arXiv subjects

Chuan Shi

Publications and source records attributed to Chuan Shi.

At least 91 records · Page 5Linked to original sources

arXiv2024

Generalizing Graph Neural Networks on Out-Of-Distribution Graphs

Graph Neural Networks (GNNs) are proposed without considering the agnostic distribution shifts between training and testing graphs, inducing the degeneration of the generalization ability of GNNs on Out-Of-Distribution (OOD) settings. The fundamental reason for such degeneration is that most GNNs are developed based on the I.I.D hypothesis. In such a setting, GNNs tend to exploit subtle statistical correlations existing in the training set for predictions, even though it is a spurious correlation. However, such spurious correlations may change in testing environments, leading to the failure of GNNs. Therefore, eliminating the impact of spurious correlations is crucial for stable GNNs. To this end, we propose a general causal representation framework, called StableGNN. The main idea is to extract high-level representations from graph data first and resort to the distinguishing ability of causal inference to help the model get rid of spurious correlations. Particularly, we exploit a graph pooling layer to extract subgraph-based representations as high-level representations. Furthermore, we propose a causal variable distinguishing regularizer to correct the biased training distribution. Hence, GNNs would concentrate more on the stable correlations. Extensive experiments on both synthetic and real-world OOD graph datasets well verify the effectiveness, flexibility and interpretability of the proposed framework.

cs.LG↗

arXiv2024

Graph Contrastive Invariant Learning from the Causal Perspective

Graph contrastive learning (GCL), learning the node representation by contrasting two augmented graphs in a self-supervised way, has attracted considerable attention. GCL is usually believed to learn the invariant representation. However, does this understanding always hold in practice? In this paper, we first study GCL from the perspective of causality. By analyzing GCL with the structural causal model (SCM), we discover that traditional GCL may not well learn the invariant representations due to the non-causal information contained in the graph. How can we fix it and encourage the current GCL to learn better invariant representations? The SCM offers two requirements and motives us to propose a novel GCL method. Particularly, we introduce the spectral graph augmentation to simulate the intervention upon non-causal factors. Then we design the invariance objective and independence objective to better capture the causal factors. Specifically, (i) the invariance objective encourages the encoder to capture the invariant information contained in causal variables, and (ii) the independence objective aims to reduce the influence of confounders on the causal variables. Experimental results demonstrate the effectiveness of our approach on node classification tasks.

cs.LG↗

arXiv2024

Learning Invariant Representations of Graph Neural Networks via Cluster Generalization

Graph neural networks (GNNs) have become increasingly popular in modeling graph-structured data due to their ability to learn node representations by aggregating local structure information. However, it is widely acknowledged that the test graph structure may differ from the training graph structure, resulting in a structure shift. In this paper, we experimentally find that the performance of GNNs drops significantly when the structure shift happens, suggesting that the learned models may be biased towards specific structure patterns. To address this challenge, we propose the Cluster Information Transfer (CIT) mechanism (Code available at https://github.com/BUPT-GAMMA/CITGNN), which can learn invariant representations for GNNs, thereby improving their generalization ability to various and unknown test graphs with structure shift. The CIT mechanism achieves this by combining different cluster information with the nodes while preserving their cluster-independent information. By generating nodes across different clusters, the mechanism significantly enhances the diversity of the nodes and helps GNNs learn the invariant representations. We provide a theoretical analysis of the CIT mechanism, showing that the impact of changing clusters during structure shift can be mitigated after transfer. Additionally, the proposed mechanism is a plug-in that can be easily used to improve existing GNNs. We comprehensively evaluate our proposed method on three typical structure shift scenarios, demonstrating its effectiveness in enhancing GNNs' performance.

cs.LG↗

arXiv2024

Directed Acyclic Graph Structure Learning from Dynamic Graphs

Estimating the structure of directed acyclic graphs (DAGs) of features (variables) plays a vital role in revealing the latent data generation process and providing causal insights in various applications. Although there have been many studies on structure learning with various types of data, the structure learning on the dynamic graph has not been explored yet, and thus we study the learning problem of node feature generation mechanism on such ubiquitous dynamic graph data. In a dynamic graph, we propose to simultaneously estimate contemporaneous relationships and time-lagged interaction relationships between the node features. These two kinds of relationships form a DAG, which could effectively characterize the feature generation process in a concise way. To learn such a DAG, we cast the learning problem as a continuous score-based optimization problem, which consists of a differentiable score function to measure the validity of the learned DAGs and a smooth acyclicity constraint to ensure the acyclicity of the learned DAGs. These two components are translated into an unconstraint augmented Lagrangian objective which could be minimized by mature continuous optimization techniques. The resulting algorithm, named GraphNOTEARS, outperforms baselines on simulated data across a wide range of settings that may encounter in real-world applications. We also apply the proposed approach on two dynamic graphs constructed from the real-world Yelp dataset, demonstrating our method could learn the connections between node features, which conforms with the domain knowledge.

