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Chuxu Zhang

Publications and source records attributed to Chuxu Zhang.

At least 37 records · Page 2Linked to original sources
arXiv2026

OPBench: A Graph Benchmark to Combat the Opioid Crisis

The opioid epidemic continues to ravage communities worldwide, straining healthcare systems, disrupting families, and demanding urgent computational solutions. To combat this lethal opioid crisis, graph learning methods have emerged as a promising paradigm for modeling complex drug-related phenomena. However, a significant gap remains: there is no comprehensive benchmark for systematically evaluating these methods across real-world opioid crisis scenarios. To bridge this gap, we introduce OPBench, the first comprehensive opioid benchmark comprising five datasets across three critical application domains: opioid overdose detection from healthcare claims, illicit drug trafficking detection from digital platforms, and drug misuse prediction from dietary patterns. Specifically, OPBench incorporates diverse graph structures, including heterogeneous graphs and hypergraphs, to preserve the rich and complex relational information among drug-related data. To address data scarcity, we collaborate with domain experts and authoritative institutions to curate and annotate datasets while adhering to privacy and ethical guidelines. Furthermore, we establish a unified evaluation framework with standardized protocols, predefined data splits, and reproducible baselines to facilitate fair and systematic comparison among graph learning methods. Through extensive experiments, we analyze the strengths and limitations of existing graph learning methods, thereby providing actionable insights for future research in combating the opioid crisis. Our source code and datasets are available at https://github.com/Tianyi-Billy-Ma/OPBench.

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arXiv2026

BHyGNN+: Unsupervised Representation Learning for Heterophilic Hypergraphs

Hypergraph Neural Networks (HyGNNs) have demonstrated remarkable success in modeling higher-order relationships among entities. However, their performance often degrades on heterophilic hypergraphs, where nodes connected by the same hyperedge tend to have dissimilar semantic representations or belong to different classes. While several HyGNNs, including our prior work BHyGNN, have been proposed to address heterophily, their reliance on labeled data significantly limits their applicability in real-world scenarios where annotations are scarce or costly. To overcome this limitation, we introduce BHyGNN+, a self-supervised learning framework that extends BHyGNN for representation learning on heterophilic hypergraphs without requiring ground-truth labels. The core idea of BHyGNN+ is hypergraph duality, a structural transformation where the roles of nodes and hyperedges are interchanged. By contrasting augmented views of a hypergraph against its dual using cosine similarity, our framework captures essential structural patterns in a fully unsupervised manner. Notably, this duality-based formulation eliminates the need for negative samples, a common requirement in existing hypergraph contrastive learning methods that is often difficult to satisfy in practice. Extensive experiments on eleven benchmark datasets demonstrate that BHyGNN+ consistently outperforms state-of-the-art supervised and self-supervised baselines on both heterophilic and homophilic hypergraphs. Our results validate the effectiveness of leveraging hypergraph duality for self-supervised learning and establish a new paradigm for representation learning on challenging, unlabeled hypergraphs.

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arXiv2026

Molecular Representations in Implicit Functional Space via Hyper-Networks

Molecular representations fundamentally shape how machine learning systems reason about molecular structure and physical properties. Most existing approaches adopt a discrete pipeline: molecules are encoded as sequences, graphs, or point clouds, mapped to fixed-dimensional embeddings, and then used for task-specific prediction. This paradigm treats molecules as discrete objects, despite their intrinsically continuous and field-like physical nature. We argue that molecular learning can instead be formulated as learning in function space. Specifically, we model each molecule as a continuous function over three-dimensional (3D) space and treat this molecular field as the primary object of representation. From this perspective, conventional molecular representations arise as particular sampling schemes of an underlying continuous object. We instantiate this formulation with MolField, a hyper-network-based framework that learns distributions over molecular fields. To ensure physical consistency, these functions are defined over canonicalized coordinates, yielding invariance to global SE(3) transformations. To enable learning directly over functions, we introduce a structured weight tokenization and train a sequence-based hyper-network to model a shared prior over molecular fields. We evaluate MolField on molecular dynamics and property prediction. Our results show that treating molecules as continuous functions fundamentally changes how molecular representations generalize across tasks and yields downstream behavior that is stable to how molecules are discretized or queried.

