arXiv subjects

Runze Yan

Publications and source records attributed to Runze Yan.

At least 19 recordsLinked to original sources

arXiv2026

Benchmarking Generalist and Specialist Time-Series Foundation Models for PPG-Based Health Assessment

Time-series Foundation Models (FMs) are pretrained on either heterogeneous corpora or specific signal domains. Using Photoplethysmography (PPG) as a representative modality, we compare generalist time-series FMs, PPG-specialist FMs, and traditional machine learning (ML) baselines for PPG-based health assessment. We conduct a two-stage benchmark. First, we evaluate multiple FM families across 23 downstream evaluations (e.g., atrial fibrillation detection, vital-sign estimation). Second, we conduct a focused four-FM comparison (MOMENT, Chronos-2, GPT-PPG, MOMENT-PPG) at multiple model sizes on an expanded 51-task suite, under both frozen-backbone and full-model tuning, to study tuning strategy, model scaling, and cross-dataset transfer. The multi-model benchmark shows that PPG-specialist FMs achieve the strongest aggregate performance, but their advantage is not uniform: generalist FMs remain competitive on several tasks, and traditional ML baselines outperform FMs on selected clinical regression tasks. The focused analysis shows that the advantage of PPG-specific pretraining appears mainly with frozen backbones and on targets that the waveform directly reflects, such as atrial fibrillation and vital signs. Full-model tuning narrows this advantage, model rankings change with the tuning strategy, and the largest model variant is the best choice in only about one-third of cases. Additionally, controlled experiments with two generalist models show that initializing PPG pretraining from generalist checkpoints provides an early advantage over training from scratch, even when the pretrained features offer little downstream benefit. Together, these findings suggest that PPG-specific pretraining is useful but task-dependent, and that FMs should be evaluated against simpler statistical, traditional ML, and clinical history-based baselines.

cs.LG↗

arXiv2026

A Guideline-Grounded Multi-Agent Framework for Personalized Exercise Prescription from Clinical and Wearable Data

Translating population-level exercise guidance into individualized prescriptions requires integrating clinical and wearable data, including diagnoses, medications, functional limitations, and baseline activity, with condition-specific recommendations, a process difficult to scale beyond specialist rehabilitation settings. We developed FITTER, a multi-agent framework that integrates these data with condition-specific guidance to generate personalized FITT-VP prescriptions and applies deterministic safety audit and repair to correct rule-checkable violations. We evaluated FITTER using data from 400 All of Us participants (300 cancer, 100 stroke) against five LLM comparators through computational evaluation, ablation, and structured clinician review. FITTER achieved 98.5% safety-constraint compliance versus 75.8-85.8% for comparators and showed greater quantitative dosing precision and guideline alignment. Cancer-cohort ablation identified safety audit and repair as the largest contributor to safety-constraint compliance. Clinicians reviewed 80 prescriptions across safety, personalization, instruction concreteness, anticipated effectiveness, and clinical acceptability. FITTER provides a clinician-facing approach integrating clinical and wearable data, guidance, and explicit safety constraints.

cs.AI↗

arXiv2026

Toward Low-Burden Image-Based Dietary Assessment Through Human-AI Collaborative Correction

Image-based dietary assessment can automate initial food logging, but meal photographs often leave food identity, hidden ingredients, preparation, and portion uncertain, making correction a recurring part of use. We introduce Human-AI Collaborative Correction, which reframes correction as communicate intent $\rightarrow$ regenerate $\rightarrow$ verify: users express what should change through text, voice, or guided clarification, the AI regenerates the linked dietary record, and users verify the result. In a within-participant study with 30 participants, compared with conventional Manual Search-and-Edit Correction, collaborative correction was associated with lower workload (Raw TLX: 35.83 vs. 55.00; p < .001), 21.0% lower recorded usage time, 51.1% fewer recorded clicks, and more favorable user-experience ratings; 90.0% preferred it overall. An exploratory nutrient analysis also found lower energy MAE. These findings support intent-driven regeneration as a promising interaction pattern for reducing correction burden while preserving user verification and making image-based dietary tracking easier to sustain.

cs.HC↗

arXiv2026

Can Personal Requirements Become Supervision for Planning?