cs.LG↗

arXiv2024

Hierarchical Contrastive Learning Enhanced Heterogeneous Graph Neural Network

Heterogeneous graph neural networks (HGNNs) as an emerging technique have shown superior capacity of dealing with heterogeneous information network (HIN). However, most HGNNs follow a semi-supervised learning manner, which notably limits their wide use in reality since labels are usually scarce in real applications. Recently, contrastive learning, a self-supervised method, becomes one of the most exciting learning paradigms and shows great potential when there are no labels. In this paper, we study the problem of self-supervised HGNNs and propose a novel co-contrastive learning mechanism for HGNNs, named HeCo. Different from traditional contrastive learning which only focuses on contrasting positive and negative samples, HeCo employs cross-view contrastive mechanism. Specifically, two views of a HIN (network schema and meta-path views) are proposed to learn node embeddings, so as to capture both of local and high-order structures simultaneously. Then the cross-view contrastive learning, as well as a view mask mechanism, is proposed, which is able to extract the positive and negative embeddings from two views. This enables the two views to collaboratively supervise each other and finally learn high-level node embeddings. Moreover, to further boost the performance of HeCo, two additional methods are designed to generate harder negative samples with high quality. Besides the invariant factors, view-specific factors complementally provide the diverse structure information between different nodes, which also should be contained into the final embeddings. Therefore, we need to further explore each view independently and propose a modified model, called HeCo++. Specifically, HeCo++ conducts hierarchical contrastive learning, including cross-view and intra-view contrasts, which aims to enhance the mining of respective structures.

cs.LG↗

arXiv2024

Minimum Topology Attacks for Graph Neural Networks

With the great popularity of Graph Neural Networks (GNNs), their robustness to adversarial topology attacks has received significant attention. Although many attack methods have been proposed, they mainly focus on fixed-budget attacks, aiming at finding the most adversarial perturbations within a fixed budget for target node. However, considering the varied robustness of each node, there is an inevitable dilemma caused by the fixed budget, i.e., no successful perturbation is found when the budget is relatively small, while if it is too large, the yielding redundant perturbations will hurt the invisibility. To break this dilemma, we propose a new type of topology attack, named minimum-budget topology attack, aiming to adaptively find the minimum perturbation sufficient for a successful attack on each node. To this end, we propose an attack model, named MiBTack, based on a dynamic projected gradient descent algorithm, which can effectively solve the involving non-convex constraint optimization on discrete topology. Extensive results on three GNNs and four real-world datasets show that MiBTack can successfully lead all target nodes misclassified with the minimum perturbation edges. Moreover, the obtained minimum budget can be used to measure node robustness, so we can explore the relationships of robustness, topology, and uncertainty for nodes, which is beyond what the current fixed-budget topology attacks can offer.

cs.AI↗

arXiv2024

GraphTranslator: Aligning Graph Model to Large Language Model for Open-ended Tasks

Large language models (LLMs) like ChatGPT, exhibit powerful zero-shot and instruction-following capabilities, have catalyzed a revolutionary transformation across diverse fields, especially for open-ended tasks. While the idea is less explored in the graph domain, despite the availability of numerous powerful graph models (GMs), they are restricted to tasks in a pre-defined form. Although several methods applying LLMs to graphs have been proposed, they fail to simultaneously handle the pre-defined and open-ended tasks, with LLM as a node feature enhancer or as a standalone predictor. To break this dilemma, we propose to bridge the pretrained GM and LLM by a Translator, named GraphTranslator, aiming to leverage GM to handle the pre-defined tasks effectively and utilize the extended interface of LLMs to offer various open-ended tasks for GM. To train such Translator, we propose a Producer capable of constructing the graph-text alignment data along node information, neighbor information and model information. By translating node representation into tokens, GraphTranslator empowers an LLM to make predictions based on language instructions, providing a unified perspective for both pre-defined and open-ended tasks. Extensive results demonstrate the effectiveness of our proposed GraphTranslator on zero-shot node classification. The graph question answering experiments reveal our GraphTranslator potential across a broad spectrum of open-ended tasks through language instructions. Our code is available at: https://github.com/alibaba/GraphTranslator.