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arXiv2026

GLEN-Bench: A Graph-Language based Benchmark for Nutritional Health

Nutritional interventions are important for managing chronic health conditions, but current computational methods provide limited support for personalized dietary guidance. We identify three key gaps: (1) dietary pattern studies often ignore real-world constraints such as socioeconomic status, comorbidities, and limited food access; (2) recommendation systems rarely explain why a particular food helps a given patient; and (3) no unified benchmark evaluates methods across the connected tasks needed for nutritional interventions. We introduce GLEN-Bench, the first comprehensive graph-language based benchmark for nutritional health assessment. We combine NHANES health records, FNDDS food composition data, and USDA food-access metrics to build a knowledge graph that links demographics, health conditions, dietary behaviors, poverty-related constraints, and nutrient needs. We test the benchmark using opioid use disorder, where models must detect subtle nutritional differences across disease stages. GLEN-Bench includes three linked tasks: risk detection identifies at-risk individuals from dietary and socioeconomic patterns; recommendation suggests personalized foods that meet clinical needs within resource constraints; and question answering provides graph-grounded, natural-language explanations to facilitate comprehension. We evaluate these graph-language approaches, including graph neural networks, large language models, and hybrid architectures, to establish solid baselines and identify practical design choices. Our analysis identifies clear dietary patterns linked to health risks, providing insights that can guide practical interventions.

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arXiv2026

LongDA: Benchmarking LLM Agents for Long-Document Data Analysis

We introduce LongDA, a data analysis benchmark for evaluating LLM-based agents under documentation-intensive analytical workflows. In contrast to existing benchmarks that assume well-specified schemas and inputs, LongDA targets real-world settings in which navigating long documentation and complex data is the primary bottleneck. To this end, we manually curate raw data files, long and heterogeneous documentation, and expert-written publications from 17 publicly available U.S. national surveys, from which we extract 505 analytical queries grounded in real analytical practice. Solving these queries requires agents to first retrieve and integrate key information from multiple unstructured documents, before performing multi-step computations and writing executable code, which remains challenging for existing data analysis agents. To support the systematic evaluation under this setting, we develop LongTA, a tool-augmented agent framework that enables document access, retrieval, and code execution, and evaluate a range of proprietary and open-source models. Our experiments reveal substantial performance gaps even among state-of-the-art models, highlighting the challenges researchers should consider before applying LLM agents for decision support in real-world, high-stakes analytical settings.

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arXiv2025

Generative Graph Pattern Machine

Graph neural networks (GNNs) have been predominantly driven by message-passing, where node representations are iteratively updated via local neighborhood aggregation. Despite their success, message-passing suffers from fundamental limitations -- including constrained expressiveness, over-smoothing, over-squashing, and limited capacity to model long-range dependencies. These issues hinder scalability: increasing data size or model size often fails to yield improved performance. To this end, we explore pathways beyond message-passing and introduce Generative Graph Pattern Machine (G$^2$PM), a generative Transformer pre-training framework for graphs. G$^2$PM represents graph instances (nodes, edges, or entire graphs) as sequences of substructures, and employs generative pre-training over the sequences to learn generalizable and transferable representations. Empirically, G$^2$PM demonstrates strong scalability: on the ogbn-arxiv benchmark, it continues to improve with model sizes up to 60M parameters, outperforming prior generative approaches that plateau at significantly smaller scales (e.g., 3M). In addition, we systematically analyze the model design space, highlighting key architectural choices that contribute to its scalability and generalization. Across diverse tasks -- including node/link/graph classification, transfer learning, and cross-graph pretraining -- G$^2$PM consistently outperforms strong baselines, establishing a compelling foundation for scalable graph learning. The code and dataset are available at https://github.com/Zehong-Wang/G2PM.

