arXiv subjects

Carl Yang

Publications and source records attributed to Carl Yang.

At least 73 records · Page 4Linked to original sources

arXiv2025

PPG-Distill: Efficient Photoplethysmography Signals Analysis via Foundation Model Distillation

Photoplethysmography (PPG) is widely used in wearable health monitoring, yet large PPG foundation models remain difficult to deploy on resource-limited devices. We present PPG-Distill, a knowledge distillation framework that transfers both global and local knowledge through prediction-, feature-, and patch-level distillation. PPG-Distill incorporates morphology distillation to preserve local waveform patterns and rhythm distillation to capture inter-patch temporal structures. On heart rate estimation and atrial fibrillation detection, PPG-Distill improves student performance by up to 21.8% while achieving 7X faster inference and reducing memory usage by 19X, enabling efficient PPG analysis on wearables.

cs.LG↗

arXiv2025

Conditional Neural ODE for Longitudinal Parkinson's Disease Progression Forecasting

Parkinson's disease (PD) shows heterogeneous, evolving brain-morphometry patterns. Modeling these longitudinal trajectories enables mechanistic insight, treatment development, and individualized 'digital-twin' forecasting. However, existing methods usually adopt recurrent neural networks and transformer architectures, which rely on discrete, regularly sampled data while struggling to handle irregular and sparse magnetic resonance imaging (MRI) in PD cohorts. Moreover, these methods have difficulty capturing individual heterogeneity including variations in disease onset, progression rate, and symptom severity, which is a hallmark of PD. To address these challenges, we propose CNODE (Conditional Neural ODE), a novel framework for continuous, individualized PD progression forecasting. The core of CNODE is to model morphological brain changes as continuous temporal processes using a neural ODE model. In addition, we jointly learn patient-specific initial time and progress speed to align individual trajectories into a shared progression trajectory. We validate CNODE on the Parkinson's Progression Markers Initiative (PPMI) dataset. Experimental results show that our method outperforms state-of-the-art baselines in forecasting longitudinal PD progression.

cs.LG↗

arXiv2025

Beyond MedQA: Towards Real-world Clinical Decision Making in the Era of LLMs

Large language models (LLMs) show promise for clinical use. They are often evaluated using datasets such as MedQA. However, Many medical datasets, such as MedQA, rely on simplified Question-Answering (Q\A) that underrepresents real-world clinical decision-making. Based on this, we propose a unifying paradigm that characterizes clinical decision-making tasks along two dimensions: Clinical Backgrounds and Clinical Questions. As the background and questions approach the real clinical environment, the difficulty increases. We summarize the settings of existing datasets and benchmarks along two dimensions. Then we review methods to address clinical decision-making, including training-time and test-time techniques, and summarize when they help. Next, we extend evaluation beyond accuracy to include efficiency, explainability. Finally, we highlight open challenges. Our paradigm clarifies assumptions, standardizes comparisons, and guides the development of clinically meaningful LLMs.

cs.CL↗

arXiv2025

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↗

arXiv2025

MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Science

We introduce MedAgentGym, a scalable and interactive training environment designed to enhance coding-based biomedical reasoning capabilities in large language model (LLM) agents. MedAgentGym comprises 72,413 task instances across 129 categories derived from 12 authentic real-world biomedical scenarios. Tasks are encapsulated within executable sandbox environments, each featuring detailed task specifications, interactive feedback mechanisms, verifiable ground truth annotations, and scalable training trajectory generation. Extensive benchmarking of 29 LLMs reveals substantial performance disparities in biomedical data science between commercial and open-source LLMs. Leveraging efficient multi-threaded and multi-turn trajectory sampling in MedAgentGym, Med-Copilot achieves performance gains of +43.02% and +45.28% from offline and online reinforcement learning, respectively, demonstrating MedAgentGym as an effective training ground while establishing itself as a cost-effective, privacy-preserving alternative competitive with proprietary LLMs (gpt-4o). By offering a unified execution environment with a comprehensive benchmark and accessible, extensible training resources, MedAgentGym delivers an integrated platform to develop LLM-based coding assistants for advanced biomedical data science.

