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Shirui Pan

Publications and source records attributed to Shirui Pan.

At least 163 records · Page 9Linked to original sources
arXiv2024

Sign is Not a Remedy: Multiset-to-Multiset Message Passing for Learning on Heterophilic Graphs

Graph Neural Networks (GNNs) have gained significant attention as a powerful modeling and inference method, especially for homophilic graph-structured data. To empower GNNs in heterophilic graphs, where adjacent nodes exhibit dissimilar labels or features, Signed Message Passing (SMP) has been widely adopted. However, there is a lack of theoretical and empirical analysis regarding the limitations of SMP. In this work, we unveil some potential pitfalls of SMP and their remedies. We first identify two limitations of SMP: undesirable representation update for multi-hop neighbors and vulnerability against oversmoothing issues. To overcome these challenges, we propose a novel message passing function called Multiset to Multiset GNN(M2M-GNN). Our theoretical analyses and extensive experiments demonstrate that M2M-GNN effectively alleviates the aforementioned limitations of SMP, yielding superior performance in comparison

cs.LG↗
arXiv2024

Large Language Model Watermark Stealing With Mixed Integer Programming

The Large Language Model (LLM) watermark is a newly emerging technique that shows promise in addressing concerns surrounding LLM copyright, monitoring AI-generated text, and preventing its misuse. The LLM watermark scheme commonly includes generating secret keys to partition the vocabulary into green and red lists, applying a perturbation to the logits of tokens in the green list to increase their sampling likelihood, thus facilitating watermark detection to identify AI-generated text if the proportion of green tokens exceeds a threshold. However, recent research indicates that watermarking methods using numerous keys are susceptible to removal attacks, such as token editing, synonym substitution, and paraphrasing, with robustness declining as the number of keys increases. Therefore, the state-of-the-art watermark schemes that employ fewer or single keys have been demonstrated to be more robust against text editing and paraphrasing. In this paper, we propose a novel green list stealing attack against the state-of-the-art LLM watermark scheme and systematically examine its vulnerability to this attack. We formalize the attack as a mixed integer programming problem with constraints. We evaluate our attack under a comprehensive threat model, including an extreme scenario where the attacker has no prior knowledge, lacks access to the watermark detector API, and possesses no information about the LLM's parameter settings or watermark injection/detection scheme. Extensive experiments on LLMs, such as OPT and LLaMA, demonstrate that our attack can successfully steal the green list and remove the watermark across all settings.

cs.CR↗
arXiv2024

Deep Learning for Time Series Anomaly Detection: A Survey

Time series anomaly detection has applications in a wide range of research fields and applications, including manufacturing and healthcare. The presence of anomalies can indicate novel or unexpected events, such as production faults, system defects, or heart fluttering, and is therefore of particular interest. The large size and complex patterns of time series have led researchers to develop specialised deep learning models for detecting anomalous patterns. This survey focuses on providing structured and comprehensive state-of-the-art time series anomaly detection models through the use of deep learning. It providing a taxonomy based on the factors that divide anomaly detection models into different categories. Aside from describing the basic anomaly detection technique for each category, the advantages and limitations are also discussed. Furthermore, this study includes examples of deep anomaly detection in time series across various application domains in recent years. It finally summarises open issues in research and challenges faced while adopting deep anomaly detection models.

cs.LG↗
arXiv2024

Regressor-free Molecule Generation to Support Drug Response Prediction

Drug response prediction (DRP) is a crucial phase in drug discovery, and the most important metric for its evaluation is the IC50 score. DRP results are heavily dependent on the quality of the generated molecules. Existing molecule generation methods typically employ classifier-based guidance, enabling sampling within the IC50 classification range. However, these methods fail to ensure the sampling space range's effectiveness, generating numerous ineffective molecules. Through experimental and theoretical study, we hypothesize that conditional generation based on the target IC50 score can obtain a more effective sampling space. As a result, we introduce regressor-free guidance molecule generation to ensure sampling within a more effective space and support DRP. Regressor-free guidance combines a diffusion model's score estimation with a regression controller model's gradient based on number labels. To effectively map regression labels between drugs and cell lines, we design a common-sense numerical knowledge graph that constrains the order of text representations. Experimental results on the real-world dataset for the DRP task demonstrate our method's effectiveness in drug discovery. The code is available at:https://anonymous.4open.science/r/RMCD-DBD1.