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arXiv2025

GraphTOP: Graph Topology-Oriented Prompting for Graph Neural Networks

Graph Neural Networks (GNNs) have revolutionized the field of graph learning by learning expressive graph representations from massive graph data. As a common pattern to train powerful GNNs, the "pre-training, adaptation" scheme first pre-trains GNNs over unlabeled graph data and subsequently adapts them to specific downstream tasks. In the adaptation phase, graph prompting is an effective strategy that modifies input graph data with learnable prompts while keeping pre-trained GNN models frozen. Typically, existing graph prompting studies mainly focus on *feature-oriented* methods that apply graph prompts to node features or hidden representations. However, these studies often achieve suboptimal performance, as they consistently overlook the potential of *topology-oriented* prompting, which adapts pre-trained GNNs by modifying the graph topology. In this study, we conduct a pioneering investigation of graph prompting in terms of graph topology. We propose the first **Graph** **T**opology-**O**riented **P**rompting (GraphTOP) framework to effectively adapt pre-trained GNN models for downstream tasks. More specifically, we reformulate topology-oriented prompting as an edge rewiring problem within multi-hop local subgraphs and relax it into the continuous probability space through reparameterization while ensuring tight relaxation and preserving graph sparsity. Extensive experiments on five graph datasets under four pre-training strategies demonstrate that our proposed GraphTOP outshines six baselines on multiple node classification datasets. Our code is available at https://github.com/xbfu/GraphTOP.

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arXiv2025

Interpretable Graph-Language Modeling for Detecting Youth Illicit Drug Use

Illicit drug use among teenagers and young adults (TYAs) remains a pressing public health concern, with rising prevalence and long-term impacts on health and well-being. To detect illicit drug use among TYAs, researchers analyze large-scale surveys such as the Youth Risk Behavior Survey (YRBS) and the National Survey on Drug Use and Health (NSDUH), which preserve rich demographic, psychological, and environmental factors related to substance use. However, existing modeling methods treat survey variables independently, overlooking latent and interconnected structures among them. To address this limitation, we propose LAMI (LAtent relation Mining with bi-modal Interpretability), a novel joint graph-language modeling framework for detecting illicit drug use and interpreting behavioral risk factors among TYAs. LAMI represents individual responses as relational graphs, learns latent connections through a specialized graph structure learning layer, and integrates a large language model to generate natural language explanations grounded in both graph structures and survey semantics. Experiments on the YRBS and NSDUH datasets show that LAMI outperforms competitive baselines in predictive accuracy. Interpretability analyses further demonstrate that LAMI reveals meaningful behavioral substructures and psychosocial pathways, such as family dynamics, peer influence, and school-related distress, that align with established risk factors for substance use.

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arXiv2025

NG-Router: Graph-Supervised Multi-Agent Collaboration for Nutrition Question Answering

Diet plays a central role in human health, and Nutrition Question Answering (QA) offers a promising path toward personalized dietary guidance and the prevention of diet-related chronic diseases. However, existing methods face two fundamental challenges: the limited reasoning capacity of single-agent systems and the complexity of designing effective multi-agent architectures, as well as contextual overload that hinders accurate decision-making. We introduce Nutritional-Graph Router (NG-Router), a novel framework that formulates nutritional QA as a supervised, knowledge-graph-guided multi-agent collaboration problem. NG-Router integrates agent nodes into heterogeneous knowledge graphs and employs a graph neural network to learn task-aware routing distributions over agents, leveraging soft supervision derived from empirical agent performance. To further address contextual overload, we propose a gradient-based subgraph retrieval mechanism that identifies salient evidence during training, thereby enhancing multi-hop and relational reasoning. Extensive experiments across multiple benchmarks and backbone models demonstrate that NG-Router consistently outperforms both single-agent and ensemble baselines, offering a principled approach to domain-aware multi-agent reasoning for complex nutritional health tasks.

