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Qiaoyu Tan

Publications and source records attributed to Qiaoyu Tan.

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

GraphSearch: Agentic Search-Augmented Reasoning for Zero-Shot Graph Learning

Recent advances in search-augmented large reasoning models (LRMs) enable the retrieval of external knowledge to reduce hallucinations in multistep reasoning. However, their ability to operate on graph-structured data, prevalent in domains such as e-commerce, social networks, and scientific citations, remains underexplored. Unlike plain text corpora, graphs encode rich topological signals that connect related entities and can serve as valuable priors for retrieval, enabling more targeted search and improved reasoning efficiency. Yet, effectively leveraging such structure poses unique challenges, including the difficulty of generating graph-expressive queries and ensuring reliable retrieval that balances structural and semantic relevance. To address this gap, we introduce GraphSearch, the first framework that extends search-augmented reasoning to graph learning, enabling zero-shot graph learning without task-specific fine-tuning. GraphSearch combines a Graph-aware Query Planner, which disentangles search space (e.g., 1-hop, multi-hop, or global neighbors) from semantic queries, with a Graph-aware Retriever, which constructs candidate sets based on topology and ranks them using a hybrid scoring function. We further instantiate two traversal modes: GraphSearch-R, which recursively expands neighborhoods hop by hop, and GraphSearch-F, which flexibly retrieves across local and global neighborhoods without hop constraints. Extensive experiments across diverse benchmarks show that GraphSearch achieves competitive or even superior performance compared to supervised graph learning methods, setting state-of-the-art results in zero-shot node classification and link prediction. These findings position GraphSearch as a flexible and generalizable paradigm for agentic reasoning over graphs.

cs.CL↗
arXiv2025

CrystalICL: Enabling In-Context Learning for Crystal Generation

Designing crystal materials with desired physicochemical properties remains a fundamental challenge in materials science. While large language models (LLMs) have demonstrated strong in-context learning (ICL) capabilities, existing LLM-based crystal generation approaches are limited to zero-shot scenarios and are unable to benefit from few-shot scenarios. In contrast, human experts typically design new materials by modifying relevant known structures which aligns closely with the few-shot ICL paradigm. Motivated by this, we propose CrystalICL, a novel model designed for few-shot crystal generation. Specifically, we introduce a space-group based crystal tokenization method, which effectively reduces the complexity of modeling crystal symmetry in LLMs. We further introduce a condition-structure aware hybrid instruction tuning framework and a multi-task instruction tuning strategy, enabling the model to better exploit ICL by capturing structure-property relationships from limited data. Extensive experiments on four crystal generation benchmarks demonstrate the superiority of CrystalICL over the leading baseline methods on conditional and unconditional generation tasks.

cs.LG↗
arXiv2025

TrustGLM: Evaluating the Robustness of GraphLLMs Against Prompt, Text, and Structure Attacks

Inspired by the success of large language models (LLMs), there is a significant research shift from traditional graph learning methods to LLM-based graph frameworks, formally known as GraphLLMs. GraphLLMs leverage the reasoning power of LLMs by integrating three key components: the textual attributes of input nodes, the structural information of node neighborhoods, and task-specific prompts that guide decision-making. Despite their promise, the robustness of GraphLLMs against adversarial perturbations remains largely unexplored-a critical concern for deploying these models in high-stakes scenarios. To bridge the gap, we introduce TrustGLM, a comprehensive study evaluating the vulnerability of GraphLLMs to adversarial attacks across three dimensions: text, graph structure, and prompt manipulations. We implement state-of-the-art attack algorithms from each perspective to rigorously assess model resilience. Through extensive experiments on six benchmark datasets from diverse domains, our findings reveal that GraphLLMs are highly susceptible to text attacks that merely replace a few semantically similar words in a node's textual attribute. We also find that standard graph structure attack methods can significantly degrade model performance, while random shuffling of the candidate label set in prompt templates leads to substantial performance drops. Beyond characterizing these vulnerabilities, we investigate defense techniques tailored to each attack vector through data-augmented training and adversarial training, which show promising potential to enhance the robustness of GraphLLMs. We hope that our open-sourced library will facilitate rapid, equitable evaluation and inspire further innovative research in this field.