Managing multiple chronic conditions through diet requires satisfying disease- and medication-specific requirements jointly across meals and days while preserving established eating habits. These requirements are public in clinical guidelines and drug labels, yet turning them into a feasible plan for one person remains difficult for language-model agents. In our dietitian-approved weekly planning evaluation built from NHANES, thirteen models, from medically fine-tuned 8B models to GPT-6.1 Sol, pass fewer than 3% of complete plans through direct generation. Explicit rules, higher reasoning effort, or model-directed tools leave GPT-6.1 Sol at no more than 8%. We present Noura, which pairs LLM planning with executable personal specifications instantiated from public clinical guidance and individual health and dietary profiles. During planning, the specification grounds foods, optimizes portions, checks the complete multi-day plan, and guides revision. Our key insight is that a specification that rejects a plan can also determine what to learn from it. Noura turns executed plans and contextually credited revisions into supervision for compact models, recovering targets even from trajectories that never achieve complete success. The same specification supplies supervised targets, preferences, and rewards for post-training. On 4,993 held-out participants, Noura-SFT raises Qwen3-14B's complete-plan pass rate from 24.0% to 72.5% within the same execution loop, cuts rule violations by 97.5% with no observed critical failures, and improves dietary quality. The locally hosted 14B planner incurs fewer rule violations than its GPT-6 Luna teacher. A matched comparison shows that executed targets reduce rule violations by 41% over model-written proposals. Across four Qwen, Phi, and Llama backbones, self-training alone reduces rule violations by 41-61% on a 1,249-person population subset.

cs.AI↗

arXiv2026

TGAge: A Phenotypic Aging Clock Based on Tabular Foundation Models and the Gompertz Law for Assisted Living Facility Residents

Biological age captures overall health status beyond chronological age, yet existing biological aging clocks are difficult to apply to assisted living facility (ALF) residents due to scarce epigenetic data. We propose TGAge, a second-generation phenotypic aging clock that estimates risk-equivalent biological age from routinely collected clinical measurements. TGAge employs a tabular foundation model to predict all-cause mortality risks over discrete time-to-death intervals and converts the resulting mortality-risk ratio into biological age acceleration via the Gompertz law. We develop and evaluate TGAge on a large cohort of ALF residents curated from a proprietary, multi-state long-term care database. TGAge outperforms clinical indices and established biological aging clocks in survival prediction. Moreover, TGAge-derived age acceleration is significantly associated with multiple aging-related comorbidities. These findings support TGAge as a practical, interpretable, and highly predictive biological aging clock for vulnerable ALF populations using only routinely collected clinical measurements.

stat.AP↗

arXiv2026

TRACE: Expert-Aligned ECG Representation Learning with Rigorous Benchmarking and Real-World Validation in Acute Cardiac Care

TRACE (Text-Reinforced Analysis of Cardio ECGs) is a multimodal electrocardiogram (ECG) representation model that learns clinically grounded signal embeddings for downstream cardiac classification. It is designed to address the limitations of existing CLIP-style training, which often struggles with noisy clinical text and fails to leverage the complementary strengths of unimodal (from ECG) and cross-modal (between ECG and matched cardiologist reports) learning. To bridge this gap, we propose a hybrid architecture that jointly learns unimodal and cross-modal representations via uncertainty-weighted multi-task learning while utilizing an LLM-based pipeline to extract high-fidelity findings from cardiologist reports. We evaluate TRACE across a spectrum of clinical urgency, establishing robust performance on public benchmarks for arrhythmia classification and structural abnormalities relative to existing unimodal and multimodal ECG models. To demonstrate real-world utility, we further validate the model on acute coronary occlusion (ACO), where the prevailing ST-elevation criteria miss 25-34% of true occlusions. Utilizing a large private ACO dataset with expert-annotated ground truth, TRACE significantly outperforms real-world clinical practice, yielding a 19.0% increase in sensitivity or a 62.6% reduction in false positive rates at the clinical baseline. This extensive evaluation confirms that TRACE delivers both strong performance on benchmark tasks and tangible clinical impact in the most acute, high-risk cardiac scenarios.

