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Jiaying Lu

Publications and source records attributed to Jiaying Lu.

At least 19 recordsLinked to original sources

HiFi-BRep: High-Fidelity Latent Representation for Robust B-Rep Generation

Boundary representation (B-Rep) generation is a fundamental task in computer-aided design, yet the direct synthesis of high-fidelity and structurally valid B-Reps remains a major challenge. Existing deep generative methods suffer from two forms of brittleness: representation brittleness, caused by padding noise and feature contamination in the latent space, and generation brittleness, stemming from sequential error propagation and a train-inference mismatch due to non-differentiable validity enforcement. We propose HiFi-BRep, a novel framework that addresses these limitations through two synergistic contributions. First, a topology-aware encoder constructs a high-fidelity latent representation by eliminating padding via learnable queries and preventing feature contamination with topology-guided attention. Second, a single-stage decoder jointly predicts geometry and topology in parallel, embedding core manifold constraints as a differentiable learning objective. This design ensures mutual guidance between geometry and topology while avoiding cascaded errors. Extensive experiments show that HiFi-BRep significantly outperforms state-of-the-art methods in both structural validity and geometric fidelity, providing a robust solution for high-quality B-Rep synthesis. Code and models are publicly available at https://github.com/1nnoh/HiFi-BRep.

cs.CV

OmniMech: All-in-one Multimodal Mechanical Benchmark for 3D Reconstruction

Recent vision-language models (VLMs) can generate executable CAD programs from images, but existing methods mainly target coarse, general-purpose 3D objects and rarely address the fine-grained geometry and millimeter-level tolerances required in industrial mechanical design. We introduce OmniMech, the first million-scale benchmark for evaluating VLMs on executable CAD generation from industrial manufacturing data. OmniMech contains more than 251,000 fully dimensioned and toleranced 2D orthographic drawings, paired with native CAD models, multi-view renderings, mesh, STEP and B-rep representations, and rich semantic annotations. The benchmark includes four tasks: (1) parametric CAD program synthesis from engineering drawings; (2) diagram-to-3D reasoning for geometrically and structurally consistent reconstruction; (3) annotation-grounded reasoning over dimensions, symbols, feature callouts, and manufacturing constraints; and (4) tool-augmented agentic reasoning using visualization, measurement, CAD execution, and verification tools. Experiments show that current VLMs and CAD-specialized models still struggle with executable program synthesis, fine-grained 3D reconstruction, and reliable enforcement of dimensions and tolerances. We will release the benchmark data, evaluation code, and tool interfaces to support future research.

cs.CV

OmniRouting: A Semantic-Coupled Multimodal Benchmark for Constraint-Aware Spatial Reasoning in PCB Routing

Recent large language models (LLMs) have demonstrated remarkable progress in constraint-aware navigation, maze reasoning, and graph reasoning. However, their ability to reason about complex routing problems under strict geometric, topological, and electrical constraints remains largely unexplored, despite routing being one of the most challenging and critical stages of electronic design automation (EDA). To bridge this gap, we introduce OmniRouting, the first large-scale benchmark designed to evaluate LLMs on printed-circuit-board (PCB) routing reasoning under real-world industrial design-rule, manufacturability, and connectivity constraints. OmniRouting contains 1,681 industrial-grade schematic-coupled PCB designs, including board geometries, routable component placements by human engineers, footprints, pad locations, netlists, stackup information, and routing constraints. The benchmark comprises four tasks: (1) geometric routing reasoning, generating physically valid copper traces, vias, and layer assignments to connect circuit nets within constrained board regions; (2) design-rule-aware routing reasoning, producing routable layouts that satisfy clearance, trace-width, via, obstacle-avoidance, and board-boundary constraints; (3) electrical functionality reasoning, preserving schematic-specified connectivity while reasoning over net names and functional roles to produce electrically correct routing; and (4) tool-augmented agentic routing, leveraging external tools for tasks (1)-(3). Our results reveal substantial limitations of current LMMs in PCB routing, including weak path-planning capabilities, poor adherence to design-rule constraints, and inconsistent preservation of electrical functionality. We will open-source all benchmark data, evaluation code, and tool interfaces to facilitate future research.