cs.LG↗
arXiv2025

Graph-MLLM: Harnessing Multimodal Large Language Models for Multimodal Graph Learning

Multimodal Large Language Models (MLLMs) have demonstrated remarkable capabilities in representing and understanding diverse modalities. However, they typically focus on modality alignment in a pairwise manner while overlooking structural relationships across data points. Integrating multimodality with structured graph information (i.e., multimodal graphs, MMGs) is essential for real-world applications such as social networks, healthcare, and recommendation systems. Existing MMG learning methods fall into three paradigms based on how they leverage MLLMs: Encoder, Aligner, and Predictor. MLLM-as-Encoder focuses on enhancing graph neural networks (GNNs) via multimodal feature fusion; MLLM-as-Aligner aligns multimodal attributes in language or hidden space to enable LLM-based graph reasoning; MLLM-as-Predictor treats MLLMs as standalone reasoners with in-context learning or fine-tuning. Despite their advances, the MMG field lacks a unified benchmark to fairly evaluate across these approaches, making it unclear what progress has been made. To bridge this gap, we present Graph-MLLM, a comprehensive benchmark for multimodal graph learning by systematically evaluating these three paradigms across six datasets with different domains. Through extensive experiments, we observe that jointly considering the visual and textual attributes of the nodes benefits graph learning, even when using pre-trained text-to-image alignment models (e.g., CLIP) as encoders. We also find that converting visual attributes into textual descriptions further improves performance compared to directly using visual inputs. Moreover, we observe that fine-tuning MLLMs on specific MMGs can achieve state-of-the-art results in most scenarios, even without explicit graph structure information. We hope that our open-sourced library will facilitate rapid, equitable evaluation and inspire further innovative research in this field.

cs.LG↗
arXiv2025

Concept-Centric Token Interpretation for Vector-Quantized Generative Models

Vector-Quantized Generative Models (VQGMs) have emerged as powerful tools for image generation. However, the key component of VQGMs -- the codebook of discrete tokens -- is still not well understood, e.g., which tokens are critical to generate an image of a certain concept? This paper introduces Concept-Oriented Token Explanation (CORTEX), a novel approach for interpreting VQGMs by identifying concept-specific token combinations. Our framework employs two methods: (1) a sample-level explanation method that analyzes token importance scores in individual images, and (2) a codebook-level explanation method that explores the entire codebook to find globally relevant tokens. Experimental results demonstrate CORTEX's efficacy in providing clear explanations of token usage in the generative process, outperforming baselines across multiple pretrained VQGMs. Besides enhancing VQGMs transparency, CORTEX is useful in applications such as targeted image editing and shortcut feature detection. Our code is available at https://github.com/YangTianze009/CORTEX.

cs.CV↗
arXiv2025

GRAPHGPT-O: Synergistic Multimodal Comprehension and Generation on Graphs

The rapid development of Multimodal Large Language Models (MLLMs) has enabled the integration of multiple modalities, including texts and images, within the large language model (LLM) framework. However, texts and images are usually interconnected, forming a multimodal attributed graph (MMAG). It is underexplored how MLLMs can incorporate the relational information (\textit{i.e.}, graph structure) and semantic information (\textit{i.e.,} texts and images) on such graphs for multimodal comprehension and generation. In this paper, we propose GraphGPT-o, which supports omni-multimodal understanding and creation on MMAGs. We first comprehensively study linearization variants to transform semantic and structural information as input for MLLMs. Then, we propose a hierarchical aligner that enables deep graph encoding, bridging the gap between MMAGs and MLLMs. Finally, we explore the inference choices, adapting MLLM to interleaved text and image generation in graph scenarios. Extensive experiments on three datasets from different domains demonstrate the effectiveness of our proposed method. Datasets and codes will be open-sourced upon acceptance.