cs.LG↗

arXiv2026

A Comprehensive Inference-Time Augmentation Framework in Physiological Signals: Application to PPG-Based AF Detection

Objective: Accurate classification of physiological signals in real-world deployments is challenged by sensor noise, motion artifacts, and distribution shifts between training and deployment data. Inference-time augmentation (ITA), which applies augmentations during inference rather than retraining, offers a simple, model-agnostic mechanism to improve robustness. However, ITA application to physiological signals has remained narrow in scope, relying on limited augmentation methods with fixed, unoptimized parameters. This work proposes a unified ITA framework to address that gap. Approach: The framework incorporates 13 augmentation methods spanning time-domain, amplitude-domain, frequency-domain, and artifact-injection transformations, with hyperparameters optimized via Bayesian optimization. We evaluate on atrial fibrillation (AF) detection from 30-second PPG signals using GPT-PPG and ResNet across five datasets comprising more than 400 patients and ${\sim}$9,800 hours of recording. Main results: Standard ITA consistently improved AUROC (up to 8.5% for GPT-PPG and 0.7% for ResNet) and AUPRC (up to 10.6% for GPT-PPG and 0.8% for ResNet). Selective ITA further reduced average FPR by up to 4.4% (GPT-PPG) and 1.3% (ResNet) on non-AF datasets. Significance: These findings establish ITA as a practical, model-agnostic approach for improving PPG-based AF classification reliability in deployment settings where retraining is not feasible, with broader applicability to physiological signal analysis.

cs.LG↗

arXiv2026

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↗

arXiv2026

PG-LRF: Physiology-Guided Latent Rectified Flow for Electro-Hemodynamic PPG-to-ECG Generation

Electrocardiography (ECG) is the clinical standard for cardiac assessment but requires dedicated hardware that does not scale to daily-life monitoring. Photoplethysmography (PPG) is ubiquitous in wearables but lacks ECG-specific diagnostic morphology and is corrupted by motion and sensor noise. PPG-to-ECG generation aims to bridge this gap by recovering electrical morphology and timing from peripheral pulse signals. However, existing methods largely rely on statistical alignment and data-driven generation. They fail to explicitly structure the latent space around physiology-aware electro-hemodynamic factors and lack constraints from forward physiological dynamics. To address these challenges, we propose PG-LRF, a physiology-guided latent rectified flow framework. PG-LRF introduces an electro-hemodynamic simulator that co-models ECG and PPG through shared cardiac phase dynamics. Guided by this simulator, a Physiology-Aware AutoEncoder learns a structured electro-hemodynamic latent space. Then we integrate this simulator guidance into a PPG-conditioned latent rectified flow, enforcing ECG-side morphology consistency and ECG-to-PPG forward hemodynamic consistency during generative transport. Experiments on the large-scale MC-MED dataset demonstrate that PG-LRF significantly improves PPG-to-ECG generation and downstream cardiovascular disease classification, proving its ability to generate ECGs that are both signal-faithful and physiologically plausible under the ECG-to-PPG hemodynamic pathway

eess.SP↗

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

NutriOrion: A Hierarchical Multi-Agent Framework for Personalized Nutrition Intervention Grounded in Clinical Guidelines

