arXiv subjects

Jundong Li

Publications and source records attributed to Jundong Li.

At least 73 records · Page 4Linked to original sources

arXiv2025

Edge Prompt Tuning for Graph Neural Networks

Pre-training powerful Graph Neural Networks (GNNs) with unlabeled graph data in a self-supervised manner has emerged as a prominent technique in recent years. However, inevitable objective gaps often exist between pre-training and downstream tasks. To bridge this gap, graph prompt tuning techniques design and learn graph prompts by manipulating input graphs or reframing downstream tasks as pre-training tasks without fine-tuning the pre-trained GNN models. While recent graph prompt tuning methods have proven effective in adapting pre-trained GNN models for downstream tasks, they overlook the crucial role of edges in graph prompt design, which can significantly affect the quality of graph representations for downstream tasks. In this study, we propose EdgePrompt, a simple yet effective graph prompt tuning method from the perspective of edges. Unlike previous studies that design prompt vectors on node features, EdgePrompt manipulates input graphs by learning additional prompt vectors for edges and incorporates the edge prompts through message passing in the pre-trained GNN models to better embed graph structural information for downstream tasks. Our method is compatible with prevalent GNN architectures pre-trained under various pre-training strategies and is universal for different downstream tasks. We provide comprehensive theoretical analyses of our method regarding its capability of handling node classification and graph classification as downstream tasks. Extensive experiments on ten graph datasets under four pre-training strategies demonstrate the superiority of our proposed method against six baselines. Our code is available at https://github.com/xbfu/EdgePrompt.

cs.LG↗

arXiv2025

CEB: Compositional Evaluation Benchmark for Fairness in Large Language Models

As Large Language Models (LLMs) are increasingly deployed to handle various natural language processing (NLP) tasks, concerns regarding the potential negative societal impacts of LLM-generated content have also arisen. To evaluate the biases exhibited by LLMs, researchers have recently proposed a variety of datasets. However, existing bias evaluation efforts often focus on only a particular type of bias and employ inconsistent evaluation metrics, leading to difficulties in comparison across different datasets and LLMs. To address these limitations, we collect a variety of datasets designed for the bias evaluation of LLMs, and further propose CEB, a Compositional Evaluation Benchmark that covers different types of bias across different social groups and tasks. The curation of CEB is based on our newly proposed compositional taxonomy, which characterizes each dataset from three dimensions: bias types, social groups, and tasks. By combining the three dimensions, we develop a comprehensive evaluation strategy for the bias in LLMs. Our experiments demonstrate that the levels of bias vary across these dimensions, thereby providing guidance for the development of specific bias mitigation methods.

cs.CL↗

arXiv2025

Virtual Nodes Can Help: Tackling Distribution Shifts in Federated Graph Learning

Federated Graph Learning (FGL) enables multiple clients to jointly train powerful graph learning models, e.g., Graph Neural Networks (GNNs), without sharing their local graph data for graph-related downstream tasks, such as graph property prediction. In the real world, however, the graph data can suffer from significant distribution shifts across clients as the clients may collect their graph data for different purposes. In particular, graph properties are usually associated with invariant label-relevant substructures (i.e., subgraphs) across clients, while label-irrelevant substructures can appear in a client-specific manner. The issue of distribution shifts of graph data hinders the efficiency of GNN training and leads to serious performance degradation in FGL. To tackle the aforementioned issue, we propose a novel FGL framework entitled FedVN that eliminates distribution shifts through client-specific graph augmentation strategies with multiple learnable Virtual Nodes (VNs). Specifically, FedVN lets the clients jointly learn a set of shared VNs while training a global GNN model. To eliminate distribution shifts, each client trains a personalized edge generator that determines how the VNs connect local graphs in a client-specific manner. Furthermore, we provide theoretical analyses indicating that FedVN can eliminate distribution shifts of graph data across clients. Comprehensive experiments on four datasets under five settings demonstrate the superiority of our proposed FedVN over nine baselines.

cs.LG↗

arXiv2025

Collaborative Retrieval for Large Language Model-based Conversational Recommender Systems