cs.AI↗
arXiv2025

GraphICL: Unlocking Graph Learning Potential in LLMs through Structured Prompt Design

The growing importance of textual and relational systems has driven interest in enhancing large language models (LLMs) for graph-structured data, particularly Text-Attributed Graphs (TAGs), where samples are represented by textual descriptions interconnected by edges. While research has largely focused on developing specialized graph LLMs through task-specific instruction tuning, a comprehensive benchmark for evaluating LLMs solely through prompt design remains surprisingly absent. Without such a carefully crafted evaluation benchmark, most if not all, tailored graph LLMs are compared against general LLMs using simplistic queries (e.g., zero-shot reasoning with LLaMA), which can potentially camouflage many advantages as well as unexpected predicaments of them. To achieve more general evaluations and unveil the true potential of LLMs for graph tasks, we introduce Graph In-context Learning (GraphICL) Benchmark, a comprehensive benchmark comprising novel prompt templates designed to capture graph structure and handle limited label knowledge. Our systematic evaluation shows that general-purpose LLMs equipped with our GraphICL outperform state-of-the-art specialized graph LLMs and graph neural network models in resource-constrained settings and out-of-domain tasks. These findings highlight the significant potential of prompt engineering to enhance LLM performance on graph learning tasks without training and offer a strong baseline for advancing research in graph LLMs.

cs.LG↗
arXiv2024

UniGLM: Training One Unified Language Model for Text-Attributed Graph Embedding

Representation learning on text-attributed graphs (TAGs), where nodes are represented by textual descriptions, is crucial for textual and relational knowledge systems and recommendation systems. Currently, state-of-the-art embedding methods for TAGs primarily focus on fine-tuning language models (e.g., BERT) using structure-aware training signals. While effective, these methods are tailored for individual TAG and cannot generalize across various graph scenarios. Given the shared textual space, leveraging multiple TAGs for joint fine-tuning, aligning text and graph structure from different aspects, would be more beneficial. Motivated by this, we introduce a novel Unified Graph Language Model (UniGLM) framework, the first graph embedding model that generalizes well to both in-domain and cross-domain TAGs. Specifically, UniGLM is trained over multiple TAGs with different domains and scales using self-supervised contrastive learning. UniGLM includes an adaptive positive sample selection technique for identifying structurally similar nodes and a lazy contrastive module that is devised to accelerate training by minimizing repetitive encoding calculations. Extensive empirical results across 9 benchmark TAGs demonstrate UniGLM's efficacy against leading embedding baselines in terms of generalization (various downstream tasks and backbones) and transfer learning (in and out of domain scenarios). The code is available at https://github.com/NYUSHCS/UniGLM.

cs.CL↗
arXiv2024

Better Late Than Never: Formulating and Benchmarking Recommendation Editing

Recommendation systems play a pivotal role in suggesting items to users based on their preferences. However, in online platforms, these systems inevitably offer unsuitable recommendations due to limited model capacity, poor data quality, or evolving user interests. Enhancing user experience necessitates efficiently rectify such unsuitable recommendation behaviors. This paper introduces a novel and significant task termed recommendation editing, which focuses on modifying known and unsuitable recommendation behaviors. Specifically, this task aims to adjust the recommendation model to eliminate known unsuitable items without accessing training data or retraining the model. We formally define the problem of recommendation editing with three primary objectives: strict rectification, collaborative rectification, and concentrated rectification. Three evaluation metrics are developed to quantitatively assess the achievement of each objective. We present a straightforward yet effective benchmark for recommendation editing using novel Editing Bayesian Personalized Ranking Loss. To demonstrate the effectiveness of the proposed method, we establish a comprehensive benchmark that incorporates various methods from related fields. Codebase is available at https://github.com/cycl2018/Recommendation-Editing.

