Missing attribute issues are prevalent in the graph learning, leading to biased outcomes in Graph Neural Networks (GNNs). Existing methods that rely on feature propagation are prone to cold start problem, particularly when dealing with attribute resetting and low-degree nodes, which hinder effective propagation and convergence. To address these challenges, we propose AttriReBoost (ARB), a novel method that incorporates propagation-based method to mitigate cold start problems in attribute-missing graphs. ARB enhances global feature propagation by redefining initial boundary conditions and strategically integrating virtual edges, thereby improving node connectivity and ensuring more stable and efficient convergence. This method facilitates gradient-free attribute reconstruction with lower computational overhead. The proposed method is theoretically grounded, with its convergence rigorously established. Extensive experiments on several real-world benchmark datasets demonstrate the effectiveness of ARB, achieving an average accuracy improvement of 5.11% over state-of-the-art methods. Additionally, ARB exhibits remarkable computational efficiency, processing a large-scale graph with 2.49 million nodes in just 16 seconds on a single GPU. Our code is available at https://github.com/limengran98/ARB.
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.
Real-world graph data environments intrinsically exist noise (e.g., link and structure errors) that inevitably disturb the effectiveness of graph representation and downstream learning tasks. For homogeneous graphs, the latest works use original node features to synthesize a similarity graph that can correct the structure of the noised graph. This idea is based on the homogeneity assumption, which states that similar nodes in the homogeneous graph tend to have direct links in the original graph. However, similar nodes in heterogeneous graphs usually do not have direct links, which can not be used to correct the original noise graph. This causes a significant challenge in noised heterogeneous graph learning. To this end, this paper proposes a novel synthesized similarity-based graph neural network compatible with noised heterogeneous graph learning. First, we calculate the original feature similarities of all nodes to synthesize a similarity-based high-order graph. Second, we propose a similarity-aware encoder to embed original and synthesized graphs with shared parameters. Then, instead of graph-to-graph supervising, we synchronously supervise the original and synthesized graph embeddings to predict the same labels. Meanwhile, a target-based graph extracted from the synthesized graph contrasts the structure of the metapath-based graph extracted from the original graph to learn the mutual information. Extensive experiments in numerous real-world datasets show the proposed method achieves state-of-the-art records in the noised heterogeneous graph learning tasks. In highlights, +5$\sim$6\% improvements are observed in several noised datasets compared with previous SOTA methods. The code and datasets are available at https://github.com/kg-cc/NoiseHGNN.
The integration of multi-omic data is pivotal for understanding complex diseases, but its high dimensionality and noise present significant challenges. Graph Neural Networks (GNNs) offer a robust framework for analyzing large-scale signaling pathways and protein-protein interaction networks, yet they face limitations in expressivity when capturing intricate biological relationships. To address this, we propose Graph Sequence Language Model (GraphSeqLM), a framework that enhances GNNs with biological sequence embeddings generated by Large Language Models (LLMs). These embeddings encode structural and biological properties of DNA, RNA, and proteins, augmenting GNNs with enriched features for analyzing sample-specific multi-omic data. By integrating topological, sequence-derived, and biological information, GraphSeqLM demonstrates superior predictive accuracy and outperforms existing methods, paving the way for more effective multi-omic data integration in precision medicine.
Incorporating multi-modal features as side information has recently become a trend in recommender systems. To elucidate user-item preferences, recent studies focus on fusing modalities via concatenation, element-wise sum, or attention mechanisms. Despite having notable success, existing approaches do not account for the modality-specific noise encapsulated within each modality. As a result, direct fusion of modalities will lead to the amplification of cross-modality noise. Moreover, the variation of noise that is unique within each modality results in noise alleviation and fusion being more challenging. In this work, we propose a new Spectrum-based Modality Representation (SMORE) fusion graph recommender that aims to capture both uni-modal and fusion preferences while simultaneously suppressing modality noise. Specifically, SMORE projects the multi-modal features into the frequency domain and leverages the spectral space for fusion. To reduce dynamic contamination that is unique to each modality, we introduce a filter to attenuate and suppress the modality noise adaptively while capturing the universal modality patterns effectively. Furthermore, we explore the item latent structures by designing a new multi-modal graph learning module to capture associative semantic correlations and universal fusion patterns among similar items. Finally, we formulate a new modality-aware preference module, which infuses behavioral features and balances the uni- and multi-modal features for precise preference modeling. This empowers SMORE with the ability to infer both user modality-specific and fusion preferences more accurately. Experiments on three real-world datasets show the efficacy of our proposed model. The source code for this work has been made publicly available at https://github.com/kennethorq/SMORE.