Personalized nutrition intervention for patients with multimorbidity is critical for improving health outcomes, yet remains challenging because it requires the simultaneous integration of heterogeneous clinical conditions, medications, and dietary guidelines. Single-agent large language models (LLMs) often suffer from context overload and attention dilution when processing such high-dimensional patient profiles. We introduce NutriOrion, a hierarchical multi-agent framework with a parallel-then-sequential reasoning topology. NutriOrion decomposes nutrition planning into specialized domain agents with isolated contexts to mitigate anchoring bias, followed by a conditional refinement stage. The framework includes a multi-objective prioritization algorithm to resolve conflicting dietary requirements and a safety constraint mechanism that injects pharmacological contraindications as hard negative constraints during synthesis, ensuring clinical validity by construction rather than post-hoc filtering. For clinical interoperability, NutriOrion maps synthesized insights into the ADIME standard and FHIR R4 resources. Evaluated on 330 stroke patients with multimorbidity, NutriOrion outperforms multiple baselines, including GPT-4.1 and alternative multi-agent architectures. It achieves a 12.1 percent drug-food interaction violation rate, demonstrates strong personalization with negative correlations (-0.26 to -0.35) between patient biomarkers and recommended risk nutrients, and yields clinically meaningful dietary improvements, including a 167 percent increase in fiber and a 27 percent increase in potassium, alongside reductions in sodium (9 percent) and sugars (12 percent).

cs.MA↗

arXiv2026

Noninvasive Intracranial Pressure Estimation Using Subspace System Identification and Bespoke Machine Learning Algorithms: A Learning-to-Rank Approach

Accurate noninvasive estimation of intracranial pressure (ICP) remains a major challenge in critical care. We developed a bespoke machine learning algorithm that integrates system identification and ranking-constrained optimization to estimate mean ICP from noninvasive signals. A machine learning framework was proposed to obtain accurate mean ICP values using arbitrary noninvasive signals. The subspace system identification algorithm is employed to identify cerebral hemodynamics models for ICP simulation using arterial blood pressure (ABP), cerebral blood velocity (CBv), and R-wave to R-wave interval (R-R interval) signals in a comprehensive database. A mapping function to describe the relationship between the features of noninvasive signals and the estimation errors is learned using innovative ranking constraints through convex optimization. Patients across multiple clinical settings were randomly split into testing and training datasets for performance evaluation of the mapping function. The results indicate that about 31.88% of testing entries achieved estimation errors within 2 mmHg and 34.07% of testing entries between 2 mmHg and 6 mmHg from the nonlinear mapping with constraints. Our results demonstrate the feasibility of the proposed noninvasive ICP estimation approach. Further validation and technical refinement are required before clinical deployment, but this work lays the foundation for safe and broadly accessible ICP monitoring in patients with acute brain injury and related conditions.

cs.LG↗

arXiv2025

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↗

arXiv2025

Estimating Clinical Lab Test Result Trajectories from PPG using Physiological Foundation Model and Patient-Aware State Space Model -- a UNIPHY+ Approach

Clinical laboratory tests provide essential biochemical measurements for diagnosis and treatment, but are limited by intermittent and invasive sampling. In contrast, photoplethysmogram (PPG) is a non-invasive, continuously recorded signal in intensive care units (ICUs) that reflects cardiovascular dynamics and can serve as a proxy for latent physiological changes. We propose UNIPHY+Lab, a framework that combines a large-scale PPG foundation model for local waveform encoding with a patient-aware Mamba model for long-range temporal modeling. Our architecture addresses three challenges: (1) capturing extended temporal trends in laboratory values, (2) accounting for patient-specific baseline variation via FiLM-modulated initial states, and (3) performing multi-task estimation for interrelated biomarkers. We evaluate our method on the two ICU datasets for predicting the five key laboratory tests. The results show substantial improvements over the LSTM and carry-forward baselines in MAE, RMSE, and $R^2$ among most of the estimation targets. This work demonstrates the feasibility of continuous, personalized lab value estimation from routine PPG monitoring, offering a pathway toward non-invasive biochemical surveillance in critical care.

