Complex Query Answering (CQA) over Knowledge Graphs (KGs) has attracted a lot of attention to potentially support many applications. Given that KGs are usually incomplete, neural models are proposed to answer the logical queries by parameterizing set operators with complex neural networks. However, such methods usually train neural set operators with a large number of entity and relation embeddings from the zero, where whether and how the embeddings or the neural set operators contribute to the performance remains not clear. In this paper, we propose a simple framework for complex query answering that decomposes the KG embeddings from neural set operators. We propose to represent the complex queries into the query graph. On top of the query graph, we propose the Logical Message Passing Neural Network (LMPNN) that connects the local one-hop inferences on atomic formulas to the global logical reasoning for complex query answering. We leverage existing effective KG embeddings to conduct one-hop inferences on atomic formulas, the results of which are regarded as the messages passed in LMPNN. The reasoning process over the overall logical formulas is turned into the forward pass of LMPNN that incrementally aggregates local information to finally predict the answers' embeddings. The complex logical inference across different types of queries will then be learned from training examples based on the LMPNN architecture. Theoretically, our query-graph represenation is more general than the prevailing operator-tree formulation, so our approach applies to a broader range of complex KG queries. Empirically, our approach yields the new state-of-the-art neural CQA model. Our research bridges the gap between complex KG query answering tasks and the long-standing achievements of knowledge graph representation learning.
Aligning users across networks using graph representation learning has been found effective where the alignment is accomplished in a low-dimensional embedding space. Yet, achieving highly precise alignment is still challenging, especially when nodes with long-range connectivity to the labeled anchors are encountered. To alleviate this limitation, we purposefully designed WL-Align which adopts a regularized representation learning framework to learn distinctive node representations. It extends the Weisfeiler-Lehman Isormorphism Test and learns the alignment in alternating phases of "across-network Weisfeiler-Lehman relabeling" and "proximity-preserving representation learning". The across-network Weisfeiler-Lehman relabeling is achieved through iterating the anchor-based label propagation and a similarity-based hashing to exploit the known anchors' connectivity to different nodes in an efficient and robust manner. The representation learning module preserves the second-order proximity within individual networks and is regularized by the across-network Weisfeiler-Lehman hash labels. Extensive experiments on real-world and synthetic datasets have demonstrated that our proposed WL-Align outperforms the state-of-the-art methods, achieving significant performance improvements in the "exact matching" scenario. Data and code of WL-Align are available at https://github.com/ChenPengGang/WLAlignCode.
Graph Neural Networks (GNNs) have shown great potential in the field of graph representation learning. Standard GNNs define a local message-passing mechanism which propagates information over the whole graph domain by stacking multiple layers. This paradigm suffers from two major limitations, over-squashing and poor long-range dependencies, that can be solved using global attention but significantly increases the computational cost to quadratic complexity. In this work, we propose an alternative approach to overcome these structural limitations by leveraging the ViT/MLP-Mixer architectures introduced in computer vision. We introduce a new class of GNNs, called Graph ViT/MLP-Mixer, that holds three key properties. First, they capture long-range dependency and mitigate the issue of over-squashing as demonstrated on Long Range Graph Benchmark and TreeNeighbourMatch datasets. Second, they offer better speed and memory efficiency with a complexity linear to the number of nodes and edges, surpassing the related Graph Transformer and expressive GNN models. Third, they show high expressivity in terms of graph isomorphism as they can distinguish at least 3-WL non-isomorphic graphs. We test our architecture on 4 simulated datasets and 7 real-world benchmarks, and show highly competitive results on all of them. The source code is available for reproducibility at: \url{https://github.com/XiaoxinHe/Graph-ViT-MLPMixer}.