Multimodal recommendation systems can learn users' preferences from existing user-item interactions as well as the semantics of multimodal data associated with items. Many existing methods model this through a multimodal user-item graph, approaching multimodal recommendation as a graph learning task. Graph Neural Networks (GNNs) have shown promising performance in this domain. Prior research has capitalized on GNNs' capability to capture neighborhood information within certain receptive fields (typically denoted by the number of hops, $K$) to enrich user and item semantics. We observe that the optimal receptive fields for GNNs can vary across different modalities. In this paper, we propose GNNs with Modality-Independent Receptive Fields, which employ separate GNNs with independent receptive fields for different modalities to enhance performance. Our results indicate that the optimal $K$ for certain modalities on specific datasets can be as low as 1 or 2, which may restrict the GNNs' capacity to capture global information. To address this, we introduce a Sampling-based Global Transformer, which utilizes uniform global sampling to effectively integrate global information for GNNs. We conduct comprehensive experiments that demonstrate the superiority of our approach over existing methods. Our code is publicly available at https://github.com/CrawlScript/MIG-GT.
Large Vision-Language Models (LVLMs) have demonstrated remarkable performance across diverse tasks. Despite great success, recent studies show that LVLMs encounter substantial limitations when engaging with visual graphs. To study the reason behind these limitations, we propose VGCure, a comprehensive benchmark covering 22 tasks for examining the fundamental graph understanding and reasoning capacities of LVLMs. Extensive evaluations conducted on 14 LVLMs reveal that LVLMs are weak in basic graph understanding and reasoning tasks, particularly those concerning relational or structurally complex information. Based on this observation, we propose a structure-aware fine-tuning framework to enhance LVLMs with structure learning abilities through 3 self-supervised learning tasks. Experiments validate the effectiveness of our method in improving LVLMs' zero-shot performance on fundamental graph learning tasks, as well as enhancing the robustness of LVLMs against complex visual graphs.
Classical neural ODEs trained with explicit methods are intrinsically limited by stability, crippling their efficiency and robustness for stiff learning problems that are common in graph learning and scientific machine learning. We present a semi-implicit neural ODE approach that exploits the partitionable structure of the underlying dynamics. Our technique leads to an implicit neural network with significant computational advantages over existing approaches because of enhanced stability and efficient linear solves during time integration. We show that our approach outperforms existing approaches on a variety of applications including graph classification and learning complex dynamical systems. We also demonstrate that our approach can train challenging neural ODEs where both explicit methods and fully implicit methods are intractable.
Session-based recommendation seeks to forecast the next item a user will be interested in, based on their interaction sequences. Due to limited interaction data, session-based recommendation faces the challenge of limited data availability. Traditional methods enhance feature learning by constructing complex models to generate positive and negative samples. This paper proposes a session-based recommendation model using Single Positive optimization loss and Graph Learning (SPGL) to deal with the problem of data sparsity, high model complexity and weak transferability. SPGL utilizes graph convolutional networks to generate global item representations and batch session representations, effectively capturing intrinsic relationships between items. The use of single positive optimization loss improves uniformity of item representations, thereby enhancing recommendation accuracy. In the intent extractor, SPGL considers the hop count of the adjacency matrix when constructing the directed global graph to fully integrate spatial information. It also takes into account the reverse positional information of items when constructing session representations to incorporate temporal information. Comparative experiments across three benchmark datasets, Tmall, RetailRocket and Diginetica, demonstrate the model's effectiveness. The source code can be accessed on https://github.com/liang-tian-tian/SPGL .