cs.AI↗

arXiv2024

Federated Heterogeneous Graph Neural Network for Privacy-preserving Recommendation

The heterogeneous information network (HIN), which contains rich semantics depicted by meta-paths, has emerged as a potent tool for mitigating data sparsity in recommender systems. Existing HIN-based recommender systems operate under the assumption of centralized storage and model training. However, real-world data is often distributed due to privacy concerns, leading to the semantic broken issue within HINs and consequent failures in centralized HIN-based recommendations. In this paper, we suggest the HIN is partitioned into private HINs stored on the client side and shared HINs on the server. Following this setting, we propose a federated heterogeneous graph neural network (FedHGNN) based framework, which facilitates collaborative training of a recommendation model using distributed HINs while protecting user privacy. Specifically, we first formalize the privacy definition for HIN-based federated recommendation (FedRec) in the light of differential privacy, with the goal of protecting user-item interactions within private HIN as well as users' high-order patterns from shared HINs. To recover the broken meta-path based semantics and ensure proposed privacy measures, we elaborately design a semantic-preserving user interactions publishing method, which locally perturbs user's high-order patterns and related user-item interactions for publishing. Subsequently, we introduce an HGNN model for recommendation, which conducts node- and semantic-level aggregations to capture recovered semantics. Extensive experiments on four datasets demonstrate that our model outperforms existing methods by a substantial margin (up to 34% in HR@10 and 42% in NDCG@10) under a reasonable privacy budget.

cs.LG↗

arXiv2024

Endowing Pre-trained Graph Models with Provable Fairness

Pre-trained graph models (PGMs) aim to capture transferable inherent structural properties and apply them to different downstream tasks. Similar to pre-trained language models, PGMs also inherit biases from human society, resulting in discriminatory behavior in downstream applications. The debiasing process of existing fair methods is generally coupled with parameter optimization of GNNs. However, different downstream tasks may be associated with different sensitive attributes in reality, directly employing existing methods to improve the fairness of PGMs is inflexible and inefficient. Moreover, most of them lack a theoretical guarantee, i.e., provable lower bounds on the fairness of model predictions, which directly provides assurance in a practical scenario. To overcome these limitations, we propose a novel adapter-tuning framework that endows pre-trained graph models with provable fairness (called GraphPAR). GraphPAR freezes the parameters of PGMs and trains a parameter-efficient adapter to flexibly improve the fairness of PGMs in downstream tasks. Specifically, we design a sensitive semantic augmenter on node representations, to extend the node representations with different sensitive attribute semantics for each node. The extended representations will be used to further train an adapter, to prevent the propagation of sensitive attribute semantics from PGMs to task predictions. Furthermore, with GraphPAR, we quantify whether the fairness of each node is provable, i.e., predictions are always fair within a certain range of sensitive attribute semantics. Experimental evaluations on real-world datasets demonstrate that GraphPAR achieves state-of-the-art prediction performance and fairness on node classification task. Furthermore, based on our GraphPAR, around 90\% nodes have provable fairness.

cs.LG↗

arXiv2024

Graph Fairness Learning under Distribution Shifts

Graph neural networks (GNNs) have achieved remarkable performance on graph-structured data. However, GNNs may inherit prejudice from the training data and make discriminatory predictions based on sensitive attributes, such as gender and race. Recently, there has been an increasing interest in ensuring fairness on GNNs, but all of them are under the assumption that the training and testing data are under the same distribution, i.e., training data and testing data are from the same graph. Will graph fairness performance decrease under distribution shifts? How does distribution shifts affect graph fairness learning? All these open questions are largely unexplored from a theoretical perspective. To answer these questions, we first theoretically identify the factors that determine bias on a graph. Subsequently, we explore the factors influencing fairness on testing graphs, with a noteworthy factor being the representation distances of certain groups between the training and testing graph. Motivated by our theoretical analysis, we propose our framework FatraGNN. Specifically, to guarantee fairness performance on unknown testing graphs, we propose a graph generator to produce numerous graphs with significant bias and under different distributions. Then we minimize the representation distances for each certain group between the training graph and generated graphs. This empowers our model to achieve high classification and fairness performance even on generated graphs with significant bias, thereby effectively handling unknown testing graphs. Experiments on real-world and semi-synthetic datasets demonstrate the effectiveness of our model in terms of both accuracy and fairness.