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arXiv2025

MAPRO: Recasting Multi-Agent Prompt Optimization as Maximum a Posteriori Inference

Large language models (LLMs) have demonstrated remarkable capabilities across diverse tasks, and LLM-based agents further extend these abilities to various practical workflows. While recent progress shows that multi-agent systems (MAS) can outperform single agents by coordinating specialized roles, designing effective MAS remains difficult due to prompt sensitivity and the compounded instability MAS creates. To cope with the challenge, recent efforts in automated prompt design have reduced manual effort. However, multi-agent prompt optimization remains largely unexplored. Challenges like exponentially expanding search space and ambiguous credit assignment together make systematic design intractable without principled methods. Therefore, we introduce M}ulti-Agent PRompt Optimization (MAPRO), a four-stage framework that first formulates MAS prompt optimization as a Maximum a Posteriori (MAP) inference problem and solves it using a language-guided variant of max-product belief propagation algorithm. To address credit assignment and updates the system iteratively, MAPRO employs a topology-aware refinement mechanism that integrates execution feedback and downstream blames to selectively update agent prompts. Through this process, MAPRO progressively converges to a coordinated set of agent-specific prompt policies. Across benchmarks in various tasks, MAPRO achieves state-of-the-art performance, consistently surpassing manually engineered baselines and recent automated alternatives. Beyond performance, our MAP-based formulation also delivers general guidelines for building more reliable and principled multi-agent systems in the future

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arXiv2025

AgentRouter: A Knowledge-Graph-Guided LLM Router for Collaborative Multi-Agent Question Answering

Large language models (LLMs) and agent-based frameworks have advanced rapidly, enabling diverse applications. Yet, with the proliferation of models and agentic strategies, practitioners face substantial uncertainty in selecting the best configuration for a downstream task. Prior studies show that different agents and backbones exhibit complementary strengths, and that larger models are not always superior, underscoring the need for adaptive routing mechanisms. Existing approaches to agent routing, however, often emphasize cost efficiency while overlooking the fine-grained contextual and relational structure inherent in QA tasks. In this paper, we propose tAgentRouter, a framework that formulates multi-agent QA as a knowledge-graph-guided routing problem supervised by empirical performance signals. Specifically, we convert QA instance into a knowledge graph that jointly encodes queries, contextual entities, and agents, and then train a heterogeneous graph neural network (GNN) to propagate information across node types and produce task-aware routing distributions over agents. By leveraging soft supervision and weighted aggregation of agent outputs, AgentRouter learns principled collaboration schemes that capture the complementary strengths of diverse agents. Extensive experiments demonstrate that our framework consistently outperforms single-agent and ensemble baselines, while generalizing across benchmarks and LLM backbones. These results highlight the effectiveness and robustness of graph-supervised multi-agent routing for question answering.

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arXiv2025

MASS: Mathematical Data Selection via Skill Graphs for Pretraining Large Language Models

High-quality data plays a critical role in the pretraining and fine-tuning of large language models (LLMs), even determining their performance ceiling to some degree. Consequently, numerous data selection methods have been proposed to identify subsets of data that can effectively and efficiently enhance model performance. However, most of these methods focus on general data selection and tend to overlook the specific nuances of domain-related data. In this paper, we introduce MASS, a \textbf{MA}thematical data \textbf{S}election framework using the \textbf{S}kill graph for pretraining LLMs in the mathematical reasoning domain. By taking into account the unique characteristics of mathematics and reasoning, we construct a skill graph that captures the mathematical skills and their interrelations from a reference dataset. This skill graph guides us in assigning quality scores to the target dataset, enabling us to select the top-ranked subset which is further used to pretrain LLMs. Experimental results demonstrate the efficiency and effectiveness of MASS across different model sizes (1B and 7B) and pretraining datasets (web data and synthetic data). Specifically, in terms of efficiency, models trained on subsets selected by MASS can achieve similar performance to models trained on the original datasets, with a significant reduction in the number of trained tokens - ranging from 50\% to 70\% fewer tokens. In terms of effectiveness, when trained on the same amount of tokens, models trained on the data selected by MASS outperform those trained on the original datasets by 3.3\% to 5.9\%. These results underscore the potential of MASS to improve both the efficiency and effectiveness of pretraining LLMs.

