arXiv subjects

Hua Xu

Publications and source records attributed to Hua Xu.

At least 37 records · Page 2Linked to original sources

arXiv2026

A NISQ-Aware Hybrid Quantum-Classical Framework for Scalable Combinatorial Optimization

Scalable combinatorial optimization under resource-constrained quantum hardware remains a fundamental challenge in the Noisy Intermediate-Scale Quantum (NISQ) era, due to the mismatch between exponentially growing solution spaces and limited quantum computational capacity. In this work, we propose a NISQ-aware hybrid quantum-classical optimization framework that reformulates large-scale combinatorial optimization as a resource-bounded distribution evolution process. Instead of directly optimizing individual solutions, the proposed framework operates on a probabilistic representation of the solution space, enabling efficient exploration under hardware constraints. Specifically, large problem instances are decomposed into qubit-compatible subproblems via clustering-based decomposition, ensuring resource-bounded optimization. Within each subproblem, a quantum genetic algorithm evolves the solution distribution, while periodically embedded amplitude amplification acts as a controlled quantum enhancement mechanism that accelerates convergence without increasing circuit depth. A classical refinement stage ensures global solution consistency. Extensive experiments on benchmark and synthetic datasets demonstrate that the proposed framework consistently outperforms classical and quantum-inspired baselines, with performance gains that become more pronounced as problem scale increases. This scale-dependent behavior indicates that scalability is achieved through structured decomposition rather than increased quantum complexity. Noise simulations further confirm robustness under realistic NISQ conditions, and ablation studies validate that both quantum evolutionary search and amplitude amplification contribute significantly to performance improvements.

quant-ph↗

arXiv2026

IRIS: time-structured manifold projections

High-dimensional biomedical data, such as cell-by-gene matrices, are increasingly generated temporally. However, Manifold Learning algorithms, like t-SNE and UMAP, cannot incorporate time-ordering in their layouts, obfuscating the dynamics of cell types or other classes. As a solution, we present IRIS, a new Manifold Learning algorithm that structures layouts both chronologically and by manifold topology. IRIS can visualize a wide range of dynamic biomedical data, including scRNA-seq, comparative metagenomics, and literature.

cs.LG↗

arXiv2026

TRACE: Temporal Routing with Autoregressive Cross-channel Experts for EEG Representation Learning

Learning transferable representations for electroencephalography (EEG) remains challenging because EEG signals are inherently multi-channel and non-stationary. Channels observed at the same time provide coupled measurements of neural activity, while the relevant temporal dynamics vary across contexts. This structure is poorly matched by architectures that apply uniform computation across time or route each channel patch independently. To this end, we propose TRACE, an autoregressive EEG pre-training framework that predicts future EEG patches from causal context while performing temporally adaptive and cross-channel coherent computation. At each temporal step, TRACE derives an expert routing decision from the causal cross-channel history and applies it jointly to all channels at that step. This preserves instantaneous cross-channel coherence while allowing different temporal regimes to activate different computation. Since routing is defined over the available channel set and causal temporal context, TRACE is compatible with heterogeneous pre-training across corpora with different channel counts, montages, sequence lengths, and recording domains. Across eight downstream EEG benchmarks, TRACE is evaluated in both settings: when downstream domains are seen only as unlabeled pre-training data and when downstream datasets are completely unseen during pre-training. It obtains the best results on several benchmarks while remaining competitive on motor imagery and clinical event classification tasks, with ablations supporting the importance of cross-channel temporal routing.

cs.LG↗

arXiv2026

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.

