Brain age estimation is clinically important as it can provide valuable information in the context of neurodegenerative diseases such as Alzheimer's. Population graphs, which include multimodal imaging information of the subjects along with the relationships among the population, have been used in literature along with Graph Convolutional Networks (GCNs) and have proved beneficial for a variety of medical imaging tasks. A population graph is usually static and constructed manually using non-imaging information. However, graph construction is not a trivial task and might significantly affect the performance of the GCN, which is inherently very sensitive to the graph structure. In this work, we propose a framework that learns a population graph structure optimized for the downstream task. An attention mechanism assigns weights to a set of imaging and non-imaging features (phenotypes), which are then used for edge extraction. The resulting graph is used to train the GCN. The entire pipeline can be trained end-to-end. Additionally, by visualizing the attention weights that were the most important for the graph construction, we increase the interpretability of the graph. We use the UK Biobank, which provides a large variety of neuroimaging and non-imaging phenotypes, to evaluate our method on brain age regression and classification. The proposed method outperforms competing static graph approaches and other state-of-the-art adaptive methods. We further show that the assigned attention scores indicate that there are both imaging and non-imaging phenotypes that are informative for brain age estimation and are in agreement with the relevant literature.
In graph representation learning, it is important that the complex geometric structure of the input graph, e.g. hidden relations among nodes, is well captured in embedding space. However, standard Euclidean embedding spaces have a limited capacity in representing graphs of varying structures. A promising candidate for the faithful embedding of data with varying structure is product manifolds of component spaces of different geometries (spherical, hyperbolic, or euclidean). In this paper, we take a closer look at the structure of product manifold embedding spaces and argue that each component space in a product contributes differently to expressing structures in the input graph, hence should be weighted accordingly. This is different from previous works which consider the roles of different components equally. We then propose WEIGHTED-PM, a data-driven method for learning embedding of heterogeneous graphs in weighted product manifolds. Our method utilizes the topological information of the input graph to automatically determine the weight of each component in product spaces. Extensive experiments on synthetic and real-world graph datasets demonstrate that WEIGHTED-PM is capable of learning better graph representations with lower geometric distortion from input data, and performs better on multiple downstream tasks, such as word similarity learning, top-$k$ recommendation, and knowledge graph embedding.
Graph neural network (GNN) has gained increasing popularity in recent years owing to its capability and flexibility in modeling complex graph structure data. Among all graph learning methods, hypergraph learning is a technique for exploring the implicit higher-order correlations when training the embedding space of the graph. In this paper, we propose a hypergraph learning framework named LFH that is capable of dynamic hyperedge construction and attentive embedding update utilizing the heterogeneity attributes of the graph. Specifically, in our framework, the high-quality features are first generated by the pairwise fusion strategy that utilizes explicit graph structure information when generating initial node embedding. Afterwards, a hypergraph is constructed through the dynamic grouping of implicit hyperedges, followed by the type-specific hypergraph learning process. To evaluate the effectiveness of our proposed framework, we conduct comprehensive experiments on several popular datasets with eleven state-of-the-art models on both node classification and link prediction tasks, which fall into categories of homogeneous pairwise graph learning, heterogeneous pairwise graph learning, and hypergraph learning. The experiment results demonstrate a significant performance gain (average 12.5% in node classification and 13.3% in link prediction) compared with recent state-of-the-art methods.
In this paper, we introduce a new self-supervised rationalization method, called KGRec, for knowledge-aware recommender systems. To effectively identify informative knowledge connections, we propose an attentive knowledge rationalization mechanism that generates rational scores for knowledge triplets. With these scores, KGRec integrates generative and contrastive self-supervised tasks for recommendation through rational masking. To highlight rationales in the knowledge graph, we design a novel generative task in the form of masking-reconstructing. By masking important knowledge with high rational scores, KGRec is trained to rebuild and highlight useful knowledge connections that serve as rationales. To further rationalize the effect of collaborative interactions on knowledge graph learning, we introduce a contrastive learning task that aligns signals from knowledge and user-item interaction views. To ensure noise-resistant contrasting, potential noisy edges in both graphs judged by the rational scores are masked. Extensive experiments on three real-world datasets demonstrate that KGRec outperforms state-of-the-art methods. We also provide the implementation codes for our approach at https://github.com/HKUDS/KGRec.