cs.CV

BioMedJImpact: A Comprehensive Dataset and LLM Pipeline for AI Engagement and Scientific Impact Analysis of Biomedical Journals

Assessing journal impact is central to scholarly communication, yet existing resources rarely capture how collaboration and artificial intelligence (AI) research jointly shape venue prestige in biomedicine. We present BioMedJImpact, a large-scale, biomedical-oriented dataset built from 1.74 million PubMed Central articles across 2,744 journals. BioMedJImpact integrates bibliometric indicators, collaboration features, and an LLM-derived AI engagement rate, defined as the proportion of AI-related articles within each journal-year. Specifically, AI engagement rate is extracted through a reproducible three-stage LLM pipeline. We analyze how collaboration intensity and AI engagement rate jointly influence scientific impact across two temporal subsets (2016-2019, 2020-2023). Two main patterns emerge: journals with larger author teams tend to have higher citation impact, while AI engagement rate is positively associated with Impact Factor only in the 2019 subset. To validate the LLM pipeline for deriving the AI engagement rate, we conduct human evaluation, confirming substantial agreement in AI relevance detection and consistent subfield classification. Together, BioMedJImpact provides both a comprehensive dataset at the interface of biomedicine and AI and a validated framework for scalable, content-aware scientometric analysis. Code and dataset are available at https://github.com/JonathanWry/BioMedJImpact.

cs.IR

LLMBDC: Language Model for Biological Domains Oriented Clustering of Gene Ontology

Gene Ontology (GO) enrichment analysis is a foundational tool for translating large-scale genomic data into biological insights, but typically yields hundreds of redundant terms that obscure overarching themes. Existing summarization tools rely on fixed similarity metrics (REVIGO, GOSemSim, clusterProfiler::simplify()), gene-overlap measures (Metascape), or static hierarchy mappings (GO-slim), and therefore cannot incorporate biological context. Manual curation provides context-aware grouping but is subjective and labor-intensive. A scalable, context-aware framework is needed to cluster GO terms into interpretable higher-order biological domains. Here we present LLMBDC (Large Language Model for Biological Domains Oriented Clustering of Gene Ontology), a training-free framework that leverages zero-shot semantic reasoning of LLMs with confidence scoring to cluster GO terms into BioDomains using only ontology information at inference time. Benchmarked across Alzheimer's disease (AD) and Fragile X syndrome (FXS) against six baseline methods including SapBERT, LLMBDC achieved substantially higher precision, recall, and clustering performance. Against ground-truth annotations, LLMBDC improved ARI from 9.7% to 73.3% (AD) and from 15.7% to 66.6% (FXS) over REVIGO, with corresponding NMI gains from 59.9% to 73.4% (AD) and 66.0% to 79.5% (FXS). A Cauchy combination test further confirmed that aggregated BioDomains retained statistically significant functional signals. LLMBDC provides a scalable, reproducible, and interpretable route to context-aware, system-level interpretation of GO enrichment results while preserving biological specificity.

q-bio.GN

TCellAlign: Cross-study T-cell Populations Alignment with Nomenclature-Guided Multi-Agent Workflow