In recent years, graph representation learning has achieved remarkable success while suffering from low-quality data problems. As a mature technology to improve data quality in computer vision, data augmentation has also attracted increasing attention in graph domain. To advance research in this emerging direction, this survey provides a comprehensive review and summary of existing graph data augmentation (GDAug) techniques. Specifically, this survey first provides an overview of various feasible taxonomies and categorizes existing GDAug studies based on multi-scale graph elements. Subsequently, for each type of GDAug technique, this survey formalizes standardized technical definition, discuss the technical details, and provide schematic illustration. The survey also reviews domain-specific graph data augmentation techniques, including those for heterogeneous graphs, temporal graphs, spatio-temporal graphs, and hypergraphs. In addition, this survey provides a summary of available evaluation metrics and design guidelines for graph data augmentation. Lastly, it outlines the applications of GDAug at both the data and model levels, discusses open issues in the field, and looks forward to future directions. The latest advances in GDAug are summarized in GitHub.
Graph convolutional networks (GCNs) have achieved great success in graph representation learning by extracting high-level features from nodes and their topology. Since GCNs generally follow a message-passing mechanism, each node aggregates information from its first-order neighbour to update its representation. As a result, the representations of nodes with edges between them should be positively correlated and thus can be considered positive samples. However, there are more non-neighbour nodes in the whole graph, which provide diverse and useful information for the representation update. Two non-adjacent nodes usually have different representations, which can be seen as negative samples. Besides the node representations, the structural information of the graph is also crucial for learning. In this paper, we used quality-diversity decomposition in determinant point processes (DPP) to obtain diverse negative samples. When defining a distribution on diverse subsets of all non-neighbouring nodes, we incorporate both graph structure information and node representations. Since the DPP sampling process requires matrix eigenvalue decomposition, we propose a new shortest-path-base method to improve computational efficiency. Finally, we incorporate the obtained negative samples into the graph convolution operation. The ideas are evaluated empirically in experiments on node classification tasks. These experiments show that the newly proposed methods not only improve the overall performance of standard representation learning but also significantly alleviate over-smoothing problems.
Unsupervised graph representation learning (UGRL) has drawn increasing research attention and achieved promising results in several graph analytic tasks. Relying on the homophily assumption, existing UGRL methods tend to smooth the learned node representations along all edges, ignoring the existence of heterophilic edges that connect nodes with distinct attributes. As a result, current methods are hard to generalize to heterophilic graphs where dissimilar nodes are widely connected, and also vulnerable to adversarial attacks. To address this issue, we propose a novel unsupervised Graph Representation learning method with Edge hEterophily discriminaTing (GREET) which learns representations by discriminating and leveraging homophilic edges and heterophilic edges. To distinguish two types of edges, we build an edge discriminator that infers edge homophily/heterophily from feature and structure information. We train the edge discriminator in an unsupervised way through minimizing the crafted pivot-anchored ranking loss, with randomly sampled node pairs acting as pivots. Node representations are learned through contrasting the dual-channel encodings obtained from the discriminated homophilic and heterophilic edges. With an effective interplaying scheme, edge discriminating and representation learning can mutually boost each other during the training phase. We conducted extensive experiments on 14 benchmark datasets and multiple learning scenarios to demonstrate the superiority of GREET.
Graph is powerful for representing various types of real-world data. The topology (edges' presence) and edges' features of a graph decides the message passing mechanism among vertices within the graph. While most existing approaches only manually define a single-value edge to describe the connectivity or strength of association between a pair of vertices, task-specific and crucial relationship cues may be disregarded by such manually defined topology and single-value edge features. In this paper, we propose the first general graph representation learning framework (called GRATIS) which can generate a strong graph representation with a task-specific topology and task-specific multi-dimensional edge features from any arbitrary input. To learn each edge's presence and multi-dimensional feature, our framework takes both of the corresponding vertices pair and their global contextual information into consideration, enabling the generated graph representation to have a globally optimal message passing mechanism for different down-stream tasks. The principled investigation results achieved for various graph analysis tasks on 11 graph and non-graph datasets show that our GRATIS can not only largely enhance pre-defined graphs but also learns a strong graph representation for non-graph data, with clear performance improvements on all tasks. In particular, the learned topology and multi-dimensional edge features provide complementary task-related cues for graph analysis tasks. Our framework is effective, robust and flexible, and is a plug-and-play module that can be combined with different backbones and Graph Neural Networks (GNNs) to generate a task-specific graph representation from various graph and non-graph data. Our code is made publicly available at https://github.com/SSYSteve/Learning-Graph-Representation-with-Task-specific-Topology-and-Multi-dimensional-Edge-Features.