Graph neural networks (GNNs) are widely used in domains like social networks and biological systems. However, the locality assumption of GNNs, which limits information exchange to neighboring nodes, hampers their ability to capture long-range dependencies and global patterns in graphs. To address this, we propose a new inductive bias based on variational analysis, drawing inspiration from the Brachistochrone problem. Our framework establishes a mapping between discrete GNN models and continuous diffusion functionals. This enables the design of application-specific objective functions in the continuous domain and the construction of discrete deep models with mathematical guarantees. To tackle over-smoothing in GNNs, we analyze the existing layer-by-layer graph embedding models and identify that they are equivalent to l2-norm integral functionals of graph gradients, which cause over-smoothing. Similar to edge-preserving filters in image denoising, we introduce total variation (TV) to align the graph diffusion pattern with global community topologies. Additionally, we devise a selective mechanism to address the trade-off between model depth and over-smoothing, which can be easily integrated into existing GNNs. Furthermore, we propose a novel generative adversarial network (GAN) that predicts spreading flows in graphs through a neural transport equation. To mitigate vanishing flows, we customize the objective function to minimize transportation within each community while maximizing inter-community flows. Our GNN models achieve state-of-the-art (SOTA) performance on popular graph learning benchmarks such as Cora, Citeseer, and Pubmed.
Traffic prediction has been an active research topic in the domain of spatial-temporal data mining. Accurate real-time traffic prediction is essential to improve the safety, stability, and versatility of smart city systems, i.e., traffic control and optimal routing. The complex and highly dynamic spatial-temporal dependencies make effective predictions still face many challenges. Recent studies have shown that spatial-temporal graph neural networks exhibit great potential applied to traffic prediction, which combines sequential models with graph convolutional networks to jointly model temporal and spatial correlations. However, a survey study of graph learning, spatial-temporal graph models for traffic, as well as a fair comparison of baseline models are pending and unavoidable issues. In this paper, we first provide a systematic review of graph learning strategies and commonly used graph convolution algorithms. Then we conduct a comprehensive analysis of the strengths and weaknesses of recently proposed spatial-temporal graph network models. Furthermore, we build a study called STG4Traffic using the deep learning framework PyTorch to establish a standardized and scalable benchmark on two types of traffic datasets. We can evaluate their performance by personalizing the model settings with uniform metrics. Finally, we point out some problems in the current study and discuss future directions. Source codes are available at https://github.com/trainingl/STG4Traffic.
Out-of-distribution (OOD) graph generalization are critical for many real-world applications. Existing methods neglect to discard spurious or noisy features of inputs, which are irrelevant to the label. Besides, they mainly conduct instance-level class-invariant graph learning and fail to utilize the structural class relationships between graph instances. In this work, we endeavor to address these issues in a unified framework, dubbed Individual and Structural Graph Information Bottlenecks (IS-GIB). To remove class spurious feature caused by distribution shifts, we propose Individual Graph Information Bottleneck (I-GIB) which discards irrelevant information by minimizing the mutual information between the input graph and its embeddings. To leverage the structural intra- and inter-domain correlations, we propose Structural Graph Information Bottleneck (S-GIB). Specifically for a batch of graphs with multiple domains, S-GIB first computes the pair-wise input-input, embedding-embedding, and label-label correlations. Then it minimizes the mutual information between input graph and embedding pairs while maximizing the mutual information between embedding and label pairs. The critical insight of S-GIB is to simultaneously discard spurious features and learn invariant features from a high-order perspective by maintaining class relationships under multiple distributional shifts. Notably, we unify the proposed I-GIB and S-GIB to form our complementary framework IS-GIB. Extensive experiments conducted on both node- and graph-level tasks consistently demonstrate the superior generalization ability of IS-GIB. The code is available at https://github.com/YangLing0818/GraphOOD.