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arXiv2025

Graph Prompting for Graph Learning Models: Recent Advances and Future Directions

Graph learning models have demonstrated great prowess in learning expressive representations from large-scale graph data in a wide variety of real-world scenarios. As a prevalent strategy for training powerful graph learning models, the "pre-training, adaptation" scheme first pre-trains graph learning models on unlabeled graph data in a self-supervised manner and then adapts them to specific downstream tasks. During the adaptation phase, graph prompting emerges as a promising approach that learns trainable prompts while keeping the pre-trained graph learning models unchanged. In this paper, we present a systematic review of recent advancements in graph prompting. First, we introduce representative graph pre-training methods that serve as the foundation step of graph prompting. Next, we review mainstream techniques in graph prompting and elaborate on how they design learnable prompts for graph prompting. Furthermore, we summarize the real-world applications of graph prompting from different domains. Finally, we discuss several open challenges in existing studies with promising future directions in this field.

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arXiv2025

Towards Graph Foundation Models: Learning Generalities Across Graphs via Task-Trees

Foundation models are pretrained on large-scale corpora to learn generalizable patterns across domains and tasks -- such as contours, textures, and edges in images, or tokens and sentences in text. In contrast, discovering such generalities in graph-structured data, especially across heterogeneous graph tasks, remains an open challenge. To address this, we propose a novel approach to cross-task generalization in graphs via task-trees, which serve as unified learning instances aligning node-, edge-, and graph-level tasks. We theoretically analyze the stability, transferability, and generalization properties of task-trees, showing that pretraining a graph neural network (GNN) on diverse task-trees with a reconstruction objective induces transferable knowledge. This enables efficient adaptation to downstream tasks with minimal fine-tuning. To validate our framework, we introduce Graph Generality Identifier on Task-Trees (GIT), a graph foundation model that demonstrates strong performance on over 30 graphs across five domains via fine-tuning, in-context learning, and zero-shot generalization. Code and data are available at https://github.com/Zehong-Wang/GIT.

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arXiv2025

Beyond Message Passing: Neural Graph Pattern Machine

Graph learning tasks often hinge on identifying key substructure patterns -- such as triadic closures in social networks or benzene rings in molecular graphs -- that underpin downstream performance. However, most existing graph neural networks (GNNs) rely on message passing, which aggregates local neighborhood information iteratively and struggles to explicitly capture such fundamental motifs, like triangles, k-cliques, and rings. This limitation hinders both expressiveness and long-range dependency modeling. In this paper, we introduce the Neural Graph Pattern Machine (GPM), a novel framework that bypasses message passing by learning directly from graph substructures. GPM efficiently extracts, encodes, and prioritizes task-relevant graph patterns, offering greater expressivity and improved ability to capture long-range dependencies. Empirical evaluations across four standard tasks -- node classification, link prediction, graph classification, and graph regression -- demonstrate that GPM outperforms state-of-the-art baselines. Further analysis reveals that GPM exhibits strong out-of-distribution generalization, desirable scalability, and enhanced interpretability. Code and datasets are available at: https://github.com/Zehong-Wang/GPM.