q-bio.MN↗
arXiv2024

A Cross-Field Fusion Strategy for Drug-Target Interaction Prediction

Drug-target interaction (DTI) prediction is a critical component of the drug discovery process. In the drug development engineering field, predicting novel drug-target interactions is extremely crucial.However, although existing methods have achieved high accuracy levels in predicting known drugs and drug targets, they fail to utilize global protein information during DTI prediction. This leads to an inability to effectively predict interaction the interactions between novel drugs and their targets. As a result, the cross-field information fusion strategy is employed to acquire local and global protein information. Thus, we propose the siamese drug-target interaction SiamDTI prediction method, which utilizes a double channel network structure for cross-field supervised learning.Experimental results on three benchmark datasets demonstrate that SiamDTI achieves higher accuracy levels than other state-of-the-art (SOTA) methods on novel drugs and targets.Additionally, SiamDTI's performance with known drugs and targets is comparable to that of SOTA approachs. The code is available at https://anonymous.4open.science/r/DDDTI-434D.

q-bio.BM↗
arXiv2024

All Nodes are created Not Equal: Node-Specific Layer Aggregation and Filtration for GNN

The ever-designed Graph Neural Networks, though opening a promising path for the modeling of the graph-structure data, unfortunately introduce two daunting obstacles to their deployment on devices. (I) Most of existing GNNs are shallow, due mostly to the over-smoothing and gradient-vanish problem as they go deeper as convolutional architectures. (II) The vast majority of GNNs adhere to the homophily assumption, where the central node and its adjacent nodes share the same label. This assumption often poses challenges for many GNNs working with heterophilic graphs. Addressing the aforementioned issue has become a looming challenge in enhancing the robustness and scalability of GNN applications. In this paper, we take a comprehensive and systematic approach to overcoming the two aforementioned challenges for the first time. We propose a Node-Specific Layer Aggregation and Filtration architecture, termed NoSAF, a framework capable of filtering and processing information from each individual nodes. NoSAF introduces the concept of "All Nodes are Created Not Equal" into every layer of deep networks, aiming to provide a reliable information filter for each layer's nodes to sieve out information beneficial for the subsequent layer. By incorporating a dynamically updated codebank, NoSAF dynamically optimizes the optimal information outputted downwards at each layer. This effectively overcomes heterophilic issues and aids in deepening the network. To compensate for the information loss caused by the continuous filtering in NoSAF, we also propose NoSAF-D (Deep), which incorporates a compensation mechanism that replenishes information in every layer of the model, allowing NoSAF to perform meaningful computations even in very deep layers.

cs.LG↗
arXiv2024

Nonnegative Matrix Factorization in Dimensionality Reduction: A Survey

Dimensionality Reduction plays a pivotal role in improving feature learning accuracy and reducing training time by eliminating redundant features, noise, and irrelevant data. Nonnegative Matrix Factorization (NMF) has emerged as a popular and powerful method for dimensionality reduction. Despite its extensive use, there remains a need for a comprehensive analysis of NMF in the context of dimensionality reduction. To address this gap, this paper presents a comprehensive survey of NMF, focusing on its applications in both feature extraction and feature selection. We introduce a classification of dimensionality reduction, enhancing understanding of the underlying concepts. Subsequently, we delve into a thorough summary of diverse NMF approaches used for feature extraction and selection. Furthermore, we discuss the latest research trends and potential future directions of NMF in dimensionality reduction, aiming to highlight areas that need further exploration and development.

cs.LG↗
arXiv2024

Knowledge Graphs and Pre-trained Language Models enhanced Representation Learning for Conversational Recommender Systems

Conversational recommender systems (CRS) utilize natural language interactions and dialogue history to infer user preferences and provide accurate recommendations. Due to the limited conversation context and background knowledge, existing CRSs rely on external sources such as knowledge graphs to enrich the context and model entities based on their inter-relations. However, these methods ignore the rich intrinsic information within entities. To address this, we introduce the Knowledge-Enhanced Entity Representation Learning (KERL) framework, which leverages both the knowledge graph and a pre-trained language model to improve the semantic understanding of entities for CRS. In our KERL framework, entity textual descriptions are encoded via a pre-trained language model, while a knowledge graph helps reinforce the representation of these entities. We also employ positional encoding to effectively capture the temporal information of entities in a conversation. The enhanced entity representation is then used to develop a recommender component that fuses both entity and contextual representations for more informed recommendations, as well as a dialogue component that generates informative entity-related information in the response text. A high-quality knowledge graph with aligned entity descriptions is constructed to facilitate our study, namely the Wiki Movie Knowledge Graph (WikiMKG). The experimental results show that KERL achieves state-of-the-art results in both recommendation and response generation tasks.