Heterogeneous Text-Attributed Graphs (HTAGs), where different types of entities are not only associated with texts but also connected by diverse relationships, have gained widespread popularity and application across various domains. However, current research on text-attributed graph learning predominantly focuses on homogeneous graphs, which feature a single node and edge type, thus leaving a gap in understanding how methods perform on HTAGs. One crucial reason is the lack of comprehensive HTAG datasets that offer original textual content and span multiple domains of varying sizes. To this end, we introduce a collection of challenging and diverse benchmark datasets for realistic and reproducible evaluation of machine learning models on HTAGs. Our HTAG datasets are multi-scale, span years in duration, and cover a wide range of domains, including movie, community question answering, academic, literature, and patent networks. We further conduct benchmark experiments on these datasets with various graph neural networks. All source data, dataset construction codes, processed HTAGs, data loaders, benchmark codes, and evaluation setup are publicly available at GitHub and Hugging Face.
The prevalence of unhealthy eating habits has become an increasingly concerning issue in the United States. However, major food recommendation platforms (e.g., Yelp) continue to prioritize users' dietary preferences over the healthiness of their choices. Although efforts have been made to develop health-aware food recommendation systems, the personalization of such systems based on users' specific health conditions remains under-explored. In addition, few research focus on the interpretability of these systems, which hinders users from assessing the reliability of recommendations and impedes the practical deployment of these systems. In response to this gap, we first establish two large-scale personalized health-aware food recommendation benchmarks at the first attempt. We then develop a novel framework, Multi-Objective Personalized Interpretable Health-aware Food Recommendation System (MOPI-HFRS), which provides food recommendations by jointly optimizing the three objectives: user preference, personalized healthiness and nutritional diversity, along with an large language model (LLM)-enhanced reasoning module to promote healthy dietary knowledge through the interpretation of recommended results. Specifically, this holistic graph learning framework first utilizes two structure learning and a structure pooling modules to leverage both descriptive features and health data. Then it employs Pareto optimization to achieve designed multi-facet objectives. Finally, to further promote the healthy dietary knowledge and awareness, we exploit an LLM by utilizing knowledge-infusion, prompting the LLMs with knowledge obtained from the recommendation model for interpretation.
Standard deep learning architectures used for classification generate label predictions with a projection head and softmax activation function. Although successful, these methods fail to leverage the relational information between samples in the batch for generating label predictions. In recent works, graph-based learning techniques, namely Laplace learning, have been heuristically combined with neural networks for both supervised and semi-supervised learning (SSL) tasks. However, prior works approximate the gradient of the loss function with respect to the graph learning algorithm or decouple the processes; end-to-end integration with neural networks is not achieved. In this work, we derive backpropagation equations, via the adjoint method, for inclusion of a general family of graph learning layers into a neural network. This allows us to precisely integrate graph Laplacian-based label propagation into a neural network layer, replacing a projection head and softmax activation function for classification tasks. Using this new framework, our experimental results demonstrate smooth label transitions across data, improved robustness to adversarial attacks, improved generalization, and improved training dynamics compared to the standard softmax-based approach.
Extraction of building footprint polygons from remotely sensed data is essential for several urban understanding tasks such as reconstruction, navigation, and mapping. Despite significant progress in the area, extracting accurate polygonal building footprints remains an open problem. In this paper, we introduce Pix2Poly, an attention-based end-to-end trainable and differentiable deep neural network capable of directly generating explicit high-quality building footprints in a ring graph format. Pix2Poly employs a generative encoder-decoder transformer to produce a sequence of graph vertex tokens whose connectivity information is learned by an optimal matching network. Compared to previous graph learning methods, ours is a truly end-to-end trainable approach that extracts high-quality building footprints and road networks without requiring complicated, computationally intensive raster loss functions and intricate training pipelines. Upon evaluating Pix2Poly on several complex and challenging datasets, we report that Pix2Poly outperforms state-of-the-art methods in several vector shape quality metrics while being an entirely explicit method. Our code is available at https://github.com/yeshwanth95/Pix2Poly.