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arXiv2025

Graph Foundation Models: A Comprehensive Survey

Graph-structured data pervades domains such as social networks, biological systems, knowledge graphs, and recommender systems. While foundation models have transformed natural language processing, vision, and multimodal learning through large-scale pretraining and generalization, extending these capabilities to graphs -- characterized by non-Euclidean structures and complex relational semantics -- poses unique challenges and opens new opportunities. To this end, Graph Foundation Models (GFMs) aim to bring scalable, general-purpose intelligence to structured data, enabling broad transfer across graph-centric tasks and domains. This survey provides a comprehensive overview of GFMs, unifying diverse efforts under a modular framework comprising three key components: backbone architectures, pretraining strategies, and adaptation mechanisms. We categorize GFMs by their generalization scope -- universal, task-specific, and domain-specific -- and review representative methods, key innovations, and theoretical insights within each category. Beyond methodology, we examine theoretical foundations including transferability and emergent capabilities, and highlight key challenges such as structural alignment, heterogeneity, scalability, and evaluation. Positioned at the intersection of graph learning and general-purpose AI, GFMs are poised to become foundational infrastructure for open-ended reasoning over structured data. This survey consolidates current progress and outlines future directions to guide research in this rapidly evolving field. Resources are available at https://github.com/Zehong-Wang/Awesome-Foundation-Models-on-Graphs.

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arXiv2025

AutoData: A Multi-Agent System for Open Web Data Collection

The exponential growth of data-driven systems and AI technologies has intensified the demand for high-quality web-sourced datasets. While existing datasets have proven valuable, conventional web data collection approaches face significant limitations in terms of human effort and scalability. Current data-collecting solutions fall into two categories: wrapper-based methods that struggle with adaptability and reproducibility, and large language model (LLM)-based approaches that incur substantial computational and financial costs. To address these challenges, we propose AutoData, a novel multi-agent system for Automated web Data collection, that requires minimal human intervention, i.e., only necessitating a natural language instruction specifying the desired dataset. In addition, AutoData is designed with a robust multi-agent architecture, featuring a novel oriented message hypergraph coordinated by a central task manager, to efficiently organize agents across research and development squads. Besides, we introduce a novel hypergraph cache system to advance the multi-agent collaboration process that enables efficient automated data collection and mitigates the token cost issues prevalent in existing LLM-based systems. Moreover, we introduce Instruct2DS, a new benchmark dataset supporting live data collection from web sources across three domains: academic, finance, and sports. Comprehensive evaluations over Instruct2DS and three existing benchmark datasets demonstrate AutoData's superior performance compared to baseline methods. Case studies on challenging tasks such as picture book collection and paper extraction from surveys further validate its applicability. Our source code and dataset are available at https://github.com/GraphResearcher/AutoData.

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arXiv2025

LLM-Empowered Class Imbalanced Graph Prompt Learning for Online Drug Trafficking Detection

As the market for illicit drugs remains extremely profitable, major online platforms have become direct-to-consumer intermediaries for illicit drug trafficking participants. These online activities raise significant social concerns that require immediate actions. Existing approaches to combating this challenge are generally impractical, due to the imbalance of classes and scarcity of labeled samples in real-world applications. To this end, we propose a novel Large Language Model-empowered Heterogeneous Graph Prompt Learning framework for illicit Drug Trafficking detection, called LLM-HetGDT, that leverages LLM to facilitate heterogeneous graph neural networks (HGNNs) to effectively identify drug trafficking activities in the class-imbalanced scenarios. Specifically, we first pre-train HGNN over a contrastive pretext task to capture the inherent node and structure information over the unlabeled drug trafficking heterogeneous graph (HG). Afterward, we employ LLM to augment the HG by generating high-quality synthetic user nodes in minority classes. Then, we fine-tune the soft prompts on the augmented HG to capture the important information in the minority classes for the downstream drug trafficking detection task. To comprehensively study online illicit drug trafficking activities, we collect a new HG dataset over Twitter, called Twitter-HetDrug. Extensive experiments on this dataset demonstrate the effectiveness, efficiency, and applicability of LLM-HetGDT.

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