Conversational recommender systems (CRS) aim to provide personalized recommendations via interactive dialogues with users. While large language models (LLMs) enhance CRS with their superior understanding of context-aware user preferences, they typically struggle to leverage behavioral data, which have proven to be important for classical collaborative filtering (CF)-based approaches. For this reason, we propose CRAG, Collaborative Retrieval Augmented Generation for LLM-based CRS. To the best of our knowledge, CRAG is the first approach that combines state-of-the-art LLMs with CF for conversational recommendations. Our experiments on two publicly available movie conversational recommendation datasets, i.e., a refined Reddit dataset (which we name Reddit-v2) as well as the Redial dataset, demonstrate the superior item coverage and recommendation performance of CRAG, compared to several CRS baselines. Moreover, we observe that the improvements are mainly due to better recommendation accuracy on recently released movies. The code and data are available at https://github.com/yaochenzhu/CRAG.

cs.IR↗

arXiv2025

Generative Risk Minimization for Out-of-Distribution Generalization on Graphs

Out-of-distribution (OOD) generalization on graphs aims at dealing with scenarios where the test graph distribution differs from the training graph distributions. Compared to i.i.d. data like images, the OOD generalization problem on graph-structured data remains challenging due to the non-i.i.d. property and complex structural information on graphs. Recently, several works on graph OOD generalization have explored extracting invariant subgraphs that share crucial classification information across different distributions. Nevertheless, such a strategy could be suboptimal for entirely capturing the invariant information, as the extraction of discrete structures could potentially lead to the loss of invariant information or the involvement of spurious information. In this paper, we propose an innovative framework, named Generative Risk Minimization (GRM), designed to generate an invariant subgraph for each input graph to be classified, instead of extraction. To address the challenge of optimization in the absence of optimal invariant subgraphs (i.e., ground truths), we derive a tractable form of the proposed GRM objective by introducing a latent causal variable, and its effectiveness is validated by our theoretical analysis. We further conduct extensive experiments across a variety of real-world graph datasets for both node-level and graph-level OOD generalization, and the results demonstrate the superiority of our framework GRM.

cs.LG↗

arXiv2025

BrainMAP: Learning Multiple Activation Pathways in Brain Networks

Functional Magnetic Resonance Image (fMRI) is commonly employed to study human brain activity, since it offers insight into the relationship between functional fluctuations and human behavior. To enhance analysis and comprehension of brain activity, Graph Neural Networks (GNNs) have been widely applied to the analysis of functional connectivities (FC) derived from fMRI data, due to their ability to capture the synergistic interactions among brain regions. However, in the human brain, performing complex tasks typically involves the activation of certain pathways, which could be represented as paths across graphs. As such, conventional GNNs struggle to learn from these pathways due to the long-range dependencies of multiple pathways. To address these challenges, we introduce a novel framework BrainMAP to learn Multiple Activation Pathways in Brain networks. BrainMAP leverages sequential models to identify long-range correlations among sequentialized brain regions and incorporates an aggregation module based on Mixture of Experts (MoE) to learn from multiple pathways. Our comprehensive experiments highlight BrainMAP's superior performance. Furthermore, our framework enables explanatory analyses of crucial brain regions involved in tasks. Our code is provided at https://github.com/LzyFischer/Graph-Mamba.

cs.AI↗

arXiv2025

Resolving Editing-Unlearning Conflicts: A Knowledge Codebook Framework for Large Language Model Updating

Large Language Models (LLMs) excel in natural language processing by encoding extensive human knowledge, but their utility relies on timely updates as knowledge evolves. Updating LLMs involves two key tasks simultaneously: unlearning to remove unwanted knowledge and editing to incorporate new information. Existing methods face two major challenges: ineffective knowledge storage (either too sparse or too dense) and task conflicts between editing and unlearning, as validated through our theoretical and experimental results. To address these issues, we propose LOKA, a conflict-free framework for LLM updating based on a knowledge codebook. During training, updated knowledge is stored in multiple codebook memories. To optimize knowledge storage, a similarity-aware knowledge mapping ensures that related knowledge pieces are clustered and allocated to the same memory. Additionally, LOKA resolves task conflicts by employing task-specific and multi-task memories guided by a conflict score. In the inference stage, LOKA retrieves the most relevant memory from the codebook and plugs it into the original LLM to apply the updated knowledge. A learning-based router controls codebook activation to further improve knowledge utilization. Extensive experiments demonstrate the effectiveness of LOKA in LLM knowledge updating tasks.