cs.CL↗

arXiv2025

Retrieval-augmented GUI Agents with Generative Guidelines

GUI agents powered by vision-language models (VLMs) show promise in automating complex digital tasks. However, their effectiveness in real-world applications is often limited by scarce training data and the inherent complexity of these tasks, which frequently require long-tailed knowledge covering rare, unseen scenarios. We propose RAG-GUI , a lightweight VLM that leverages web tutorials at inference time. RAG-GUI is first warm-started via supervised finetuning (SFT) and further refined through self-guided rejection sampling finetuning (RSF). Designed to be model-agnostic, RAG-GUI functions as a generic plug-in that enhances any VLM-based agent. Evaluated across three distinct tasks, it consistently outperforms baseline agents and surpasses other inference baselines by 2.6% to 13.3% across two model sizes, demonstrating strong generalization and practical plug-and-play capabilities in real-world scenarios.

cs.CL↗

arXiv2025

AceSearcher: Bootstrapping Reasoning and Search for LLMs via Reinforced Self-Play

Search-augmented LLMs often struggle with complex reasoning tasks due to ineffective multi-hop retrieval and limited reasoning ability. We propose AceSearcher, a cooperative self-play framework that trains a single large language model (LLM) to alternate between two roles: a decomposer that breaks down complex queries and a solver that integrates retrieved contexts for answer generation. AceSearcher couples supervised fine-tuning on a diverse mixture of search, reasoning, and decomposition tasks with reinforcement fine-tuning optimized for final answer accuracy, eliminating the need for intermediate annotations. Extensive experiments on three reasoning-intensive tasks across 10 datasets show that AceSearcher outperforms state-of-the-art baselines, achieving an average exact match improvement of 7.6%. Remarkably, on document-level finance reasoning tasks, AceSearcher-32B matches the performance of the DeepSeek-V3 model using less than 5% of its parameters. Even at smaller scales (1.5B and 8B), AceSearcher often surpasses existing search-augmented LLMs with up to 9x more parameters, highlighting its exceptional efficiency and effectiveness in tackling complex reasoning tasks. Our code will be published at https://github.com/ritaranx/AceSearcher and https://huggingface.co/AceSearcher.

cs.CL↗

arXiv2025

MANI-Pure: Magnitude-Adaptive Noise Injection for Adversarial Purification

Adversarial purification with diffusion models has emerged as a promising defense strategy, but existing methods typically rely on uniform noise injection, which indiscriminately perturbs all frequencies, corrupting semantic structures and undermining robustness. Our empirical study reveals that adversarial perturbations are not uniformly distributed: they are predominantly concentrated in high-frequency regions, with heterogeneous magnitude intensity patterns that vary across frequencies and attack types. Motivated by this observation, we introduce MANI-Pure, a magnitude-adaptive purification framework that leverages the magnitude spectrum of inputs to guide the purification process. Instead of injecting homogeneous noise, MANI-Pure adaptively applies heterogeneous, frequency-targeted noise, effectively suppressing adversarial perturbations in fragile high-frequency, low-magnitude bands while preserving semantically critical low-frequency content. Extensive experiments on CIFAR-10 and ImageNet-1K validate the effectiveness of MANI-Pure. It narrows the clean accuracy gap to within 0.59 of the original classifier, while boosting robust accuracy by 2.15, and achieves the top-1 robust accuracy on the RobustBench leaderboard, surpassing the previous state-of-the-art method.

cs.CV↗

arXiv2025

Are Your LLM-based Text-to-SQL Models Secure? Exploring SQL Injection via Backdoor Attacks

Large language models (LLMs) have shown state-of-the-art results in translating natural language questions into SQL queries (Text-to-SQL), a long-standing challenge within the database community. However, security concerns remain largely unexplored, particularly the threat of backdoor attacks, which can introduce malicious behaviors into models through fine-tuning with poisoned datasets. In this work, we systematically investigate the vulnerabilities of LLM-based Text-to-SQL models and present ToxicSQL, a novel backdoor attack framework. Our approach leverages stealthy {semantic and character-level triggers} to make backdoors difficult to detect and remove, ensuring that malicious behaviors remain covert while maintaining high model accuracy on benign inputs. Furthermore, we propose leveraging SQL injection payloads as backdoor targets, enabling the generation of malicious yet executable SQL queries, which pose severe security and privacy risks in language model-based SQL development. We demonstrate that injecting only 0.44% of poisoned data can result in an attack success rate of 79.41%, posing a significant risk to database security. Additionally, we propose detection and mitigation strategies to enhance model reliability. Our findings highlight the urgent need for security-aware Text-to-SQL development, emphasizing the importance of robust defenses against backdoor threats.