Cell type standardization plays a central role in integrating biological knowledge across single-cell studies. While standardized resources (e.g., Cell Ontology, Nomenclature Frameworks) provide unified vocabularies of cell populations, scientific publications and public datasets continue to use heterogeneous study-specific labels, making cross-study comparison difficult even when biologically equivalent cell populations are described. In this work, we are the first to formulate this challenge as an evidence-grounded cell population alignment problem and propose TCellAlign, a multi-agent framework that includes literature retrieval, information extraction, nomenclature-guided label alignment, and evidence-based adjudication. This modular design preserves the original terminology and supporting evidence reported by each study while producing standardized labels that can be compared across studies. We further construct a manually validated benchmark dataset linking study-specific labels, CZ CELLxGENE annotations, and standardized T-cell nomenclature across 44 manually curated, published studies (including over seven million cells) spanning four biological categories: healthy, cancer, infectious disease and inflammatory diseases. Across the evaluated tasks, TCellAlign achieves stronger semantic agreement than ontology-based baselines and maintains transcriptomic coherence with both open-source and closed-source large language models (LLM) backbones. By connecting literature, datasets, and expert's nomenclature, TCellAlign enables consistent interpretation of T-cell subtypes and states across studies, facilitating biological knowledge integration and the development of future foundation models built upon standardized cellular representations.

q-bio.QM

NutriMLLM: Multimodal Large Language Models for Dietary Micronutrient Analysis

Comprehensive estimation of dietary micronutrients from food images could improve clinical nutrition care, but training such models requires large multimodal datasets linking diverse foods to complete nutrient profiles. We first show that existing multimodal large language models (MLLMs), including leading proprietary models, are unreliable for this task. Across five model families and four independent evaluation benchmarks (ASA24, SNAPMe, FNDDS, and NutriBench), models frequently abstained or returned statistically implausible values. To address this gap without costly expert annotation, we repurposed a decade of population-scale 24-hour dietary recalls as structured prompts for text-to-image generation. This pipeline produced a synthetic corpus of about 1.1 million image-description-nutrient triplets, each pairing a generated food image with a complete 65-nutrient label. To our knowledge, this is the largest synthetic food-image corpus with comprehensive micronutrient annotation planned for public release upon publication. Fine-tuning Qwen3-VL (2B/4B/8B/30B) and GLM-4.6V-Flash on this corpus yielded NutriMLLM, the first family of vision-language models specialized for comprehensive dietary micronutrient estimation. We evaluate these models with a four-component framework that separately measures abstention, hallucination, overall usability, and per-nutrient numerical accuracy. On real food images, every NutriMLLM variant achieved near-complete coverage across all 65 nutrients, and the largest variant matched or exceeded proprietary baselines (GPT-5, Gemini 3, and Claude Sonnet 4.5) in accuracy on most nutrients. These results show that recall-driven synthetic supervision can make image-based comprehensive micronutrient estimation a tractable engineering problem and support dietary assessment, personalized nutrition guidance, and population-scale micronutrient surveillance.

cs.CV

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

LLM-MINE: Large Language Model based Alzheimer's Disease and Related Dementias Phenotypes Mining from Clinical Notes

Accurate extraction of Alzheimer's Disease and Related Dementias (ADRD) phenotypes from electronic health records (EHR) is critical for early-stage detection and disease staging. However, this information is usually embedded in unstructured textual data rather than tabular data, making it difficult to be extracted accurately. We therefore propose LLM-MINE, a Large Language Model-based phenotype mining framework for automatic extraction of ADRD phenotypes from clinical notes. Using two expert-defined phenotype lists, we evaluate the extracted phenotypes by examining their statistical significance across cohorts and their utility for unsupervised disease staging. Chi-square analyses confirm statistically significant phenotype differences across cohorts, with memory impairment being the strongest discriminator. Few-shot prompting with the combined phenotype lists achieves the best clustering performance (ARI=0.290, NMI=0.232), substantially outperforming biomedical NER and dictionary-based baselines. Our results demonstrate that LLM-based phenotype extraction is a promising tool for discovering clinically meaningful ADRD signals from unstructured notes.

cs.AI

ClinNoteAgents: An LLM Multi-Agent System for Predicting and Interpreting Heart Failure 30-Day Readmission from Clinical Notes