Heterogeneous graph neural networks (HGNNs) have been widely applied in heterogeneous information network tasks, while most HGNNs suffer from poor scalability or weak representation when they are applied to large-scale heterogeneous graphs. To address these problems, we propose a novel Relation-aware Heterogeneous Graph Neural Network with Contrastive Learning (RHCO) for large-scale heterogeneous graph representation learning. Unlike traditional heterogeneous graph neural networks, we adopt the contrastive learning mechanism to deal with the complex heterogeneity of large-scale heterogeneous graphs. We first learn relation-aware node embeddings under the network schema view. Then we propose a novel positive sample selection strategy to choose meaningful positive samples. After learning node embeddings under the positive sample graph view, we perform a cross-view contrastive learning to obtain the final node representations. Moreover, we adopt the label smoothing technique to boost the performance of RHCO. Extensive experiments on three large-scale academic heterogeneous graph datasets show that RHCO achieves best performance over the state-of-the-art models.
Graph representation learning models have demonstrated great capability in many real-world applications. Nevertheless, prior research indicates that these models can learn biased representations leading to discriminatory outcomes. A few works have been proposed to mitigate the bias in graph representations. However, most existing works require exceptional time and computing resources for training and fine-tuning. To this end, we study the problem of efficient fair graph representation learning and propose a novel framework FairMILE. FairMILE is a multi-level paradigm that can efficiently learn graph representations while enforcing fairness and preserving utility. It can work in conjunction with any unsupervised embedding approach and accommodate various fairness constraints. Extensive experiments across different downstream tasks demonstrate that FairMILE significantly outperforms state-of-the-art baselines in terms of running time while achieving a superior trade-off between fairness and utility.
Community detection is the task of discovering groups of nodes sharing similar patterns within a network. With recent advancements in deep learning, methods utilizing graph representation learning and deep clustering have shown great results in community detection. However, these methods often rely on the topology of networks (i) ignoring important features such as network heterogeneity, temporality, multimodality, and other possibly relevant features. Besides, (ii) the number of communities is not known a priori and is often left to model selection. In addition, (iii) in multimodal networks all nodes are assumed to be symmetrical in their features; while true for homogeneous networks, most of the real-world networks are heterogeneous where feature availability often varies. In this paper, we propose a novel framework (named MGTCOM) that overcomes the above challenges (i)--(iii). MGTCOM identifies communities through multimodal feature learning by leveraging a new sampling technique for unsupervised learning of temporal embeddings. Importantly, MGTCOM is an end-to-end framework optimizing network embeddings, communities, and the number of communities in tandem. In order to assess its performance, we carried out an extensive evaluation on a number of multimodal networks. We found out that our method is competitive against state-of-the-art and performs well in inductive inference.
Graphons are general and powerful models for generating graphs of varying size. In this paper, we propose to directly model graphons using neural networks, obtaining Implicit Graphon Neural Representation (IGNR). Existing work in modeling and reconstructing graphons often approximates a target graphon by a fixed resolution piece-wise constant representation. Our IGNR has the benefit that it can represent graphons up to arbitrary resolutions, and enables natural and efficient generation of arbitrary sized graphs with desired structure once the model is learned. Furthermore, we allow the input graph data to be unaligned and have different sizes by leveraging the Gromov-Wasserstein distance. We first demonstrate the effectiveness of our model by showing its superior performance on a graphon learning task. We then propose an extension of IGNR that can be incorporated into an auto-encoder framework, and demonstrate its good performance under a more general setting of graphon learning. We also show that our model is suitable for graph representation learning and graph generation.