cs.AI↗

arXiv2026

Foundation Models to Unlock Real-World Evidence from Nationwide Medical Claims

Evidence derived from large-scale real-world data (RWD) is increasingly informing regulatory evaluation and healthcare decision-making. Administrative claims provide population-scale, longitudinal records of healthcare utilization, expenditure, and detailed coding of diagnoses, procedures, and medications, yet their potential as a substrate for healthcare foundation models remains largely unexplored. Here we present ReClaim, a generative transformer trained from scratch on 43.8 billion medical events from more than 200 million enrollees in the MarketScan claims data spanning 2008-2022. ReClaim models longitudinal trajectories across diagnoses, procedures, medications, and expenditure, and was scaled to 140 million, 700 million, and 1.7 billion parameters. Across over 1,000 disease-onset prediction tasks, ReClaim achieved a mean AUC of 75.6%, substantially outperforming disease-specific LightGBM (66.3%) and the transformer-based Delphi model (69.4%), with the largest gains for rare diseases. These advantages held across retrospective and prospective evaluations and in external validation on two independent datasets. Performance improved monotonically with scale, and post-training added 13.8 percentage points over pre-training alone. Beyond disease prediction, ReClaim captured financial outcomes and improved real-world evidence (RWE) analyses: for healthcare expenditure forecasting it increased explained variance from 0.28 to 0.37 relative to LightGBM, and in a target trial emulation it reduced systematic bias by 72% on average relative to Delphi. Together, these results establish administrative claims as a scalable substrate for healthcare foundation models and show that learned representations generalize across time periods and data sources, supporting disease surveillance, expenditure forecasting, and RWE generation.

cs.AI↗

arXiv2026

Quantum-Enhanced Recurrent Neural Networks via Variational Quantum Gating for Battery State of Health Prediction

Accurate state-of-health (SOH) estimation for lithium-ion batteries remains a challenging problem due to complex electrochemical degradation mechanisms and long-range temporal dependencies. In this work, we propose a quantum-enhanced recurrent framework, termed QLSTM, in which variational quantum circuits are directly embedded into the gating mechanisms of long short-term memory networks. By replacing classical affine transformations with parameterized unitary operations, the proposed model introduces structured nonlinear transformations into the recurrent state-transition process. Extensive experiments on multiple benchmark battery datasets demonstrate that QLSTM consistently outperforms classical sequence models in both predictive accuracy and robustness, achieving significant reductions in mean absolute error (MAE), with improvements on the order of 20% compared with classical LSTM baselines. Ablation studies further confirm that these improvements arise primarily from quantum-enhanced gating rather than input-level transformations. Additional analyses on qubit scaling and noise robustness reveal that model performance is governed by a balance between expressive capacity and trainability. These results provide empirical evidence that embedding quantum computational primitives within recurrent architectures offers a structurally grounded approach to improving sequence modeling capability. The proposed framework establishes a new design paradigm for integrating quantum operators into temporal learning models, with potential applications in complex dynamical system prediction tasks.

quant-ph↗

arXiv2026

Advancing AI Research Assistants with Expert-Involved Learning

Large language models (LLMs) and large multimodal models (LMMs) promise to accelerate biomedical discovery, yet their reliability remains unclear. We introduce ARIEL (AI Research Assistant for Expert-in-the-Loop Learning), an open-source evaluation and optimization framework that pairs a curated multimodal biomedical corpus with expert-vetted tasks to probe two capabilities: full-length article summarization and fine-grained figure interpretation. Using uniform protocols and blinded PhD-level evaluation, we find that state-of-the-art models generate fluent but incomplete summaries, whereas LMMs struggle with detailed visual reasoning. We later observe that prompt engineering and lightweight fine-tuning substantially improve textual coverage, and a compute-scaled inference strategy enhances visual question answering. We build an ARIEL agent that integrates textual and visual cues, and we show it can propose testable mechanistic hypotheses. ARIEL delineates current strengths and limitations of foundation models, and provides a reproducible platform for advancing trustworthy AI in biomedicine.

cs.AI↗

arXiv2026

TeamPath: Building MultiModal Pathology Experts with Reasoning AI Copilots

Advances in AI have introduced several strong models in computational pathology to usher it into the era of multi-modal diagnosis, analysis, and interpretation. However, the current pathology-specific visual language models still lack capacities in making the diagnosis with rigorous reasoning paths as well as handling divergent tasks, and thus, challenges of building AI Copilots for real scenarios still exist. Here we introduce TeamPath, an AI system powered by reinforcement learning and router-enhanced solutions based on large-scale histopathology multimodal datasets, to work as a virtual assistant for expert-level disease diagnosis, patch-level information summarization, and cross-modality generation to integrate transcriptomic information for clinical usage. We also collaborate with pathologists from Yale School of Medicine to demonstrate that TeamPath can assist them in working more efficiently by identifying and correcting expert conclusions and reasoning paths. We also discuss the human evaluation results to support the reasoning quality from TeamPath. Overall, TeamPath can flexibly choose the best settings according to the needs, and serve as an innovative and reliable system for information communication across different modalities and experts.