cs.LG↗

arXiv2025

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↗

arXiv2025

Learning ECG Representations via Poly-Window Contrastive Learning

Electrocardiogram (ECG) analysis is foundational for cardiovascular disease diagnosis, yet the performance of deep learning models is often constrained by limited access to annotated data. Self-supervised contrastive learning has emerged as a powerful approach for learning robust ECG representations from unlabeled signals. However, most existing methods generate only pairwise augmented views and fail to leverage the rich temporal structure of ECG recordings. In this work, we present a poly-window contrastive learning framework. We extract multiple temporal windows from each ECG instance to construct positive pairs and maximize their agreement via statistics. Inspired by the principle of slow feature analysis, our approach explicitly encourages the model to learn temporally invariant and physiologically meaningful features that persist across time. We validate our approach through extensive experiments and ablation studies on the PTB-XL dataset. Our results demonstrate that poly-window contrastive learning consistently outperforms conventional two-view methods in multi-label superclass classification, achieving higher AUROC (0.891 vs. 0.888) and F1 scores (0.680 vs. 0.679) while requiring up to four times fewer pre-training epochs (32 vs. 128) and 14.8% in total wall clock pre-training time reduction. Despite processing multiple windows per sample, we achieve a significant reduction in the number of training epochs and total computation time, making our method practical for training foundational models. Through extensive ablations, we identify optimal design choices and demonstrate robustness across various hyperparameters. These findings establish poly-window contrastive learning as a highly efficient and scalable paradigm for automated ECG analysis and provide a promising general framework for self-supervised representation learning in biomedical time-series data.

cs.LG↗

arXiv2025

Measuring Spiritual Values and Bias of Large Language Models

Large language models (LLMs) have become integral tool for users from various backgrounds. LLMs, trained on vast corpora, reflect the linguistic and cultural nuances embedded in their pre-training data. However, the values and perspectives inherent in this data can influence the behavior of LLMs, leading to potential biases. As a result, the use of LLMs in contexts involving spiritual or moral values necessitates careful consideration of these underlying biases. Our work starts with verification of our hypothesis by testing the spiritual values of popular LLMs. Experimental results show that LLMs' spiritual values are quite diverse, as opposed to the stereotype of atheists or secularists. We then investigate how different spiritual values affect LLMs in social-fairness scenarios e.g., hate speech identification). Our findings reveal that different spiritual values indeed lead to different sensitivity to different hate target groups. Furthermore, we propose to continue pre-training LLMs on spiritual texts, and empirical results demonstrate the effectiveness of this approach in mitigating spiritual bias.

cs.CL↗

arXiv2025

Offline Guarded Safe Reinforcement Learning for Medical Treatment Optimization Strategies

When applying offline reinforcement learning (RL) in healthcare scenarios, the out-of-distribution (OOD) issues pose significant risks, as inappropriate generalization beyond clinical expertise can result in potentially harmful recommendations. While existing methods like conservative Q-learning (CQL) attempt to address the OOD issue, their effectiveness is limited by only constraining action selection by suppressing uncertain actions. This action-only regularization imitates clinician actions that prioritize short-term rewards, but it fails to regulate downstream state trajectories, thereby limiting the discovery of improved long-term treatment strategies. To safely improve policy beyond clinician recommendations while ensuring that state-action trajectories remain in-distribution, we propose \textit{Offline Guarded Safe Reinforcement Learning} ($\mathsf{OGSRL}$), a theoretically grounded model-based offline RL framework. $\mathsf{OGSRL}$ introduces a novel dual constraint mechanism for improving policy with reliability and safety. First, the OOD guardian is established to specify clinically validated regions for safe policy exploration. By constraining optimization within these regions, it enables the reliable exploration of treatment strategies that outperform clinician behavior by leveraging the full patient state history, without drifting into unsupported state-action trajectories. Second, we introduce a safety cost constraint that encodes medical knowledge about physiological safety boundaries, providing domain-specific safeguards even in areas where training data might contain potentially unsafe interventions. Notably, we provide theoretical guarantees on safety and near-optimality: policies that satisfy these constraints remain in safe and reliable regions and achieve performance close to the best possible policy supported by the data.

cs.LG↗