cs.CL↗

arXiv2025

Collaborative Diffusion Model for Recommender System

Diffusion-based recommender systems (DR) have gained increasing attention for their advanced generative and denoising capabilities. However, existing DR face two central limitations: (i) a trade-off between enhancing generative capacity via noise injection and retaining the loss of personalized information. (ii) the underutilization of rich item-side information. To address these challenges, we present a Collaborative Diffusion model for Recommender System (CDiff4Rec). Specifically, CDiff4Rec generates pseudo-users from item features and leverages collaborative signals from both real and pseudo personalized neighbors identified through behavioral similarity, thereby effectively reconstructing nuanced user preferences. Experimental results on three public datasets show that CDiff4Rec outperforms competitors by effectively mitigating the loss of personalized information through the integration of item content and collaborative signals.

cs.IR↗

arXiv2025

Enhancing Distribution and Label Consistency for Graph Out-of-Distribution Generalization

To deal with distribution shifts in graph data, various graph out-of-distribution (OOD) generalization techniques have been recently proposed. These methods often employ a two-step strategy that first creates augmented environments and subsequently identifies invariant subgraphs to improve generalizability. Nevertheless, this approach could be suboptimal from the perspective of consistency. First, the process of augmenting environments by altering the graphs while preserving labels may lead to graphs that are not realistic or meaningfully related to the origin distribution, thus lacking distribution consistency. Second, the extracted subgraphs are obtained from directly modifying graphs, and may not necessarily maintain a consistent predictive relationship with their labels, thereby impacting label consistency. In response to these challenges, we introduce an innovative approach that aims to enhance these two types of consistency for graph OOD generalization. We propose a modifier to obtain both augmented and invariant graphs in a unified manner. With the augmented graphs, we enrich the training data without compromising the integrity of label-graph relationships. The label consistency enhancement in our framework further preserves the supervision information in the invariant graph. We conduct extensive experiments on real-world datasets to demonstrate the superiority of our framework over other state-of-the-art baselines.

cs.LG↗

arXiv2025

KG-CF: Knowledge Graph Completion with Context Filtering under the Guidance of Large Language Models

Large Language Models (LLMs) have shown impressive performance in various tasks, including knowledge graph completion (KGC). However, current studies mostly apply LLMs to classification tasks, like identifying missing triplets, rather than ranking-based tasks, where the model ranks candidate entities based on plausibility. This focus limits the practical use of LLMs in KGC, as real-world applications prioritize highly plausible triplets. Additionally, while graph paths can help infer the existence of missing triplets and improve completion accuracy, they often contain redundant information. To address these issues, we propose KG-CF, a framework tailored for ranking-based KGC tasks. KG-CF leverages LLMs' reasoning abilities to filter out irrelevant contexts, achieving superior results on real-world datasets. The code and datasets are available at \url{https://anonymous.4open.science/r/KG-CF}.

cs.AI↗

arXiv2024

ST-FiT: Inductive Spatial-Temporal Forecasting with Limited Training Data

Spatial-temporal graphs are widely used in a variety of real-world applications. Spatial-Temporal Graph Neural Networks (STGNNs) have emerged as a powerful tool to extract meaningful insights from this data. However, in real-world applications, most nodes may not possess any available temporal data during training. For example, the pandemic dynamics of most cities on a geographical graph may not be available due to the asynchronous nature of outbreaks. Such a phenomenon disagrees with the training requirements of most existing spatial-temporal forecasting methods, which jeopardizes their effectiveness and thus blocks broader deployment. In this paper, we propose to formulate a novel problem of inductive forecasting with limited training data. In particular, given a spatial-temporal graph, we aim to learn a spatial-temporal forecasting model that can be easily generalized onto those nodes without any available temporal training data. To handle this problem, we propose a principled framework named ST-FiT. ST-FiT consists of two key learning components: temporal data augmentation and spatial graph topology learning. With such a design, ST-FiT can be used on top of any existing STGNNs to achieve superior performance on the nodes without training data. Extensive experiments verify the effectiveness of ST-FiT in multiple key perspectives.