cs.CL↗
arXiv2024

FedPFT: Federated Proxy Fine-Tuning of Foundation Models

Adapting Foundation Models (FMs) for downstream tasks through Federated Learning (FL) emerges a promising strategy for protecting data privacy and valuable FMs. Existing methods fine-tune FM by allocating sub-FM to clients in FL, however, leading to suboptimal performance due to insufficient tuning and inevitable error accumulations of gradients. In this paper, we propose Federated Proxy Fine-Tuning (FedPFT), a novel method enhancing FMs adaptation in downstream tasks through FL by two key modules. First, the sub-FM construction module employs a layer-wise compression approach, facilitating comprehensive FM fine-tuning across all layers by emphasizing those crucial neurons. Second, the sub-FM alignment module conducts a two-step distillations-layer-level and neuron-level-before and during FL fine-tuning respectively, to reduce error of gradient by accurately aligning sub-FM with FM under theoretical guarantees. Experimental results on seven commonly used datasets (i.e., four text and three vision) demonstrate the superiority of FedPFT.

cs.LG↗
arXiv2024

Optimizing OOD Detection in Molecular Graphs: A Novel Approach with Diffusion Models

The open-world test dataset is often mixed with out-of-distribution (OOD) samples, where the deployed models will struggle to make accurate predictions. Traditional detection methods need to trade off OOD detection and in-distribution (ID) classification performance since they share the same representation learning model. In this work, we propose to detect OOD molecules by adopting an auxiliary diffusion model-based framework, which compares similarities between input molecules and reconstructed graphs. Due to the generative bias towards reconstructing ID training samples, the similarity scores of OOD molecules will be much lower to facilitate detection. Although it is conceptually simple, extending this vanilla framework to practical detection applications is still limited by two significant challenges. First, the popular similarity metrics based on Euclidian distance fail to consider the complex graph structure. Second, the generative model involving iterative denoising steps is time-consuming especially when it runs on the enormous pool of drugs. To address these challenges, our research pioneers an approach of Prototypical Graph Reconstruction for Molecular OOD Detection, dubbed as PGR-MOOD and hinges on three innovations: i) An effective metric to comprehensively quantify the matching degree of input and reconstructed molecules; ii) A creative graph generator to construct prototypical graphs that are in line with ID but away from OOD; iii) An efficient and scalable OOD detector to compare the similarity between test samples and pre-constructed prototypical graphs and omit the generative process on every new molecule. Extensive experiments on ten benchmark datasets and six baselines are conducted to demonstrate our superiority.

cs.LG↗
arXiv2024

Gradformer: Graph Transformer with Exponential Decay

Graph Transformers (GTs) have demonstrated their advantages across a wide range of tasks. However, the self-attention mechanism in GTs overlooks the graph's inductive biases, particularly biases related to structure, which are crucial for the graph tasks. Although some methods utilize positional encoding and attention bias to model inductive biases, their effectiveness is still suboptimal analytically. Therefore, this paper presents Gradformer, a method innovatively integrating GT with the intrinsic inductive bias by applying an exponential decay mask to the attention matrix. Specifically, the values in the decay mask matrix diminish exponentially, correlating with the decreasing node proximities within the graph structure. This design enables Gradformer to retain its ability to capture information from distant nodes while focusing on the graph's local details. Furthermore, Gradformer introduces a learnable constraint into the decay mask, allowing different attention heads to learn distinct decay masks. Such an design diversifies the attention heads, enabling a more effective assimilation of diverse structural information within the graph. Extensive experiments on various benchmarks demonstrate that Gradformer consistently outperforms the Graph Neural Network and GT baseline models in various graph classification and regression tasks. Additionally, Gradformer has proven to be an effective method for training deep GT models, maintaining or even enhancing accuracy compared to shallow models as the network deepens, in contrast to the significant accuracy drop observed in other GT models.Codes are available at \url{https://github.com/LiuChuang0059/Gradformer}.