cs.IR↗
arXiv2024

Gradient Rewiring for Editable Graph Neural Network Training

Deep neural networks are ubiquitously adopted in many applications, such as computer vision, natural language processing, and graph analytics. However, well-trained neural networks can make prediction errors after deployment as the world changes. \textit{Model editing} involves updating the base model to correct prediction errors with less accessible training data and computational resources. Despite recent advances in model editors in computer vision and natural language processing, editable training in graph neural networks (GNNs) is rarely explored. The challenge with editable GNN training lies in the inherent information aggregation across neighbors, which can lead model editors to affect the predictions of other nodes unintentionally. In this paper, we first observe the gradient of cross-entropy loss for the target node and training nodes with significant inconsistency, which indicates that directly fine-tuning the base model using the loss on the target node deteriorates the performance on training nodes. Motivated by the gradient inconsistency observation, we propose a simple yet effective \underline{G}radient \underline{R}ewiring method for \underline{E}ditable graph neural network training, named \textbf{GRE}. Specifically, we first store the anchor gradient of the loss on training nodes to preserve the locality. Subsequently, we rewire the gradient of the loss on the target node to preserve performance on the training node using anchor gradient. Experiments demonstrate the effectiveness of GRE on various model architectures and graph datasets in terms of multiple editing situations. The source code is available at \url{https://github.com/zhimengj0326/Gradient_rewiring_editing}

cs.LG↗
arXiv2024

MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction

Molecular property prediction (MPP) is a fundamental and crucial task in drug discovery. However, prior methods are limited by the requirement for a large number of labeled molecules and their restricted ability to generalize for unseen and new tasks, both of which are essential for real-world applications. To address these challenges, we present MolecularGPT for few-shot MPP. From a perspective on instruction tuning, we fine-tune large language models (LLMs) based on curated molecular instructions spanning over 1000 property prediction tasks. This enables building a versatile and specialized LLM that can be adapted to novel MPP tasks without any fine-tuning through zero- and few-shot in-context learning (ICL). MolecularGPT exhibits competitive in-context reasoning capabilities across 10 downstream evaluation datasets, setting new benchmarks for few-shot molecular prediction tasks. More importantly, with just two-shot examples, MolecularGPT can outperform standard supervised graph neural network methods on 4 out of 7 datasets. It also excels state-of-the-art LLM baselines by up to 15.7% increase on classification accuracy and decrease of 17.9 on regression metrics (e.g., RMSE) under zero-shot. This study demonstrates the potential of LLMs as effective few-shot molecular property predictors. The code is available at https://github.com/NYUSHCS/MolecularGPT.

q-bio.QM↗
arXiv2024

Retrieval-enhanced Knowledge Editing in Language Models for Multi-Hop Question Answering

Large Language Models (LLMs) have shown proficiency in question-answering tasks but often struggle to integrate real-time knowledge, leading to potentially outdated or inaccurate responses. This problem becomes even more challenging when dealing with multi-hop questions, since they require LLMs to update and integrate multiple knowledge pieces relevant to the questions. To tackle the problem, we propose the Retrieval-Augmented model Editing (RAE) framework for multi-hop question answering. RAE first retrieves edited facts and then refines the language model through in-context learning. Specifically, our retrieval approach, based on mutual information maximization, leverages the reasoning abilities of LLMs to identify chain facts that traditional similarity-based searches might miss. In addition, our framework includes a pruning strategy to eliminate redundant information from the retrieved facts, which enhances the editing accuracy and mitigates the hallucination problem. Our framework is supported by theoretical justification for its fact retrieval efficacy. Finally, comprehensive evaluation across various LLMs validates RAE's ability in providing accurate answers with updated knowledge. Our code is available at: https://github.com/sycny/RAE.

cs.CL↗
arXiv2024

Reasoning Like a Doctor: Improving Medical Dialogue Systems via Diagnostic Reasoning Process Alignment