Graph Neural Networks (GNNs) demonstrate superior performance in various graph learning tasks, yet their wider real-world application is hindered by the computational overhead when applied to large-scale graphs. To address the issue, the Graph Lottery Hypothesis (GLT) has been proposed, advocating the identification of subgraphs and subnetworks, \textit{i.e.}, winning tickets, without compromising performance. The effectiveness of current GLT methods largely stems from the use of iterative magnitude pruning (IMP), which offers higher stability and better performance than one-shot pruning. However, identifying GLTs is highly computationally expensive, due to the iterative pruning and retraining required by IMP. In this paper, we reevaluate the correlation between one-shot pruning and IMP: while one-shot tickets are suboptimal compared to IMP, they offer a \textit{fast track} to tickets with a stronger performance. We introduce a one-shot pruning and denoising framework to validate the efficacy of the \textit{fast track}. Compared to current IMP-based GLT methods, our framework achieves a double-win situation of graph lottery tickets with \textbf{higher sparsity} and \textbf{faster speeds}. Through extensive experiments across 4 backbones and 6 datasets, our method demonstrates $1.32\% - 45.62\%$ improvement in weight sparsity and a $7.49\% - 22.71\%$ increase in graph sparsity, along with a $1.7-44 \times$ speedup over IMP-based methods and $95.3\%-98.6\%$ MAC savings.
Graph Neural Networks (GNNs) have seen significant advances in recent years, yet their application to multigraphs, where parallel edges exist between the same pair of nodes, remains under-explored. Standard GNNs, designed for simple graphs, compute node representations by combining all connected edges at once, without distinguishing between edges from different neighbors. There are some GNN architectures proposed specifically for multigraphs, yet these architectures perform only node-level aggregation in their message passing layers, which limits their expressive power. Furthermore, these approaches either lack permutation equivariance when a strict total edge ordering is absent, or fail to preserve the topological structure of the multigraph. To address all these shortcomings, we propose MEGA-GNN, a unified framework for message passing on multigraphs that can effectively perform diverse graph learning tasks. Our approach introduces a two-stage aggregation process in the message passing layers: first, parallel edges are aggregated, followed by a node-level aggregation of messages from distinct neighbors. We show that MEGA-GNN is not only permutation equivariant but also universal given a strict total ordering on the edges. Experiments show that MEGA-GNN significantly outperforms state-of-the-art solutions by up to 13\% on Anti-Money Laundering datasets and is on par with their accuracy on real-world phishing classification datasets in terms of minority class F1 score.
Automatically constructing GUI groups of different granularities constitutes a critical intelligent step towards automating GUI design and implementation tasks. Specifically, in the industrial GUI-to-code process, fragmented layers may decrease the readability and maintainability of generated code, which can be alleviated by grouping semantically consistent fragmented layers in the design prototypes. This study aims to propose a graph-learning-based approach to tackle the fragmented layer grouping problem according to multi-modal information in design prototypes. Our graph learning module consists of self-attention and graph neural network modules. By taking the multimodal fused representation of GUI layers as input, we innovatively group fragmented layers by classifying GUI layers and regressing the bounding boxes of the corresponding GUI components simultaneously. Experiments on two real-world datasets demonstrate that our model achieves state-of-the-art performance. A further user study is also conducted to validate that our approach can assist an intelligent downstream tool in generating more maintainable and readable front-end code.
Temporal Graph Learning (TGL) is crucial for capturing the evolving nature of stock markets. Traditional methods often ignore the interplay between dynamic temporal changes and static relational structures between stocks. To address this issue, we propose the Dynamic Graph Representation with Contrastive Learning (DGRCL) framework, which integrates dynamic and static graph relations to improve the accuracy of stock trend prediction. Our framework introduces two key components: the Embedding Enhancement (EE) module and the Contrastive Constrained Training (CCT) module. The EE module focuses on dynamically capturing the temporal evolution of stock data, while the CCT module enforces static constraints based on stock relations, refined within contrastive learning. This dual-relation approach allows for a more comprehensive understanding of stock market dynamics. Our experiments on two major U.S. stock market datasets, NASDAQ and NYSE, demonstrate that DGRCL significantly outperforms state-of-the-art TGL baselines. Ablation studies indicate the importance of both modules. Overall, DGRCL not only enhances prediction ability but also provides a robust framework for integrating temporal and relational data in dynamic graphs. Code and data are available for public access.