cs.CR↗

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

Graph-oriented Instruction Tuning of Large Language Models for Generic Graph Mining

Graphs with abundant attributes are essential in modeling interconnected entities and enhancing predictions across various real-world applications. Traditional Graph Neural Networks (GNNs) often require re-training for different graph tasks and datasets. Although the emergence of Large Language Models (LLMs) has introduced new paradigms in natural language processing, their potential for generic graph mining, training a single model to simultaneously handle diverse tasks and datasets, remains under-explored. To this end, our novel framework MuseGraph, seamlessly integrates the strengths of GNNs and LLMs into one foundation model for graph mining across tasks and datasets. This framework first features a compact graph description to encapsulate key graph information within language token limitations. Then, we propose a diverse instruction generation mechanism with Chain-of-Thought (CoT)-based instruction packages to distill the reasoning capabilities from advanced LLMs like GPT-4. Finally, we design a graph-aware instruction tuning strategy to facilitate mutual enhancement across multiple tasks and datasets while preventing catastrophic forgetting of LLMs' generative abilities. Our experimental results demonstrate significant improvements in five graph tasks and ten datasets, showcasing the potential of our MuseGraph in enhancing the accuracy of graph-oriented downstream tasks while improving the generation abilities of LLMs.

cs.CL↗

arXiv2025

HypKG: Hypergraph-based Knowledge Graph Contextualization for Precision Healthcare

Knowledge graphs (KGs) are important products of the semantic web, which are widely used in various application domains. Healthcare is one of such domains where KGs are intensively used, due to the high requirement for knowledge accuracy and interconnected nature of healthcare data. However, KGs storing general factual information often lack the ability to account for important contexts of the knowledge such as the status of specific patients, which are crucial in precision healthcare. Meanwhile, electronic health records (EHRs) provide rich personal data, including various diagnoses and medications, which provide natural contexts for general KGs. In this paper, we propose HypKG, a framework that integrates patient information from EHRs into KGs to generate contextualized knowledge representations for accurate healthcare predictions. Using advanced entity-linking techniques, we connect relevant knowledge from general KGs with patient information from EHRs, and then utilize a hypergraph model to "contextualize" the knowledge with the patient information. Finally, we employ hypergraph transformers guided by downstream prediction tasks to jointly learn proper contextualized representations for both KGs and patients, fully leveraging existing knowledge in KGs and patient contexts in EHRs. In experiments using a large biomedical KG and two real-world EHR datasets, HypKG demonstrates significant improvements in healthcare prediction tasks across multiple evaluation metrics. Additionally, by integrating external contexts, HypKG can learn to adjust the representations of entities and relations in KG, potentially improving the quality and real-world utility of knowledge.

cs.AI↗

arXiv2025

RAG in the Wild: On the (In)effectiveness of LLMs with Mixture-of-Knowledge Retrieval Augmentation

Retrieval-augmented generation (RAG) enhances large language models (LLMs) by integrating external knowledge retrieved at inference time. While RAG demonstrates strong performance on benchmarks largely derived from general-domain corpora like Wikipedia, its effectiveness under realistic, diverse retrieval scenarios remains underexplored. We evaluated RAG systems using MassiveDS, a large-scale datastore with mixture of knowledge, and identified critical limitations: retrieval mainly benefits smaller models, rerankers add minimal value, and no single retrieval source consistently excels. Moreover, current LLMs struggle to route queries across heterogeneous knowledge sources. These findings highlight the need for adaptive retrieval strategies before deploying RAG in real-world settings. Our code and data can be found at https://github.com/ritaranx/RAG_in_the_Wild.

cs.CL↗

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

KERAP: A Knowledge-Enhanced Reasoning Approach for Accurate Zero-shot Diagnosis Prediction Using Multi-agent LLMs