Medical dialogue systems have attracted significant attention for their potential to act as medical assistants. Enabling these medical systems to emulate clinicians' diagnostic reasoning process has been the long-standing research focus. Previous studies rudimentarily realized the simulation of clinicians' diagnostic process by fine-tuning language models on high-quality dialogue datasets. Nonetheless, they overly focus on the outcomes of the clinician's reasoning process while ignoring their internal thought processes and alignment with clinician preferences. Our work aims to build a medical dialogue system that aligns with clinicians' diagnostic reasoning processes. We propose a novel framework, Emulation, designed to generate an appropriate response that relies on abductive and deductive diagnostic reasoning analyses and aligns with clinician preferences through thought process modeling. Experimental results on two datasets confirm the efficacy of Emulation. Crucially, our framework furnishes clear explanations for the generated responses, enhancing its transparency in medical consultations.

cs.CL↗
arXiv2024

GAugLLM: Improving Graph Contrastive Learning for Text-Attributed Graphs with Large Language Models

This work studies self-supervised graph learning for text-attributed graphs (TAGs) where nodes are represented by textual attributes. Unlike traditional graph contrastive methods that perturb the numerical feature space and alter the graph's topological structure, we aim to improve view generation through language supervision. This is driven by the prevalence of textual attributes in real applications, which complement graph structures with rich semantic information. However, this presents challenges because of two major reasons. First, text attributes often vary in length and quality, making it difficulty to perturb raw text descriptions without altering their original semantic meanings. Second, although text attributes complement graph structures, they are not inherently well-aligned. To bridge the gap, we introduce GAugLLM, a novel framework for augmenting TAGs. It leverages advanced large language models like Mistral to enhance self-supervised graph learning. Specifically, we introduce a mixture-of-prompt-expert technique to generate augmented node features. This approach adaptively maps multiple prompt experts, each of which modifies raw text attributes using prompt engineering, into numerical feature space. Additionally, we devise a collaborative edge modifier to leverage structural and textual commonalities, enhancing edge augmentation by examining or building connections between nodes. Empirical results across five benchmark datasets spanning various domains underscore our framework's ability to enhance the performance of leading contrastive methods as a plug-in tool. Notably, we observe that the augmented features and graph structure can also enhance the performance of standard generative methods, as well as popular graph neural networks. The open-sourced implementation of our GAugLLM is available at Github.

cs.LG↗
arXiv2024

GraphFM: A Comprehensive Benchmark for Graph Foundation Model

Foundation Models (FMs) serve as a general class for the development of artificial intelligence systems, offering broad potential for generalization across a spectrum of downstream tasks. Despite extensive research into self-supervised learning as the cornerstone of FMs, several outstanding issues persist in Graph Foundation Models that rely on graph self-supervised learning, namely: 1) Homogenization. The extent of generalization capability on downstream tasks remains unclear. 2) Scalability. It is unknown how effectively these models can scale to large datasets. 3) Efficiency. The training time and memory usage of these models require evaluation. 4) Training Stop Criteria. Determining the optimal stopping strategy for pre-training across multiple tasks to maximize performance on downstream tasks. To address these questions, we have constructed a rigorous benchmark that thoroughly analyzes and studies the generalization and scalability of self-supervised Graph Neural Network (GNN) models. Regarding generalization, we have implemented and compared the performance of various self-supervised GNN models, trained to generate node representations, across tasks such as node classification, link prediction, and node clustering. For scalability, we have compared the performance of various models after training using full-batch and mini-batch strategies. Additionally, we have assessed the training efficiency of these models by conducting experiments to test their GPU memory usage and throughput. Through these experiments, we aim to provide insights to motivate future research. The code for this benchmark is publicly available at https://github.com/NYUSHCS/GraphFM.