cs.LG↗

arXiv2024

Graph Neural Networks Are More Than Filters: Revisiting and Benchmarking from A Spectral Perspective

Graph Neural Networks (GNNs) have achieved remarkable success in various graph-based learning tasks. While their performance is often attributed to the powerful neighborhood aggregation mechanism, recent studies suggest that other components such as non-linear layers may also significantly affecting how GNNs process the input graph data in the spectral domain. Such evidence challenges the prevalent opinion that neighborhood aggregation mechanisms dominate the behavioral characteristics of GNNs in the spectral domain. To demystify such a conflict, this paper introduces a comprehensive benchmark to measure and evaluate GNNs' capability in capturing and leveraging the information encoded in different frequency components of the input graph data. Specifically, we first conduct an exploratory study demonstrating that GNNs can flexibly yield outputs with diverse frequency components even when certain frequencies are absent or filtered out from the input graph data. We then formulate a novel research problem of measuring and benchmarking the performance of GNNs from a spectral perspective. To take an initial step towards a comprehensive benchmark, we design an evaluation protocol supported by comprehensive theoretical analysis. Finally, we introduce a comprehensive benchmark on real-world datasets, revealing insights that challenge prevalent opinions from a spectral perspective. We believe that our findings will open new avenues for future advancements in this area. Our implementations can be found at: https://github.com/yushundong/Spectral-benchmark.

cs.LG↗

arXiv2024

Large Language Models for Data Annotation and Synthesis: A Survey

Data annotation and synthesis generally refers to the labeling or generating of raw data with relevant information, which could be used for improving the efficacy of machine learning models. The process, however, is labor-intensive and costly. The emergence of advanced Large Language Models (LLMs), exemplified by GPT-4, presents an unprecedented opportunity to automate the complicated process of data annotation and synthesis. While existing surveys have extensively covered LLM architecture, training, and general applications, we uniquely focus on their specific utility for data annotation. This survey contributes to three core aspects: LLM-Based Annotation Generation, LLM-Generated Annotations Assessment, and LLM-Generated Annotations Utilization. Furthermore, this survey includes an in-depth taxonomy of data types that LLMs can annotate, a comprehensive review of learning strategies for models utilizing LLM-generated annotations, and a detailed discussion of the primary challenges and limitations associated with using LLMs for data annotation and synthesis. Serving as a key guide, this survey aims to assist researchers and practitioners in exploring the potential of the latest LLMs for data annotation, thereby fostering future advancements in this critical field.

cs.CL↗

arXiv2024

Instance-Aware Graph Prompt Learning

Graph neural networks stand as the predominant technique for graph representation learning owing to their strong expressive power, yet the performance highly depends on the availability of high-quality labels in an end-to-end manner. Thus the pretraining and fine-tuning paradigm has been proposed to mitigate the label cost issue. Subsequently, the gap between the pretext tasks and downstream tasks has spurred the development of graph prompt learning which inserts a set of graph prompts into the original graph data with minimal parameters while preserving competitive performance. However, the current exploratory works are still limited since they all concentrate on learning fixed task-specific prompts which may not generalize well across the diverse instances that the task comprises. To tackle this challenge, we introduce Instance-Aware Graph Prompt Learning (IA-GPL) in this paper, aiming to generate distinct prompts tailored to different input instances. The process involves generating intermediate prompts for each instance using a lightweight architecture, quantizing these prompts through trainable codebook vectors, and employing the exponential moving average technique to ensure stable training. Extensive experiments conducted on multiple datasets and settings showcase the superior performance of IA-GPL compared to state-of-the-art baselines.