cs.LG↗

arXiv2023

Graph Invariant Learning with Subgraph Co-mixup for Out-Of-Distribution Generalization

Graph neural networks (GNNs) have been demonstrated to perform well in graph representation learning, but always lacking in generalization capability when tackling out-of-distribution (OOD) data. Graph invariant learning methods, backed by the invariance principle among defined multiple environments, have shown effectiveness in dealing with this issue. However, existing methods heavily rely on well-predefined or accurately generated environment partitions, which are hard to be obtained in practice, leading to sub-optimal OOD generalization performances. In this paper, we propose a novel graph invariant learning method based on invariant and variant patterns co-mixup strategy, which is capable of jointly generating mixed multiple environments and capturing invariant patterns from the mixed graph data. Specifically, we first adopt a subgraph extractor to identify invariant subgraphs. Subsequently, we design one novel co-mixup strategy, i.e., jointly conducting environment Mixup and invariant Mixup. For the environment Mixup, we mix the variant environment-related subgraphs so as to generate sufficiently diverse multiple environments, which is important to guarantee the quality of the graph invariant learning. For the invariant Mixup, we mix the invariant subgraphs, further encouraging to capture invariant patterns behind graphs while getting rid of spurious correlations for OOD generalization. We demonstrate that the proposed environment Mixup and invariant Mixup can mutually promote each other. Extensive experiments on both synthetic and real-world datasets demonstrate that our method significantly outperforms state-of-the-art under various distribution shifts.

cs.LG↗

arXiv2023

Which Matters Most in Making Fund Investment Decisions? A Multi-granularity Graph Disentangled Learning Framework

In this paper, we highlight that both conformity and risk preference matter in making fund investment decisions beyond personal interest and seek to jointly characterize these aspects in a disentangled manner. Consequently, we develop a novel M ulti-granularity Graph Disentangled Learning framework named MGDL to effectively perform intelligent matching of fund investment products. Benefiting from the well-established fund graph and the attention module, multi-granularity user representations are derived from historical behaviors to separately express personal interest, conformity and risk preference in a fine-grained way. To attain stronger disentangled representations with specific semantics, MGDL explicitly involve two self-supervised signals, i.e., fund type based contrasts and fund popularity. Extensive experiments in offline and online environments verify the effectiveness of MGDL.

cs.LG↗

arXiv2023

Graph Mining for Cybersecurity: A Survey

The explosive growth of cyber attacks nowadays, such as malware, spam, and intrusions, caused severe consequences on society. Securing cyberspace has become an utmost concern for organizations and governments. Traditional Machine Learning (ML) based methods are extensively used in detecting cyber threats, but they hardly model the correlations between real-world cyber entities. In recent years, with the proliferation of graph mining techniques, many researchers investigated these techniques for capturing correlations between cyber entities and achieving high performance. It is imperative to summarize existing graph-based cybersecurity solutions to provide a guide for future studies. Therefore, as a key contribution of this paper, we provide a comprehensive review of graph mining for cybersecurity, including an overview of cybersecurity tasks, the typical graph mining techniques, and the general process of applying them to cybersecurity, as well as various solutions for different cybersecurity tasks. For each task, we probe into relevant methods and highlight the graph types, graph approaches, and task levels in their modeling. Furthermore, we collect open datasets and toolkits for graph-based cybersecurity. Finally, we outlook the potential directions of this field for future research.