Heart failure (HF) is one of the leading causes of rehospitalization among older adults in the United States. Although clinical notes contain rich, detailed patient information and make up a large portion of electronic health records (EHRs), they remain underutilized for HF readmission risk analysis. Traditional computational models for HF readmission often rely on expert-crafted rules, medical thesauri, and ontologies to interpret clinical notes, which are typically written under time pressure and may contain misspellings, abbreviations, and domain-specific jargon. We present ClinNoteAgents, an LLM-based multi-agent framework that transforms free-text clinical notes into (1) structured representations of clinical and social risk factors for association analysis and (2) clinician-style abstractions for HF 30-day readmission prediction. We evaluate ClinNoteAgents on 3,544 notes from 2,065 patients (readmission rate=35.16%), demonstrating high extraction fidelity for clinical variables (conditional accuracy >= 90% for multiple vitals), key risk factor identification, and preservation of predictive signal despite 60 to 90% text reduction. By reducing reliance on structured fields and minimizing manual annotation and model training, ClinNoteAgents provides a scalable and interpretable approach to note-based HF readmission risk modeling in data-limited healthcare systems.

cs.AI

Knowledge Graph Augmented Large Language Models for Disease Prediction

Electronic health records (EHRs) enable strong clinical prediction, but explanations are often coarse and hard to use for patient-level decisions. We propose a knowledge graph (KG)-guided chain-of-thought (CoT) framework for visit-level disease prediction on MIMIC-III. We map ICD-9 codes to PrimeKG, mine disease-relevant nodes and paths, and use these paths to scaffold temporally consistent CoT rationales, retaining only samples whose conclusions match observed outcomes. We fine-tune lightweight instruction-tuned LLMs (LLaMA-3.1-Instruct-8B and Gemma-7B) on two small cohorts (400 and 1,000 index visits) across ten PrimeKG-mapped diseases. Our models outperform strong classical baselines, reaching AUROC 0.66-0.70 and macro-AUPR 0.40-0.47. Without additional training, the models transfer zero-shot to the CRADLE cohort, improving accuracy from 0.40-0.51 to 0.72-0.77. In a blinded clinician study, KG-guided CoT rationales are consistently preferred for clarity, relevance, and correctness. Code is available at: https://github.com/JonathanWry/KG-guided-LLM-pipeline

cs.AI

EnECG: Efficient Ensemble Learning for Electrocardiogram Multi-task Foundation Model

Electrocardiogram (ECG) analysis plays a vital role in the early detection, monitoring, and management of various cardiovascular conditions. While existing models have achieved notable success in ECG interpretation, they fail to leverage the interrelated nature of various cardiac abnormalities. Conversely, developing a specific model capable of extracting all relevant features for multiple ECG tasks remains a significant challenge. Large-scale foundation models, though powerful, are not typically pretrained on ECG data, making full re-training or fine-tuning computationally expensive. To address these challenges, we propose EnECG(Mixture of Experts-based Ensemble Learning for ECG Multi-tasks), an ensemble-based framework that integrates multiple specialized foundation models, each excelling in different aspects of ECG interpretation. Instead of relying on a single model or single task, EnECG leverages the strengths of multiple specialized models to tackle a variety of ECG-based tasks. To mitigate the high computational cost of full re-training or fine-tuning, we introduce a lightweight adaptation strategy: attaching dedicated output layers to each foundation model and applying Low-Rank Adaptation (LoRA) only to these newly added parameters. We then adopt a Mixture of Experts (MoE) mechanism to learn ensemble weights, effectively combining the complementary expertise of individual models. Our experimental results demonstrate that by minimizing the scope of fine-tuning, EnECG can help reduce computational and memory costs while maintaining the strong representational power of foundation models. This framework not only enhances feature extraction and predictive performance but also ensures practical efficiency for real-world clinical applications. The code is available at https://github.com/yuhaoxu99/EnECG.git.

cs.LG

An Electrocardiogram Multi-task Benchmark with Comprehensive Evaluations and Insightful Findings