cs.LG↗
arXiv2024

Towards a Unified Framework of Clustering-based Anomaly Detection

Unsupervised Anomaly Detection (UAD) plays a crucial role in identifying abnormal patterns within data without labeled examples, holding significant practical implications across various domains. Although the individual contributions of representation learning and clustering to anomaly detection are well-established, their interdependencies remain under-explored due to the absence of a unified theoretical framework. Consequently, their collective potential to enhance anomaly detection performance remains largely untapped. To bridge this gap, in this paper, we propose a novel probabilistic mixture model for anomaly detection to establish a theoretical connection among representation learning, clustering, and anomaly detection. By maximizing a novel anomaly-aware data likelihood, representation learning and clustering can effectively reduce the adverse impact of anomalous data and collaboratively benefit anomaly detection. Meanwhile, a theoretically substantiated anomaly score is naturally derived from this framework. Lastly, drawing inspiration from gravitational analysis in physics, we have devised an improved anomaly score that more effectively harnesses the combined power of representation learning and clustering. Extensive experiments, involving 17 baseline methods across 30 diverse datasets, validate the effectiveness and generalization capability of the proposed method, surpassing state-of-the-art methods.

cs.LG↗
arXiv2024

E2GNN: Efficient Graph Neural Network Ensembles for Semi-Supervised Classification

This work studies ensemble learning for graph neural networks (GNNs) under the popular semi-supervised setting. Ensemble learning has shown superiority in improving the accuracy and robustness of traditional machine learning by combining the outputs of multiple weak learners. However, adopting a similar idea to integrate different GNN models is challenging because of two reasons. First, GNN is notorious for its poor inference ability, so naively assembling multiple GNN models would deteriorate the inference efficiency. Second, when GNN models are trained with few labeled nodes, their performance are limited. In this case, the vanilla ensemble approach, e.g., majority vote, may be sub-optimal since most base models, i.e., GNNs, may make the wrong predictions. To this end, in this paper, we propose an efficient ensemble learner--E2GNN to assemble multiple GNNs in a learnable way by leveraging both labeled and unlabeled nodes. Specifically, we first pre-train different GNN models on a given data scenario according to the labeled nodes. Next, instead of directly combing their outputs for label inference, we train a simple multi-layer perceptron--MLP model to mimic their predictions on both labeled and unlabeled nodes. Then the unified MLP model is deployed to infer labels for unlabeled or new nodes. Since the predictions of unlabeled nodes from different GNN models may be incorrect, we develop a reinforced discriminator to effectively filter out those wrongly predicted nodes to boost the performance of MLP. By doing this, we suggest a principled approach to tackle the inference issues of GNN ensembles and maintain the merit of ensemble learning: improved performance. Comprehensive experiments over both transductive and inductive settings, across different GNN backbones and 8 benchmark datasets, demonstrate the superiority of E2GNN.

cs.LG↗
arXiv2023

OpenGSL: A Comprehensive Benchmark for Graph Structure Learning

Graph Neural Networks (GNNs) have emerged as the de facto standard for representation learning on graphs, owing to their ability to effectively integrate graph topology and node attributes. However, the inherent suboptimal nature of node connections, resulting from the complex and contingent formation process of graphs, presents significant challenges in modeling them effectively. To tackle this issue, Graph Structure Learning (GSL), a family of data-centric learning approaches, has garnered substantial attention in recent years. The core concept behind GSL is to jointly optimize the graph structure and the corresponding GNN models. Despite the proposal of numerous GSL methods, the progress in this field remains unclear due to inconsistent experimental protocols, including variations in datasets, data processing techniques, and splitting strategies. In this paper, we introduce OpenGSL, the first comprehensive benchmark for GSL, aimed at addressing this gap. OpenGSL enables a fair comparison among state-of-the-art GSL methods by evaluating them across various popular datasets using uniform data processing and splitting strategies. Through extensive experiments, we observe that existing GSL methods do not consistently outperform vanilla GNN counterparts. We also find that there is no significant correlation between the homophily of the learned structure and task performance, challenging the common belief. Moreover, we observe that the learned graph structure demonstrates a strong generalization ability across different GNN models, despite the high computational and space consumption. We hope that our open-sourced library will facilitate rapid and equitable evaluation and inspire further innovative research in this field. The code of the benchmark can be found in https://github.com/OpenGSL/OpenGSL.

cs.LG↗