cs.LG↗

arXiv2024

Invariant Shape Representation Learning For Image Classification

Geometric shape features have been widely used as strong predictors for image classification. Nevertheless, most existing classifiers such as deep neural networks (DNNs) directly leverage the statistical correlations between these shape features and target variables. However, these correlations can often be spurious and unstable across different environments (e.g., in different age groups, certain types of brain changes have unstable relations with neurodegenerative disease); hence leading to biased or inaccurate predictions. In this paper, we introduce a novel framework that for the first time develops invariant shape representation learning (ISRL) to further strengthen the robustness of image classifiers. In contrast to existing approaches that mainly derive features in the image space, our model ISRL is designed to jointly capture invariant features in latent shape spaces parameterized by deformable transformations. To achieve this goal, we develop a new learning paradigm based on invariant risk minimization (IRM) to learn invariant representations of image and shape features across multiple training distributions/environments. By embedding the features that are invariant with regard to target variables in different environments, our model consistently offers more accurate predictions. We validate our method by performing classification tasks on both simulated 2D images, real 3D brain and cine cardiovascular magnetic resonance images (MRIs). Our code is publicly available at https://github.com/tonmoy-hossain/ISRL.

cs.CV↗

arXiv2024

Federated Graph Learning with Graphless Clients

Federated Graph Learning (FGL) is tasked with training machine learning models, such as Graph Neural Networks (GNNs), for multiple clients, each with its own graph data. Existing methods usually assume that each client has both node features and graph structure of its graph data. In real-world scenarios, however, there exist federated systems where only a part of the clients have such data while other clients (i.e. graphless clients) may only have node features. This naturally leads to a novel problem in FGL: how to jointly train a model over distributed graph data with graphless clients? In this paper, we propose a novel framework FedGLS to tackle the problem in FGL with graphless clients. In FedGLS, we devise a local graph learner on each graphless client which learns the local graph structure with the structure knowledge transferred from other clients. To enable structure knowledge transfer, we design a GNN model and a feature encoder on each client. During local training, the feature encoder retains the local graph structure knowledge together with the GNN model via knowledge distillation, and the structure knowledge is transferred among clients in global update. Our extensive experiments demonstrate the superiority of the proposed FedGLS over five baselines.

cs.LG↗

arXiv2024

Global Graph Counterfactual Explanation: A Subgraph Mapping Approach

Graph Neural Networks (GNNs) have been widely deployed in various real-world applications. However, most GNNs are black-box models that lack explanations. One strategy to explain GNNs is through counterfactual explanation, which aims to find minimum perturbations on input graphs that change the GNN predictions. Existing works on GNN counterfactual explanations primarily concentrate on the local-level perspective (i.e., generating counterfactuals for each individual graph), which suffers from information overload and lacks insights into the broader cross-graph relationships. To address such issues, we propose GlobalGCE, a novel global-level graph counterfactual explanation method. GlobalGCE aims to identify a collection of subgraph mapping rules as counterfactual explanations for the target GNN. According to these rules, substituting certain significant subgraphs with their counterfactual subgraphs will change the GNN prediction to the desired class for most graphs (i.e., maximum coverage). Methodologically, we design a significant subgraph generator and a counterfactual subgraph autoencoder in our GlobalGCE, where the subgraphs and the rules can be effectively generated. Extensive experiments demonstrate the superiority of our GlobalGCE compared to existing baselines. Our code can be found at https://anonymous.4open.science/r/GlobalGCE-92E8.

cs.LG↗

arXiv2024

Explaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective for Molecular Property Prediction

In recent years, Graph Neural Networks (GNNs) have become successful in molecular property prediction tasks such as toxicity analysis. However, due to the black-box nature of GNNs, their outputs can be concerning in high-stakes decision-making scenarios, e.g., drug discovery. Facing such an issue, Graph Counterfactual Explanation (GCE) has emerged as a promising approach to improve GNN transparency. However, current GCE methods usually fail to take domain-specific knowledge into consideration, which can result in outputs that are not easily comprehensible by humans. To address this challenge, we propose a novel GCE method, LLM-GCE, to unleash the power of large language models (LLMs) in explaining GNNs for molecular property prediction. Specifically, we utilize an autoencoder to generate the counterfactual graph topology from a set of counterfactual text pairs (CTPs) based on an input graph. Meanwhile, we also incorporate a CTP dynamic feedback module to mitigate LLM hallucination, which provides intermediate feedback derived from the generated counterfactuals as an attempt to give more faithful guidance. Extensive experiments demonstrate the superior performance of LLM-GCE. Our code is released on https://github.com/YinhanHe123/new\_LLM4GNNExplanation.

cs.LG↗