Spatial-temporal graph learning has emerged as a promising solution for modeling structured spatial-temporal data and learning region representations for various urban sensing tasks such as crime forecasting and traffic flow prediction. However, most existing models are vulnerable to the quality of the generated region graph due to the inaccurate graph-structured information aggregation schema. The ubiquitous spatial-temporal data noise and incompleteness in real-life scenarios pose challenges in generating high-quality region representations. To address this challenge, we propose a new spatial-temporal graph learning model (GraphST) for enabling effective self-supervised learning. Our proposed model is an adversarial contrastive learning paradigm that automates the distillation of crucial multi-view self-supervised information for robust spatial-temporal graph augmentation. We empower GraphST to adaptively identify hard samples for better self-supervision, enhancing the representation discrimination ability and robustness. In addition, we introduce a cross-view contrastive learning paradigm to model the inter-dependencies across view-specific region representations and preserve underlying relation heterogeneity. We demonstrate the superiority of our proposed GraphST method in various spatial-temporal prediction tasks on real-life datasets. We release our model implementation via the link: \url{https://github.com/HKUDS/GraphST}.
Finding multiple temporal relationships among locations can benefit a bunch of urban applications, such as dynamic offline advertising and smart public transport planning. While some efforts have been made on finding static relationships among locations, little attention is focused on studying time-aware location relationships. Indeed, abundant location-based human activities are time-varying and the availability of these data enables a new paradigm for understanding the dynamic relationships in a period among connective locations. To this end, we propose to study a new problem, namely multi-Temporal relationship inference among locations (Trial for short), where the major challenge is how to integrate dynamic and geographical influence under the relationship sparsity constraint. Specifically, we propose a solution to Trial with a graph learning scheme, which includes a spatially evolving graph neural network (SEENet) with two collaborative components: spatially evolving graph convolution module (SEConv) and spatially evolving self-supervised learning strategy (SE-SSL). SEConv performs the intra-time aggregation and inter-time propagation to capture the multifaceted spatially evolving contexts from the view of location message passing. In addition, SE-SSL designs time-aware self-supervised learning tasks in a global-local manner with additional evolving constraint to enhance the location representation learning and further handle the relationship sparsity. Finally, experiments on four real-world datasets demonstrate the superiority of our method over several state-of-the-art approaches.
Molecular property prediction is an important problem in drug discovery and materials science. As geometric structures have been demonstrated necessary for molecular property prediction, 3D information has been combined with various graph learning methods to boost prediction performance. However, obtaining the geometric structure of molecules is not feasible in many real-world applications due to the high computational cost. In this work, we propose a novel 3D pre-training framework (dubbed 3D PGT), which pre-trains a model on 3D molecular graphs, and then fine-tunes it on molecular graphs without 3D structures. Based on fact that bond length, bond angle, and dihedral angle are three basic geometric descriptors corresponding to a complete molecular 3D conformer, we first develop a multi-task generative pre-train framework based on these three attributes. Next, to automatically fuse these three generative tasks, we design a surrogate metric using the \textit{total energy} to search for weight distribution of the three pretext task since total energy corresponding to the quality of 3D conformer.Extensive experiments on 2D molecular graphs are conducted to demonstrate the accuracy, efficiency and generalization ability of the proposed 3D PGT compared to various pre-training baselines.
Temporal Graph Learning, which aims to model the time-evolving nature of graphs, has gained increasing attention and achieved remarkable performance recently. However, in reality, graph structures are often incomplete and noisy, which hinders temporal graph networks (TGNs) from learning informative representations. Graph contrastive learning uses data augmentation to generate plausible variations of existing data and learn robust representations. However, rule-based augmentation approaches may be suboptimal as they lack learnability and fail to leverage rich information from downstream tasks. To address these issues, we propose a Time-aware Graph Structure Learning (TGSL) approach via sequence prediction on temporal graphs, which learns better graph structures for downstream tasks through adding potential temporal edges. In particular, it predicts time-aware context embedding based on previously observed interactions and uses the Gumble-Top-K to select the closest candidate edges to this context embedding. Additionally, several candidate sampling strategies are proposed to ensure both efficiency and diversity. Furthermore, we jointly learn the graph structure and TGNs in an end-to-end manner and perform inference on the refined graph. Extensive experiments on temporal link prediction benchmarks demonstrate that TGSL yields significant gains for the popular TGNs such as TGAT and GraphMixer, and it outperforms other contrastive learning methods on temporal graphs. We release the code at https://github.com/ViktorAxelsen/TGSL.