q-bio.QM↗

arXiv2026

Evolutionary Multimodal Reasoning via Hierarchical Semantic Representation for Intent Recognition

Multimodal intent recognition aims to infer human intents by jointly modeling various modalities, playing a pivotal role in real-world dialogue systems. However, current methods struggle to model hierarchical semantics underlying complex intents and lack the capacity for self-evolving reasoning over multimodal representations. To address these issues, we propose HIER, a novel method that integrates HIerarchical semantic representation with Evolutionary Reasoning based on Multimodal Large Language Model (MLLM). Inspired by human cognition, HIER introduces a structured reasoning paradigm that organizes multimodal semantics into three progressively abstracted levels. It starts with modality-specific tokens capturing localized semantic cues, which are then clustered via a label-guided strategy to form mid-level semantic concepts. To capture higher-order structure, inter-concept relations are selected using JS divergence scores to highlight salient dependencies across concepts. These hierarchical representations are then injected into MLLM via CoT-driven prompting, enabling step-wise reasoning. Besides, HIER utilizes a self-evolution mechanism that refines semantic representations through MLLM feedback, allowing dynamic adaptation during inference. Experiments on three challenging benchmarks show that HIER consistently outperforms state-of-the-art methods and MLLMs with 1-3% gains across all metrics. Code and more results are available at https://github.com/thuiar/HIER.

cs.MM↗

arXiv2026

An artificial intelligence framework for end-to-end rare disease phenotyping from clinical notes using large language models

Phenotyping is fundamental to rare disease diagnosis, but manual curation of structured phenotypes from clinical notes is labor-intensive and difficult to scale. Existing artificial intelligence approaches typically optimize individual components of phenotyping but do not operationalize the full clinical workflow of extracting features from clinical text, standardizing them to Human Phenotype Ontology (HPO) terms, and prioritizing diagnostically informative HPO terms. We developed RARE-PHENIX, an end-to-end AI framework for rare disease phenotyping that integrates large language model-based phenotype extraction, ontology-grounded standardization to HPO terms, and supervised ranking of diagnostically informative phenotypes. We trained RARE-PHENIX using data from 2,671 patients across 11 Undiagnosed Diseases Network clinical sites, and externally validated it on 16,357 real-world clinical notes from Vanderbilt University Medical Center. Using clinician-curated HPO terms as the gold standard, RARE-PHENIX consistently outperformed a state-of-the-art deep learning baseline (PhenoBERT) across ontology-based similarity and precision-recall-F1 metrics in end-to-end evaluation (i.e., ontology-based similarity of 0.70 vs. 0.58). Ablation analyses demonstrated performance improvements with the addition of each module in RARE-PHENIX (extraction, standardization, and prioritization), supporting the value of modeling the full clinical phenotyping workflow. By modeling phenotyping as a clinically aligned workflow rather than a single extraction task, RARE-PHENIX provides structured, ranked phenotypes that are more concordant with clinician curation and has the potential to support human-in-the-loop rare disease diagnosis in real-world settings.

cs.AI↗

arXiv2026

High-Throughput In-Situ Fabrication of Fibrous Membranes Enables Scalable Passive Radiative Cooling

Deploying fibrous membranes for passive daytime radiative cooling (PDRC) on large and irregular surfaces is highly desirable but remains challenging, owing to the slow deposition rates and the need for electrically conductive substrates in conventional electrospinning. Here, we demonstrate a high-throughput in-situ strategy for fabricating nanocomposite PDRC fibrous membranes via solution blow spinning. This method achieves deposition rates 8-12 times faster than electrospinning and can be applied directly onto nonplanar, nonconductive objects. The resulting membranes, composed of styrene-ethylene-butylene-styrene (SEBS) fibers embedded with Y2O3 nanoparticles, achieve sub-ambient cooling of up to 7.0 °C outdoors, effectively delaying ice melting. Moreover, they are fully recyclable through simple cleaning, dissolution, and reprocessing. This scalable and sustainable fabrication route provides a versatile and practical platform for integrating PDRC fibrous membranes across diverse surfaces, paving the way toward real-world thermal management applications.