In the process of patient diagnosis, non-invasive measurements are widely used due to their low risks and quick results. Electrocardiogram (ECG), as a non-invasive method to collect heart activities, is used to diagnose cardiac conditions. Analyzing the ECG typically requires domain expertise, which is a roadblock to applying artificial intelligence (AI) for healthcare. Through advances in self-supervised learning and foundation models, AI systems can now acquire and leverage domain knowledge without relying solely on human expertise. However, there is a lack of comprehensive analyses over the foundation models' performance on ECG. This study aims to answer the research question: "Are Foundation Models Useful for ECG Analysis?" To address it, we evaluate language/general time-series/ECG foundation models in comparison with time-series deep learning models. The experimental results show that general time-series/ECG foundation models achieve a top performance rate of 80%, indicating their effectiveness in ECG analysis. In-depth analyses and insights are provided along with comprehensive experimental results. This study highlights the limitations and potential of foundation models in advancing physiological waveform analysis. The data and code for this benchmark are publicly available at https://github.com/yuhaoxu99/ECGMultitasks-Benchmark.

cs.LG

BioMedJImpact: A Comprehensive Dataset and LLM Pipeline for AI Engagement and Scientific Impact Analysis of Biomedical Journals

Assessing journal impact is central to scholarly communication, yet existing open resources rarely capture how collaboration structures and artificial intelligence (AI) research jointly shape venue prestige in biomedicine. We present BioMedJImpact, a large-scale, biomedical-oriented dataset designed to advance journal-level analysis of scientific impact and AI engagement. Built from 1.74 million PubMed Central articles across 2,744 journals, BioMedJImpact integrates bibliometric indicators, collaboration features, and LLM-derived semantic indicators for AI engagement. Specifically, the AI engagement feature is extracted through a reproducible three-stage LLM pipeline that we propose. Using this dataset, we analyze how collaboration intensity and AI engagement jointly influence scientific impact across pre- and post-pandemic periods (2016-2019, 2020-2023). Two consistent trends emerge: journals with higher collaboration intensity, particularly those with larger and more diverse author teams, tend to achieve greater citation impact, and AI engagement has become an increasingly strong correlate of journal prestige, especially in quartile rankings. To further validate the three-stage LLM pipeline we proposed for deriving the AI engagement feature, we conduct human evaluation, confirming substantial agreement in AI relevance detection and consistent subfield classification. Together, these contributions demonstrate that BioMedJImpact serves as both a comprehensive dataset capturing the intersection of biomedicine and AI, and a validated methodological framework enabling scalable, content-aware scientometric analysis of scientific impact and innovation dynamics. Code is available at https://github.com/JonathanWry/BioMedJImpact.

cs.CL

Integrating Epigenetic and Phenotypic Features for Biological Age Estimation in Cancer Patients via Multimodal Learning

Biological age, which may be older or younger than chronological age due to factors such as genetic predisposition, environmental exposures, serves as a meaningful biomarker of aging processes and can inform risk stratification, treatment planning, and survivorship care in cancer patients. We propose EpiCAge, a multimodal framework that integrates epigenetic and phenotypic data to improve biological age prediction. Evaluated on eight internal and four external cancer cohorts, EpiCAge consistently outperforms existing epigenetic and phenotypic age clocks. Our analyses show that EpiCAge identifies biologically relevant markers, and its derived age acceleration is significantly associated with mortality risk. These results highlight EpiCAge as a promising multimodal machine learning tool for biological age assessment in oncology.

q-bio.GN

Generalist vs Specialist Time Series Foundation Models: Investigating Potential Emergent Behaviors in Assessing Human Health Using PPG Signals

