibration in tool-use agents, revealing a fundamental confidence dichotomy driven by tool type. Specifically, our pilot study identifies that evidence tools (e.g., web search) systematically induce severe overconfidence due to inherent noise in retrieved information, while verification tools (e.g., code interpreters) can ground reasoning through deterministic feedback and mitigate miscalibration. To robustly improve calibration across tool types, we propose a reinforcement learning (RL) fine-tuning framework that jointly optimizes task accuracy and calibration, supported by a holistic benchmark of reward designs. We demonstrate that our trained agents not only achieve superior calibration but also exhibit robust generalization from local training environments to noisy web settings and to distinct domains such as mathematical reasoning. Our results highlight the necessity of domain-specific calibration strategies for tool-use agents. More broadly, this work establishes a foundation for building self-aware agents that can reliably communicate uncertainty in high-stakes, real-world deployments.

preprint2026arXiv

The Pragmatic Mind of Machines: Tracing the Emergence of Pragmatic Competence in Large Language Models

Current large language models (LLMs) have demonstrated emerging capabilities in social intelligence tasks, including implicature resolution and theory-of-mind reasoning, both of which require substantial pragmatic understanding. However, how LLMs acquire this pragmatic competence throughout the training process remains poorly understood. In this work, we introduce ALTPRAG, a dataset grounded in the pragmatic concept of alternatives, to evaluate whether LLMs at different training stages can accurately infer nuanced speaker intentions. Each instance pairs two equally plausible yet pragmatically divergent continuations and requires the model to (i) infer the speaker's intended meaning and (ii) explain when and why a speaker would choose one utterance over its alternative, thus directly probing pragmatic competence through contrastive reasoning. We systematically evaluate 22 LLMs across 3 key training stages: after pre-training, supervised fine-tuning (SFT), and preference optimization, to examine the development of pragmatic competence. Our results show that even base models exhibit notable sensitivity to pragmatic cues, which improves consistently with increases in model and data scale. Additionally, SFT and RLHF contribute further gains, particularly in cognitive-pragmatic scenarios. These findings highlight pragmatic competence as an emergent and compositional property of LLM training and offer new insights for aligning models with human communicative norms.

preprint2026arXiv

Toward Global Large Language Models in Medicine

Despite continuous advances in medical technology, the global distribution of health care resources remains uneven. The development of large language models (LLMs) has transformed the landscape of medicine and holds promise for improving health care quality and expanding access to medical information globally. However, existing LLMs are primarily trained on high-resource languages, limiting their applicability in global medical scenarios. To address this gap, we constructed GlobMed, a large multilingual medical dataset, containing over 500,000 entries spanning 12 languages, including four low-resource languages. Building on this, we established GlobMed-Bench, which systematically assesses 56 state-of-the-art proprietary and open-weight LLMs across multiple multilingual medical tasks, revealing significant performance disparities across languages, particularly for low-resource languages. Additionally, we introduced GlobMed-LLMs, a suite of multilingual medical LLMs trained on GlobMed, with parameters ranging from 1.7B to 8B. GlobMed-LLMs achieved an average performance improvement of over 40% relative to baseline models, with a more than threefold increase in performance on low-resource languages. Together, these resources provide an important foundation for advancing the equitable development and application of LLMs globally, enabling broader language communities to benefit from technological advances.

preprint2026arXiv

Towards Valid Student Simulation with Large Language Models

This paper presents a conceptual and methodological framework for large language model (LLM) based student simulation in educational settings. The authors identify a core failure mode, termed the "competence paradox" in which broadly capable LLMs are asked to emulate partially knowledgeable learners, leading to unrealistic error patterns and learning dynamics. To address this, the paper reframes student simulation as a constrained generation problem governed by an explicit Epistemic State Specification (ESS), which defines what a simulated learner can access, how errors are structured, and how learner state evolves over time. The work further introduces a Goal-by-Environment framework to situate simulated student systems according to behavioral objectives and deployment contexts. Rather than proposing a new system or benchmark, the paper synthesizes prior literature, formalizes key design dimensions, and articulates open challenges related to validity, evaluation, and ethical risks. Overall, the paper argues for epistemic fidelity over surface realism as a prerequisite for using LLM-based simulated students as reliable scientific and pedagogical instruments.

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