Graph Neural Networks (GNNs) have demonstrated their effectiveness in various graph learning tasks, yet their reliance on neighborhood aggregation during inference poses challenges for deployment in latency-sensitive applications, such as real-time financial fraud detection. To address this limitation, recent studies have proposed distilling knowledge from teacher GNNs into student Multi-Layer Perceptrons (MLPs) trained on node content, aiming to accelerate inference. However, these approaches often inadequately explore structural information when inferring unseen nodes. To this end, we introduce SimMLP, a Self-supervised framework for learning MLPs on graphs, designed to fully integrate rich structural information into MLPs. Notably, SimMLP is the first MLP-learning method that can achieve equivalence to GNNs in the optimal case. The key idea is to employ self-supervised learning to align the representations encoded by graph context-aware GNNs and neighborhood dependency-free MLPs, thereby fully integrating the structural information into MLPs. We provide a comprehensive theoretical analysis, demonstrating the equivalence between SimMLP and GNNs based on mutual information and inductive bias, highlighting SimMLP's advanced structural learning capabilities. Additionally, we conduct extensive experiments on 20 benchmark datasets, covering node classification, link prediction, and graph classification, to showcase SimMLP's superiority over state-of-the-art baselines, particularly in scenarios involving unseen nodes (e.g., inductive and cold-start node classification) where structural insights are crucial. Our codes are available at: https://github.com/Zehong-Wang/SimMLP.
Self-supervised heterogeneous graph learning (SHGL) has shown promising potential in diverse scenarios. However, while existing SHGL methods share a similar essential with clustering approaches, they encounter two significant limitations: (i) noise in graph structures is often introduced during the message-passing process to weaken node representations, and (ii) cluster-level information may be inadequately captured and leveraged, diminishing the performance in downstream tasks. In this paper, we address these limitations by theoretically revisiting SHGL from the spectral clustering perspective and introducing a novel framework enhanced by rank and dual consistency constraints. Specifically, our framework incorporates a rank-constrained spectral clustering method that refines the affinity matrix to exclude noise effectively. Additionally, we integrate node-level and cluster-level consistency constraints that concurrently capture invariant and clustering information to facilitate learning in downstream tasks. We theoretically demonstrate that the learned representations are divided into distinct partitions based on the number of classes and exhibit enhanced generalization ability across tasks. Experimental results affirm the superiority of our method, showcasing remarkable improvements in several downstream tasks compared to existing methods.
We address two fundamental challenges in Graph Neural Networks (GNNs): (1) the lack of theoretical support for invariance learning, a critical property in image processing, and (2) the absence of a unified model capable of excelling on both homophilic and heterophilic graph datasets. To tackle these issues, we establish and prove scale invariance in graphs, extending this key property to graph learning, and validate it through experiments on real-world datasets. Leveraging directed multi-scaled graphs and an adaptive self-loop strategy, we propose ScaleNet, a unified network architecture that achieves state-of-the-art performance across four homophilic and two heterophilic benchmark datasets. Furthermore, we show that through graph transformation based on scale invariance, uniform weights can replace computationally expensive edge weights in digraph inception networks while maintaining or improving performance. For another popular GNN approach to digraphs, we demonstrate the equivalence between Hermitian Laplacian methods and GraphSAGE with incidence normalization. ScaleNet bridges the gap between homophilic and heterophilic graph learning, offering both theoretical insights into scale invariance and practical advancements in unified graph learning. Our implementation is publicly available at https://github.com/Qin87/ScaleNet/tree/Aug23.