physics.optics↗

arXiv2026

MedViz: An Agent-based, Visual-guided Research Assistant for Navigating Biomedical Literature

Biomedical researchers face increasing challenges in navigating millions of publications in diverse domains. Traditional search engines typically return articles as ranked text lists, offering little support for global exploration or in-depth analysis. Although recent advances in generative AI and large language models have shown promise in tasks such as summarization, extraction, and question answering, their dialog-based implementations are poorly integrated with literature search workflows. To address this gap, we introduce MedViz, a visual analytics system that integrates multiple AI agents with interactive visualization to support the exploration of the large-scale biomedical literature. MedViz combines a semantic map of millions of articles with agent-driven functions for querying, summarizing, and hypothesis generation, allowing researchers to iteratively refine questions, identify trends, and uncover hidden connections. By bridging intelligent agents with interactive visualization, MedViz transforms biomedical literature search into a dynamic, exploratory process that accelerates knowledge discovery.

cs.IR↗

arXiv2026

ctELM: Decoding and Manipulating Embeddings of Clinical Trials with Embedding Language Models

Text embeddings have become an essential part of a variety of language applications. However, methods for interpreting, exploring and reversing embedding spaces are limited, reducing transparency and precluding potentially valuable generative use cases. In this work, we align Large Language Models to embeddings of clinical trials using the recently reported Embedding Language Model (ELM) method. We develop an open-source, domain-agnostic ELM architecture and training framework, design training tasks for clinical trials, and introduce an expert-validated synthetic dataset. We then train a series of ELMs exploring the impact of tasks and training regimes. Our final model, ctELM, can accurately describe and compare unseen clinical trials from embeddings alone and produce plausible clinical trials from novel vectors. We further show that generated trial abstracts are responsive to moving embeddings along concept vectors for age and sex of study subjects. Our public ELM implementation and experimental results will aid the alignment of Large Language Models to embedding spaces in the biomedical domain and beyond.

cs.CL↗

arXiv2026

BioPulse-QA: A Dynamic Biomedical Question-Answering Benchmark for Evaluating Factuality, Robustness, and Bias in Large Language Models

Objective: Large language models (LLMs) are increasingly applied in biomedical settings, and existing benchmark datasets have played an important role in supporting model development and evaluation. However, these benchmarks often have limitations. Many rely on static or outdated datasets that fail to capture the dynamic, context-rich, and high-stakes nature of biomedical knowledge. They also carry increasing risk of data leakage due to overlap with model pretraining corpora and often overlook critical dimensions such as robustness to linguistic variation and potential demographic biases. Materials and Methods: To address these gaps, we introduce BioPulse-QA, a benchmark that evaluates LLMs on answering questions from newly published biomedical documents including drug labels, trial protocols, and clinical guidelines. BioPulse-QA includes 2,280 expert-verified question answering (QA) pairs and perturbed variants, covering both extractive and abstractive formats. We evaluate four LLMs - GPT-4o, GPT-o1, Gemini-2.0-Flash, and LLaMA-3.1 8B Instruct - released prior to the publication dates of the benchmark documents. Results: GPT-o1 achieves the highest relaxed F1 score (0.92), followed by Gemini-2.0-Flash (0.90) on drug labels. Clinical trials are the most challenging source, with extractive F1 scores as low as 0.36. Discussion and Conclusion: Performance differences are larger for paraphrasing than for typographical errors, while bias testing shows negligible differences. BioPulse-QA provides a scalable and clinically relevant framework for evaluating biomedical LLMs.

cs.CL↗

arXiv2026

EHRNavigator: A Multi-Agent System for Patient-Level Clinical Question Answering over Heterogeneous Electronic Health Records

Clinical decision-making increasingly relies on timely and context-aware access to patient information within Electronic Health Records (EHRs), yet most existing natural language question-answering (QA) systems are evaluated solely on benchmark datasets, limiting their practical relevance. To overcome this limitation, we introduce EHRNavigator, a multi-agent framework that harnesses AI agents to perform patient-level question answering across heterogeneous and multimodal EHR data. We assessed its performance using both public benchmark and institutional datasets under realistic hospital conditions characterized by diverse schemas, temporal reasoning demands, and multimodal evidence integration. Through quantitative evaluation and clinician-validated chart review, EHRNavigator demonstrated strong generalization, achieving 86% accuracy on real-world cases while maintaining clinically acceptable response times. Overall, these findings confirm that EHRNavigator effectively bridges the gap between benchmark evaluation and clinical deployment, offering a robust, adaptive, and efficient solution for real-world EHR question answering.