The issue of distribution shifts is emerging as a critical concern in graph representation learning. From the perspective of invariant learning and stable learning, a recently well-established paradigm for out-of-distribution generalization, stable features of the graph are assumed to causally determine labels, while environmental features tend to be unstable and can lead to the two primary types of distribution shifts. The correlation shift is often caused by the spurious correlation between environmental features and labels that differs between the training and test data; the covariate shift often stems from the presence of new environmental features in test data. However, most strategies, such as invariant learning or graph augmentation, typically struggle with limited training environments or perturbed stable features, thus exposing limitations in handling the problem of covariate shift. To address this challenge, we propose a simple-yet-effective data augmentation strategy, Adversarial Invariant Augmentation (AIA), to handle the covariate shift on graphs. Specifically, given the training data, AIA aims to extrapolate and generate new environments, while concurrently preserving the original stable features during the augmentation process. Such a design equips the graph classification model with an enhanced capability to identify stable features in new environments, thereby effectively tackling the covariate shift in data. Extensive experiments with in-depth empirical analysis demonstrate the superiority of our approach. The implementation codes are publicly available at https://github.com/yongduosui/AIA.
The field of geometric deep learning has had a profound impact on the development of innovative and powerful graph neural network architectures. Disciplines such as computer vision and computational biology have benefited significantly from such methodological advances, which has led to breakthroughs in scientific domains such as protein structure prediction and design. In this work, we introduce GCPNet, a new geometry-complete, SE(3)-equivariant graph neural network designed for 3D molecular graph representation learning. Rigorous experiments across four distinct geometric tasks demonstrate that GCPNet's predictions (1) for protein-ligand binding affinity achieve a statistically significant correlation of 0.608, more than 5% greater than current state-of-the-art methods; (2) for protein structure ranking achieve statistically significant target-local and dataset-global correlations of 0.616 and 0.871, respectively; (3) for Newtownian many-body systems modeling achieve a task-averaged mean squared error less than 0.01, more than 15% better than current methods; and (4) for molecular chirality recognition achieve a state-of-the-art prediction accuracy of 98.7%, better than any other machine learning method to date. The source code, data, and instructions to train new models or reproduce our results are freely available at https://github.com/BioinfoMachineLearning/GCPNet.
Aside from graph neural networks (GNNs) attracting significant attention as a powerful framework revolutionizing graph representation learning, there has been an increasing demand for explaining GNN models. Although various explanation methods for GNNs have been developed, most studies have focused on instance-level explanations, which produce explanations tailored to a given graph instance. In our study, we propose Prototype-bAsed GNN-Explainer (PAGE), a novel model-level GNN explanation method that explains what the underlying GNN model has learned for graph classification by discovering human-interpretable prototype graphs. Our method produces explanations for a given class, thus being capable of offering more concise and comprehensive explanations than those of instance-level explanations. First, PAGE selects embeddings of class-discriminative input graphs on the graph-level embedding space after clustering them. Then, PAGE discovers a common subgraph pattern by iteratively searching for high matching node tuples using node-level embeddings via a prototype scoring function, thereby yielding a prototype graph as our explanation. Using six graph classification datasets, we demonstrate that PAGE qualitatively and quantitatively outperforms the state-of-the-art model-level explanation method. We also carry out systematic experimental studies by demonstrating the relationship between PAGE and instance-level explanation methods, the robustness of PAGE to input data scarce environments, and the computational efficiency of the proposed prototype scoring function in PAGE.
Heterogeneous graph neural network has unleashed great potential on graph representation learning and shown superior performance on downstream tasks such as node classification and clustering. Existing heterogeneous graph learning networks are primarily designed to either rely on pre-defined meta-paths or use attention mechanisms for type-specific attentive message propagation on different nodes/edges, incurring many customization efforts and computational costs. To this end, we design a relation-centered Pooling and Convolution for Heterogeneous Graph learning Network, namely PC-HGN, to enable relation-specific sampling and cross-relation convolutions, from which the structural heterogeneity of the graph can be better encoded into the embedding space through the adaptive training process. We evaluate the performance of the proposed model by comparing with state-of-the-art graph learning models on three different real-world datasets, and the results show that PC-HGN consistently outperforms all the baseline and improves the performance maximumly up by 17.8%.