cs.LG↗
arXiv2024

Self-Supervised Learning for Time Series Analysis: Taxonomy, Progress, and Prospects

Self-supervised learning (SSL) has recently achieved impressive performance on various time series tasks. The most prominent advantage of SSL is that it reduces the dependence on labeled data. Based on the pre-training and fine-tuning strategy, even a small amount of labeled data can achieve high performance. Compared with many published self-supervised surveys on computer vision and natural language processing, a comprehensive survey for time series SSL is still missing. To fill this gap, we review current state-of-the-art SSL methods for time series data in this article. To this end, we first comprehensively review existing surveys related to SSL and time series, and then provide a new taxonomy of existing time series SSL methods by summarizing them from three perspectives: generative-based, contrastive-based, and adversarial-based. These methods are further divided into ten subcategories with detailed reviews and discussions about their key intuitions, main frameworks, advantages and disadvantages. To facilitate the experiments and validation of time series SSL methods, we also summarize datasets commonly used in time series forecasting, classification, anomaly detection, and clustering tasks. Finally, we present the future directions of SSL for time series analysis.

cs.LG↗
arXiv2024

IME: Integrating Multi-curvature Shared and Specific Embedding for Temporal Knowledge Graph Completion

Temporal Knowledge Graphs (TKGs) incorporate a temporal dimension, allowing for a precise capture of the evolution of knowledge and reflecting the dynamic nature of the real world. Typically, TKGs contain complex geometric structures, with various geometric structures interwoven. However, existing Temporal Knowledge Graph Completion (TKGC) methods either model TKGs in a single space or neglect the heterogeneity of different curvature spaces, thus constraining their capacity to capture these intricate geometric structures. In this paper, we propose a novel Integrating Multi-curvature shared and specific Embedding (IME) model for TKGC tasks. Concretely, IME models TKGs into multi-curvature spaces, including hyperspherical, hyperbolic, and Euclidean spaces. Subsequently, IME incorporates two key properties, namely space-shared property and space-specific property. The space-shared property facilitates the learning of commonalities across different curvature spaces and alleviates the spatial gap caused by the heterogeneous nature of multi-curvature spaces, while the space-specific property captures characteristic features. Meanwhile, IME proposes an Adjustable Multi-curvature Pooling (AMP) approach to effectively retain important information. Furthermore, IME innovatively designs similarity, difference, and structure loss functions to attain the stated objective. Experimental results clearly demonstrate the superior performance of IME over existing state-of-the-art TKGC models.

cs.AI↗
arXiv2024

Emerging Trends in Federated Learning: From Model Fusion to Federated X Learning

Federated learning is a new learning paradigm that decouples data collection and model training via multi-party computation and model aggregation. As a flexible learning setting, federated learning has the potential to integrate with other learning frameworks. We conduct a focused survey of federated learning in conjunction with other learning algorithms. Specifically, we explore various learning algorithms to improve the vanilla federated averaging algorithm and review model fusion methods such as adaptive aggregation, regularization, clustered methods, and Bayesian methods. Following the emerging trends, we also discuss federated learning in the intersection with other learning paradigms, termed federated X learning, where X includes multitask learning, meta-learning, transfer learning, unsupervised learning, and reinforcement learning. In addition to reviewing state-of-the-art studies, this paper also identifies key challenges and applications in this field, while also highlighting promising future directions.

cs.LG↗
arXiv2024

Unraveling Privacy Risks of Individual Fairness in Graph Neural Networks

Graph neural networks (GNNs) have gained significant attraction due to their expansive real-world applications. To build trustworthy GNNs, two aspects - fairness and privacy - have emerged as critical considerations. Previous studies have separately examined the fairness and privacy aspects of GNNs, revealing their trade-off with GNN performance. Yet, the interplay between these two aspects remains unexplored. In this paper, we pioneer the exploration of the interaction between the privacy risks of edge leakage and the individual fairness of a GNN. Our theoretical analysis unravels that edge privacy risks unfortunately escalate when the nodes' individual fairness improves. Such an issue hinders the accomplishment of privacy and fairness of GNNs at the same time. To balance fairness and privacy, we carefully introduce fairness-aware loss reweighting based on influence function and privacy-aware graph structure perturbation modules within a fine-tuning mechanism. Experimental results underscore the effectiveness of our approach in achieving GNN fairness with limited performance compromise and controlled privacy risks. This work contributes to the comprehensively developing trustworthy GNNs by simultaneously addressing both fairness and privacy aspects.