cs.CL↗

arXiv2025

PDA in Action: Ten Principles for High-Quality Multi-Site Clinical Evidence Generation

Background: Distributed Research Networks (DRNs) offer significant opportunities for collaborative multi-site research and have significantly advanced healthcare research based on clinical observational data. However, generating high-quality real-world evidence using fit-for-use data from multi-site studies faces important challenges, including biases associated with various types of heterogeneity within and across sites and data sharing difficulties. Over the last ten years, Privacy-Preserving Distributed Algorithms (PDA) have been developed and utilized in numerous national and international real-world studies spanning diverse domains, from comparative effectiveness research, target trial emulation, to healthcare delivery, policy evaluation, and system performance assessment. Despite these advances, there remains a lack of comprehensive and clear guiding principles for generating high-quality real-world evidence through collaborative studies leveraging the methods under PDA. Objective: The paper aims to establish ten principles of best practice for conducting high-quality multi-site studies using PDA. These principles cover all phases of research, including study preparation, protocol development, analysis, and final reporting. Discussion: The ten principles for conducting a PDA study outline a principled, efficient, and transparent framework for employing distributed learning algorithms within DRNs to generate reliable and reproducible real-world evidence.

cs.CY↗

arXiv2025

LitFM: A Retrieval Augmented Structure-aware Foundation Model For Citation Graphs

With the advent of large language models (LLMs), managing scientific literature via LLMs has become a promising direction of research. However, existing approaches often overlook the rich structural and semantic relevance among scientific literature, limiting their ability to discern the relationships between pieces of scientific knowledge, and suffer from various types of hallucinations. These methods also focus narrowly on individual downstream tasks, limiting their applicability across use cases. Here we propose LitFM, the first literature foundation model designed for a wide variety of practical downstream tasks on domain-specific literature, with a focus on citation information. At its core, LitFM contains a novel graph retriever to integrate graph structure by navigating citation graphs and extracting relevant literature, thereby enhancing model reliability. LitFM also leverages a knowledge-infused LLM, fine-tuned through a well-developed instruction paradigm. It enables LitFM to extract domain-specific knowledge from literature and reason relationships among them. By integrating citation graphs during both training and inference, LitFM can generalize to unseen papers and accurately assess their relevance within existing literature. Additionally, we introduce new large-scale literature citation benchmark datasets on three academic fields, featuring sentence-level citation information and local context. Extensive experiments validate the superiority of LitFM, achieving 28.1% improvement on retrieval task in precision, and an average improvement of 7.52% over state-of-the-art across six downstream literature-related tasks

cs.SI↗

arXiv2025

MAC-SLU: Multi-Intent Automotive Cabin Spoken Language Understanding Benchmark

Spoken Language Understanding (SLU), which aims to extract user semantics to execute downstream tasks, is a crucial component of task-oriented dialog systems. Existing SLU datasets generally lack sufficient diversity and complexity, and there is an absence of a unified benchmark for the latest Large Language Models (LLMs) and Large Audio Language Models (LALMs). This work introduces MAC-SLU, a novel Multi-Intent Automotive Cabin Spoken Language Understanding Dataset, which increases the difficulty of the SLU task by incorporating authentic and complex multi-intent data. Based on MAC-SLU, we conducted a comprehensive benchmark of leading open-source LLMs and LALMs, covering methods like in-context learning, supervised fine-tuning (SFT), and end-to-end (E2E) and pipeline paradigms. Our experiments show that while LLMs and LALMs have the potential to complete SLU tasks through in-context learning, their performance still lags significantly behind SFT. Meanwhile, E2E LALMs demonstrate performance comparable to pipeline approaches and effectively avoid error propagation from speech recognition. Code\footnote{https://github.com/Gatsby-web/MAC\_SLU} and datasets\footnote{huggingface.co/datasets/Gatsby1984/MAC\_SLU} are released publicly.

cs.CL↗