Medical diagnosis prediction plays a critical role in disease detection and personalized healthcare. While machine learning (ML) models have been widely adopted for this task, their reliance on supervised training limits their ability to generalize to unseen cases, particularly given the high cost of acquiring large, labeled datasets. Large language models (LLMs) have shown promise in leveraging language abilities and biomedical knowledge for diagnosis prediction. However, they often suffer from hallucinations, lack structured medical reasoning, and produce useless outputs. To address these challenges, we propose KERAP, a knowledge graph (KG)-enhanced reasoning approach that improves LLM-based diagnosis prediction through a multi-agent architecture. Our framework consists of a linkage agent for attribute mapping, a retrieval agent for structured knowledge extraction, and a prediction agent that iteratively refines diagnosis predictions. Experimental results demonstrate that KERAP enhances diagnostic reliability efficiently, offering a scalable and interpretable solution for zero-shot medical diagnosis prediction.

cs.AI↗

arXiv2025

Graph ODEs and Beyond: A Comprehensive Survey on Integrating Differential Equations with Graph Neural Networks

Graph Neural Networks (GNNs) and differential equations (DEs) are two rapidly advancing areas of research that have shown remarkable synergy in recent years. GNNs have emerged as powerful tools for learning on graph-structured data, while differential equations provide a principled framework for modeling continuous dynamics across time and space. The intersection of these fields has led to innovative approaches that leverage the strengths of both, enabling applications in physics-informed learning, spatiotemporal modeling, and scientific computing. This survey aims to provide a comprehensive overview of the burgeoning research at the intersection of GNNs and DEs. We will categorize existing methods, discuss their underlying principles, and highlight their applications across domains such as molecular modeling, traffic prediction, and epidemic spreading. Furthermore, we identify open challenges and outline future research directions to advance this interdisciplinary field. A comprehensive paper list is provided at https://github.com/Emory-Melody/Awesome-Graph-NDEs. This survey serves as a resource for researchers and practitioners seeking to understand and contribute to the fusion of GNNs and DEs

cs.LG↗

arXiv2025

Correlation-Aware Graph Convolutional Networks for Multi-Label Node Classification

Multi-label node classification is an important yet under-explored domain in graph mining as many real-world nodes belong to multiple categories rather than just a single one. Although a few efforts have been made by utilizing Graph Convolution Networks (GCNs) to learn node representations and model correlations between multiple labels in the embedding space, they still suffer from the ambiguous feature and ambiguous topology induced by multiple labels, which reduces the credibility of the messages delivered in graphs and overlooks the label correlations on graph data. Therefore, it is crucial to reduce the ambiguity and empower the GCNs for accurate classification. However, this is quite challenging due to the requirement of retaining the distinctiveness of each label while fully harnessing the correlation between labels simultaneously. To address these issues, in this paper, we propose a Correlation-aware Graph Convolutional Network (CorGCN) for multi-label node classification. By introducing a novel Correlation-Aware Graph Decomposition module, CorGCN can learn a graph that contains rich label-correlated information for each label. It then employs a Correlation-Enhanced Graph Convolution to model the relationships between labels during message passing to further bolster the classification process. Extensive experiments on five datasets demonstrate the effectiveness of our proposed CorGCN.

cs.LG↗

arXiv2025

How to Use Graph Data in the Wild to Help Graph Anomaly Detection?

In recent years, graph anomaly detection has found extensive applications in various domains such as social, financial, and communication networks. However, anomalies in graph-structured data present unique challenges, including label scarcity, ill-defined anomalies, and varying anomaly types, making supervised or semi-supervised methods unreliable. Researchers often adopt unsupervised approaches to address these challenges, assuming that anomalies deviate significantly from the normal data distribution. Yet, when the available data is insufficient, capturing the normal distribution accurately and comprehensively becomes difficult. To overcome this limitation, we propose to utilize external graph data (i.e., graph data in the wild) to help anomaly detection tasks. This naturally raises the question: How can we use external data to help graph anomaly detection tasks? To answer this question, we propose a framework called Wild-GAD. It is built upon a unified database, UniWildGraph, which comprises a large and diverse collection of graph data with broad domain coverage, ample data volume, and a unified feature space. Further, we develop selection criteria based on representativity and diversity to identify the most suitable external data for anomaly detection task. Extensive experiments on six real-world datasets demonstrate the effectiveness of Wild-GAD. Compared to the baseline methods, our framework has an average 18% AUCROC and 32% AUCPR improvement over the best-competing methods.

cs.LG↗