cs.LG↗
arXiv2024

Online GNN Evaluation Under Test-time Graph Distribution Shifts

Evaluating the performance of a well-trained GNN model on real-world graphs is a pivotal step for reliable GNN online deployment and serving. Due to a lack of test node labels and unknown potential training-test graph data distribution shifts, conventional model evaluation encounters limitations in calculating performance metrics (e.g., test error) and measuring graph data-level discrepancies, particularly when the training graph used for developing GNNs remains unobserved during test time. In this paper, we study a new research problem, online GNN evaluation, which aims to provide valuable insights into the well-trained GNNs's ability to effectively generalize to real-world unlabeled graphs under the test-time graph distribution shifts. Concretely, we develop an effective learning behavior discrepancy score, dubbed LeBeD, to estimate the test-time generalization errors of well-trained GNN models. Through a novel GNN re-training strategy with a parameter-free optimality criterion, the proposed LeBeD comprehensively integrates learning behavior discrepancies from both node prediction and structure reconstruction perspectives. This enables the effective evaluation of the well-trained GNNs' ability to capture test node semantics and structural representations, making it an expressive metric for estimating the generalization error in online GNN evaluation. Extensive experiments on real-world test graphs under diverse graph distribution shifts could verify the effectiveness of the proposed method, revealing its strong correlation with ground-truth test errors on various well-trained GNN models.

cs.LG↗
arXiv2024

Revisiting Edge Perturbation for Graph Neural Network in Graph Data Augmentation and Attack

Edge perturbation is a basic method to modify graph structures. It can be categorized into two veins based on their effects on the performance of graph neural networks (GNNs), i.e., graph data augmentation and attack. Surprisingly, both veins of edge perturbation methods employ the same operations, yet yield opposite effects on GNNs' accuracy. A distinct boundary between these methods in using edge perturbation has never been clearly defined. Consequently, inappropriate perturbations may lead to undesirable outcomes, necessitating precise adjustments to achieve desired effects. Therefore, questions of ``why edge perturbation has a two-faced effect?'' and ``what makes edge perturbation flexible and effective?'' still remain unanswered. In this paper, we will answer these questions by proposing a unified formulation and establishing a clear boundary between two categories of edge perturbation methods. Specifically, we conduct experiments to elucidate the differences and similarities between these methods and theoretically unify the workflow of these methods by casting it to one optimization problem. Then, we devise Edge Priority Detector (EPD) to generate a novel priority metric, bridging these methods up in the workflow. Experiments show that EPD can make augmentation or attack flexibly and achieve comparable or superior performance to other counterparts with less time overhead.

cs.LG↗
arXiv2024

Graph Learning under Distribution Shifts: A Comprehensive Survey on Domain Adaptation, Out-of-distribution, and Continual Learning

Graph learning plays a pivotal role and has gained significant attention in various application scenarios, from social network analysis to recommendation systems, for its effectiveness in modeling complex data relations represented by graph structural data. In reality, the real-world graph data typically show dynamics over time, with changing node attributes and edge structure, leading to the severe graph data distribution shift issue. This issue is compounded by the diverse and complex nature of distribution shifts, which can significantly impact the performance of graph learning methods in degraded generalization and adaptation capabilities, posing a substantial challenge to their effectiveness. In this survey, we provide a comprehensive review and summary of the latest approaches, strategies, and insights that address distribution shifts within the context of graph learning. Concretely, according to the observability of distributions in the inference stage and the availability of sufficient supervision information in the training stage, we categorize existing graph learning methods into several essential scenarios, including graph domain adaptation learning, graph out-of-distribution learning, and graph continual learning. For each scenario, a detailed taxonomy is proposed, with specific descriptions and discussions of existing progress made in distribution-shifted graph learning. Additionally, we discuss the potential applications and future directions for graph learning under distribution shifts with a systematic analysis of the current state in this field. The survey is positioned to provide general guidance for the development of effective graph learning algorithms in handling graph distribution shifts, and to stimulate future research and advancements in this area.

cs.LG↗