cs.CR↗

arXiv2023

xTrimoABFold: De novo Antibody Structure Prediction without MSA

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

q-bio.QM↗

arXiv2023

A Post-Training Framework for Improving Heterogeneous Graph Neural Networks

Recent years have witnessed the success of heterogeneous graph neural networks (HGNNs) in modeling heterogeneous information networks (HINs). In this paper, we focus on the benchmark task of HGNNs, i.e., node classification, and empirically find that typical HGNNs are not good at predicting the label of a test node whose receptive field (1) has few training nodes from the same category or (2) has multiple training nodes from different categories. A possible explanation is that their message passing mechanisms may involve noises from different categories, and cannot fully explore task-specific knowledge such as the label dependency between distant nodes. Therefore, instead of introducing a new HGNN model, we propose a general post-training framework that can be applied on any pretrained HGNNs to further inject task-specific knowledge and enhance their prediction performance. Specifically, we first design an auxiliary system that estimates node labels based on (1) a global inference module of multi-channel label propagation and (2) a local inference module of network schema-aware prediction. The mechanism of our auxiliary system can complement the pretrained HGNNs by providing extra task-specific knowledge. During the post-training process, we will strengthen both system-level and module-level consistencies to encourage the cooperation between a pretrained HGNN and our auxiliary system. In this way, both systems can learn from each other for better performance. In experiments, we apply our framework to four typical HGNNs. Experimental results on three benchmark datasets show that compared with pretrained HGNNs, our post-training framework can enhance Micro-F1 by a relative improvement of 3.9% on average. Code, data and appendix are available at https://github.com/GXM1141/HGPF.

cs.SI↗

arXiv2023

Abnormal Event Detection via Hypergraph Contrastive Learning

Abnormal event detection, which refers to mining unusual interactions among involved entities, plays an important role in many real applications. Previous works mostly over-simplify this task as detecting abnormal pair-wise interactions. However, real-world events may contain multi-typed attributed entities and complex interactions among them, which forms an Attributed Heterogeneous Information Network (AHIN). With the boom of social networks, abnormal event detection in AHIN has become an important, but seldom explored task. In this paper, we firstly study the unsupervised abnormal event detection problem in AHIN. The events are considered as star-schema instances of AHIN and are further modeled by hypergraphs. A novel hypergraph contrastive learning method, named AEHCL, is proposed to fully capture abnormal event patterns. AEHCL designs the intra-event and inter-event contrastive modules to exploit self-supervised AHIN information. The intra-event contrastive module captures the pair-wise and multivariate interaction anomalies within an event, and the inter-event module captures the contextual anomalies among events. These two modules collaboratively boost the performance of each other and improve the detection results. During the testing phase, a contrastive learning-based abnormal event score function is further proposed to measure the abnormality degree of events. Extensive experiments on three datasets in different scenarios demonstrate the effectiveness of AEHCL, and the results improve state-of-the-art baselines up to 12.0% in Average Precision (AP) and 4.6% in Area Under Curve (AUC) respectively.

cs.LG↗

arXiv2023

Specformer: Spectral Graph Neural Networks Meet Transformers

Spectral graph neural networks (GNNs) learn graph representations via spectral-domain graph convolutions. However, most existing spectral graph filters are scalar-to-scalar functions, i.e., mapping a single eigenvalue to a single filtered value, thus ignoring the global pattern of the spectrum. Furthermore, these filters are often constructed based on some fixed-order polynomials, which have limited expressiveness and flexibility. To tackle these issues, we introduce Specformer, which effectively encodes the set of all eigenvalues and performs self-attention in the spectral domain, leading to a learnable set-to-set spectral filter. We also design a decoder with learnable bases to enable non-local graph convolution. Importantly, Specformer is equivariant to permutation. By stacking multiple Specformer layers, one can build a powerful spectral GNN. On synthetic datasets, we show that our Specformer can better recover ground-truth spectral filters than other spectral GNNs. Extensive experiments of both node-level and graph-level tasks on real-world graph datasets show that our Specformer outperforms state-of-the-art GNNs and learns meaningful spectrum patterns. Code and data are available at https://github.com/bdy9527/Specformer.

cs.LG↗

arXiv2023

A Survey on Spectral Graph Neural Networks

Graph neural networks (GNNs) have attracted considerable attention from the research community. It is well established that GNNs are usually roughly divided into spatial and spectral methods. Despite that spectral GNNs play an important role in both graph signal processing and graph representation learning, existing studies are biased toward spatial approaches, and there is no comprehensive review on spectral GNNs so far. In this paper, we summarize the recent development of spectral GNNs, including model, theory, and application. Specifically, we first discuss the connection between spatial GNNs and spectral GNNs, which shows that spectral GNNs can capture global information and have better expressiveness and interpretability. Next, we categorize existing spectral GNNs according to the spectrum information they use, \ie, eigenvalues or eigenvectors. In addition, we review major theoretical results and applications of spectral GNNs, followed by a quantitative experiment to benchmark some popular spectral GNNs. Finally, we conclude the paper with some future directions.

cs.LG↗