We investigate novel random graph embeddings that can be computed in expected polynomial time and that are able to distinguish all non-isomorphic graphs in expectation. Previous graph embeddings have limited expressiveness and either cannot distinguish all graphs or cannot be computed efficiently for every graph. To be able to approximate arbitrary functions on graphs, we are interested in efficient alternatives that become arbitrarily expressive with increasing resources. Our approach is based on Lov\'asz' characterisation of graph isomorphism through an infinite dimensional vector of homomorphism counts. Our empirical evaluation shows competitive results on several benchmark graph learning tasks.
Relational inference aims to identify interactions between parts of a dynamical system from the observed dynamics. Current state-of-the-art methods fit the dynamics with a graph neural network (GNN) on a learnable graph. They use one-step message-passing GNNs -- intuitively the right choice since non-locality of multi-step or spectral GNNs may confuse direct and indirect interactions. But the \textit{effective} interaction graph depends on the sampling rate and it is rarely localized to direct neighbors, leading to poor local optima for the one-step model. In this work, we propose a \textit{graph dynamics prior} (GDP) for relational inference. GDP constructively uses error amplification in non-local polynomial filters to steer the solution to the ground-truth graph. To deal with non-uniqueness, GDP simultaneously fits a ``shallow'' one-step model and a polynomial multi-step model with shared graph topology. Experiments show that GDP reconstructs graphs far more accurately than earlier methods, with remarkable robustness to under-sampling. Since appropriate sampling rates for unknown dynamical systems are not known a priori, this robustness makes GDP suitable for real applications in scientific machine learning. Reproducible code is available at https://github.com/DaDaCheng/GDP.
Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in the effect of one drug to the presence of another drug in the human body, which plays an essential role in drug discovery and clinical research. DDIs prediction through traditional clinical trials and experiments is an expensive and time-consuming process. To correctly apply the advanced AI and deep learning, the developer and user meet various challenges such as the availability and encoding of data resources, and the design of computational methods. This review summarizes chemical structure based, network based, NLP based and hybrid methods, providing an updated and accessible guide to the broad researchers and development community with different domain knowledge. We introduce widely-used molecular representation and describe the theoretical frameworks of graph neural network models for representing molecular structures. We present the advantages and disadvantages of deep and graph learning methods by performing comparative experiments. We discuss the potential technical challenges and highlight future directions of deep and graph learning models for accelerating DDIs prediction.
The nature of heterophilous graphs is significantly different from that of homophilous graphs, which causes difficulties in early graph neural network models and suggests aggregations beyond the 1-hop neighborhood. In this paper, we develop a new way to implement multi-scale extraction via constructing Haar-type graph framelets with desired properties of permutation equivariance, efficiency, and sparsity, for deep learning tasks on graphs. We further design a graph framelet neural network model PEGFAN (Permutation Equivariant Graph Framelet Augmented Network) based on our constructed graph framelets. The experiments are conducted on a synthetic dataset and 9 benchmark datasets to compare performance with other state-of-the-art models. The result shows that our model can achieve the best performance on certain datasets of heterophilous graphs (including the majority of heterophilous datasets with relatively larger sizes and denser connections) and competitive performance on the remaining.
Vulnerability detection is a critical problem in software security and attracts growing attention both from academia and industry. Traditionally, software security is safeguarded by designated rule-based detectors that heavily rely on empirical expertise, requiring tremendous effort from software experts to generate rule repositories for large code corpus. Recent advances in deep learning, especially Graph Neural Networks (GNN), have uncovered the feasibility of automatic detection of a wide range of software vulnerabilities. However, prior learning-based works only break programs down into a sequence of word tokens for extracting contextual features of codes, or apply GNN largely on homogeneous graph representation (e.g., AST) without discerning complex types of underlying program entities (e.g., methods, variables). In this work, we are one of the first to explore heterogeneous graph representation in the form of Code Property Graph and adapt a well-known heterogeneous graph network with a dual-supervisor structure for the corresponding graph learning task. Using the prototype built, we have conducted extensive experiments on both synthetic datasets and real-world projects. Compared with the state-of-the-art baselines, the results demonstrate promising effectiveness in this research direction in terms of vulnerability detection performance (average F1 improvements over 10\% in real-world projects) and transferability from C/C++ to other programming languages (average F1 improvements over 11%).