Foundation models are large-scale machine learning models that are pre-trained on massive amounts of data and can be adapted for various downstream tasks. They have been extensively applied to tasks in Natural Language Processing and Computer Vision with models such as GPT, BERT, and CLIP. They are now also increasingly gaining attention in time-series analysis, particularly for physiological sensing. However, most time series foundation models are specialist models - with data in pre-training and testing of the same type, such as Electrocardiogram, Electroencephalogram, and Photoplethysmogram (PPG). Recent works, such as MOMENT, train a generalist time series foundation model with data from multiple domains, such as weather, traffic, and electricity. This paper aims to conduct a comprehensive benchmarking study to compare the performance of generalist and specialist models, with a focus on PPG signals. Through an extensive suite of total 51 tasks covering cardiac state assessment, laboratory value estimation, and cross-modal inference, we comprehensively evaluate both models across seven dimensions, including win score, average performance, feature quality, tuning gain, performance variance, transferability, and scalability. These metrics jointly capture not only the models' capability but also their adaptability, robustness, and efficiency under different fine-tuning strategies, providing a holistic understanding of their strengths and limitations for diverse downstream scenarios. In a full-tuning scenario, we demonstrate that the specialist model achieves a 27% higher win score. Finally, we provide further analysis on generalization, fairness, attention visualizations, and the importance of training data choice.

cs.LG

Longitudinal Progression Prediction of Alzheimer's Disease with Tabular Foundation Model

Alzheimer's disease is a progressive neurodegenerative disorder that remains challenging to predict due to its multifactorial etiology and the complexity of multimodal clinical data. Accurate forecasting of clinically relevant biomarkers, including diagnostic and quantitative measures, is essential for effective monitoring of disease progression. This work introduces L2C-TabPFN, a method that integrates a longitudinal-to-cross-sectional (L2C) transformation with a pre-trained Tabular Foundation Model (TabPFN) to predict Alzheimer's disease outcomes using the TADPOLE dataset. L2C-TabPFN converts sequential patient records into fixed-length feature vectors, enabling robust prediction of diagnosis, cognitive scores, and ventricular volume. Experimental results demonstrate that, while L2C-TabPFN achieves competitive performance on diagnostic and cognitive outcomes, it provides state-of-the-art results in ventricular volume prediction. This key imaging biomarker reflects neurodegeneration and progression in Alzheimer's disease. These findings highlight the potential of tabular foundational models for advancing longitudinal prediction of clinically relevant imaging markers in Alzheimer's disease.

cs.LG

Towards Synthesizing Normative Data for Cognitive Assessments Using Generative Multimodal Large Language Models

Cognitive assessments require normative data as essential benchmarks for evaluating individual performance. Hence, developing new cognitive tests based on novel image stimuli is challenging due to the lack of readily available normative data. Traditional data collection methods are costly, time-consuming, and infrequently updated, limiting their practical utility. Recent advancements in generative multimodal large language models (MLLMs) offer a new approach to generate synthetic normative data from existing cognitive test images. We investigated the feasibility of using MLLMs, specifically GPT-4o and GPT-4o-mini, to synthesize normative textual responses for established image-based cognitive assessments, such as the "Cookie Theft" picture description task. Two distinct prompting strategies-naive prompts with basic instructions and advanced prompts enriched with contextual guidance-were evaluated. Responses were analyzed using embeddings to assess their capacity to distinguish diagnostic groups and demographic variations. Performance metrics included BLEU, ROUGE, BERTScore, and an LLM-as-a-judge evaluation. Advanced prompting strategies produced synthetic responses that more effectively distinguished between diagnostic groups and captured demographic diversity compared to naive prompts. Superior models generated responses exhibiting higher realism and diversity. BERTScore emerged as the most reliable metric for contextual similarity assessment, while BLEU was less effective for evaluating creative outputs. The LLM-as-a-judge approach provided promising preliminary validation results. Our study demonstrates that generative multimodal LLMs, guided by refined prompting methods, can feasibly generate robust synthetic normative data for existing cognitive tests, thereby laying the groundwork for developing novel image-based cognitive assessments without the traditional limitations.

cs.LG