Transformers use the dense self-attention mechanism which gives a lot of flexibility for long-range connectivity. Over multiple layers of a deep transformer, the number of possible connectivity patterns increases exponentially. However, very few of these contribute to the performance of the network, and even fewer are essential. We hypothesize that there are sparsely connected sub-networks within a transformer, called information pathways which can be trained independently. However, the dynamic (i.e., input-dependent) nature of these pathways makes it difficult to prune dense self-attention during training. But the overall distribution of these pathways is often predictable. We take advantage of this fact to propose Stochastically Subsampled self-Attention (SSA) - a general-purpose training strategy for transformers that can reduce both the memory and computational cost of self-attention by 4 to 8 times during training while also serving as a regularization method - improving generalization over dense training. We show that an ensemble of sub-models can be formed from the subsampled pathways within a network, which can achieve better performance than its densely attended counterpart. We perform experiments on a variety of NLP, computer vision and graph learning tasks in both generative and discriminative settings to provide empirical evidence for our claims and show the effectiveness of the proposed method.
Label errors have been found to be prevalent in popular text, vision, and audio datasets, which heavily influence the safe development and evaluation of machine learning algorithms. Despite increasing efforts towards improving the quality of generic data types, such as images and texts, the problem of mislabel detection in graph data remains underexplored. To bridge the gap, we explore mislabelling issues in popular real-world graph datasets and propose GraphCleaner, a post-hoc method to detect and correct these mislabelled nodes in graph datasets. GraphCleaner combines the novel ideas of 1) Synthetic Mislabel Dataset Generation, which seeks to generate realistic mislabels; and 2) Neighborhood-Aware Mislabel Detection, where neighborhood dependency is exploited in both labels and base classifier predictions. Empirical evaluations on 6 datasets and 6 experimental settings demonstrate that GraphCleaner outperforms the closest baseline, with an average improvement of 0.14 in F1 score, and 0.16 in MCC. On real-data case studies, GraphCleaner detects real and previously unknown mislabels in popular graph benchmarks: PubMed, Cora, CiteSeer and OGB-arxiv; we find that at least 6.91% of PubMed data is mislabelled or ambiguous, and simply removing these mislabelled data can boost evaluation performance from 86.71% to 89.11%.
Heterogeneous Graph Neural Networks (HGNNs) have gained significant popularity in various heterogeneous graph learning tasks. However, most existing HGNNs rely on spatial domain-based methods to aggregate information, i.e., manually selected meta-paths or some heuristic modules, lacking theoretical guarantees. Furthermore, these methods cannot learn arbitrary valid heterogeneous graph filters within the spectral domain, which have limited expressiveness. To tackle these issues, we present a positive spectral heterogeneous graph convolution via positive noncommutative polynomials. Then, using this convolution, we propose PSHGCN, a novel Positive Spectral Heterogeneous Graph Convolutional Network. PSHGCN offers a simple yet effective method for learning valid heterogeneous graph filters. Moreover, we demonstrate the rationale of PSHGCN in the graph optimization framework. We conducted an extensive experimental study to show that PSHGCN can learn diverse heterogeneous graph filters and outperform all baselines on open benchmarks. Notably, PSHGCN exhibits remarkable scalability, efficiently handling large real-world graphs comprising millions of nodes and edges. Our codes are available at https://github.com/ivam-he/PSHGCN.
Graph Neural Networks (GNNs) have exhibited impressive performance in many graph learning tasks. Nevertheless, the performance of GNNs can deteriorate when the input graph data suffer from weak information, i.e., incomplete structure, incomplete features, and insufficient labels. Most prior studies, which attempt to learn from the graph data with a specific type of weak information, are far from effective in dealing with the scenario where diverse data deficiencies exist and mutually affect each other. To fill the gap, in this paper, we aim to develop an effective and principled approach to the problem of graph learning with weak information (GLWI). Based on the findings from our empirical analysis, we derive two design focal points for solving the problem of GLWI, i.e., enabling long-range propagation in GNNs and allowing information propagation to those stray nodes isolated from the largest connected component. Accordingly, we propose D$^2$PT, a dual-channel GNN framework that performs long-range information propagation not only on the input graph with incomplete structure, but also on a global graph that encodes global semantic similarities. We further develop a prototype contrastive alignment algorithm that aligns the class-level prototypes learned from two channels, such that the two different information propagation processes can mutually benefit from each other and the finally learned model can well handle the GLWI problem. Extensive experiments on eight real-world benchmark datasets demonstrate the effectiveness and efficiency of our proposed methods in various GLWI scenarios.