Most existing deep learning-based acoustic scene classification (ASC) approaches directly utilize representations extracted from spectrograms to identify target scenes. However, these approaches pay little attention to the audio events occurring in the scene despite they provide crucial semantic information. This paper conducts the first study that investigates whether real-life acoustic scenes can be reliably recognized based only on the features that describe a limited number of audio events. To model the task-specific relationships between coarse-grained acoustic scenes and fine-grained audio events, we propose an event relational graph representation learning (ERGL) framework for ASC. Specifically, ERGL learns a graph representation of an acoustic scene from the input audio, where the embedding of each event is treated as a node, while the relationship cues derived from each pair of event embeddings are described by a learned multidimensional edge feature. Experiments on a polyphonic acoustic scene dataset show that the proposed ERGL achieves competitive performance on ASC by using only a limited number of embeddings of audio events without any data augmentations. The validity of the proposed ERGL framework proves the feasibility of recognizing diverse acoustic scenes based on the event relational graph. Our code is available on our homepage (https://github.com/Yuanbo2020/ERGL).
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which yields the variation across multiple copies of chromosomes. Variations among fast evolving viruses that lead to different strains (called quasispecies) are also deciphered with similar approaches. In both these cases, high-throughput sequencing technologies that provide oversampled mixtures of large noisy fragments (reads) of genomes, are used to infer constituent components (haplotypes or quasispecies). The problem is harder for polyploid species where there are more than two copies of chromosomes. State-of-the-art neural approaches to solve this NP-hard problem do not adequately model relations among the reads that are important for deconvolving the input signal. We address this problem by developing a new method, called NeurHap, that combines graph representation learning with combinatorial optimization. Our experiments demonstrate substantially better performance of NeurHap in real and synthetic datasets compared to competing approaches.
Unsupervised representation learning for dynamic graphs has attracted a lot of research attention in recent years. Compared with static graph, the dynamic graph is a comprehensive embodiment of both the intrinsic stable characteristics of nodes and the time-related dynamic preference. However, existing methods generally mix these two types of information into a single representation space, which may lead to poor explanation, less robustness, and a limited ability when applied to different downstream tasks. To solve the above problems, in this paper, we propose a novel disenTangled representation learning framework for discrete-time Dynamic graphs, namely DyTed. We specially design a temporal-clips contrastive learning task together with a structure contrastive learning to effectively identify the time-invariant and time-varying representations respectively. To further enhance the disentanglement of these two types of representation, we propose a disentanglement-aware discriminator under an adversarial learning framework from the perspective of information theory. Extensive experiments on Tencent and five commonly used public datasets demonstrate that DyTed, as a general framework that can be applied to existing methods, achieves state-of-the-art performance on various downstream tasks, as well as be more robust against noise.
Graph contrastive learning (GCL) has recently emerged as an effective learning paradigm to alleviate the reliance on labelling information for graph representation learning. The core of GCL is to maximise the mutual information between the representation of a node and its contextual representation (i.e., the corresponding instance with similar semantic information) summarised from the contextual scope (e.g., the whole graph or 1-hop neighbourhood). This scheme distils valuable self-supervision signals for GCL training. However, existing GCL methods still suffer from limitations, such as the incapacity or inconvenience in choosing a suitable contextual scope for different datasets and building biased contrastiveness. To address aforementioned problems, we present a simple self-supervised learning method termed Unifying Graph Contrastive Learning with Flexible Contextual Scopes (UGCL for short). Our algorithm builds flexible contextual representations with tunable contextual scopes by controlling the power of an adjacency matrix. Additionally, our method ensures contrastiveness is built within connected components to reduce the bias of contextual representations. Based on representations from both local and contextual scopes, UGCL optimises a very simple contrastive loss function for graph representation learning. Essentially, the architecture of UGCL can be considered as a general framework to unify existing GCL methods. We have conducted intensive experiments and achieved new state-of-the-art performance in six out of eight benchmark datasets compared with self-supervised graph representation learning baselines. Our code has been open-sourced.
In recent years, graph representation learning has gained significant popularity, which aims to generate node embeddings that capture features of graphs. One of the methods to achieve this is employing a technique called random walks that captures node sequences in a graph and then learns embeddings for each node using a natural language processing technique called Word2Vec. These embeddings are then used for deep learning on graph data for classification tasks, such as link prediction or node classification. Prior work operates on pre-collected temporal graph data and is not designed to handle updates on a graph in real-time. Real world graphs change dynamically and their entire temporal updates are not available upfront. In this paper, we propose an end-to-end graph learning pipeline that performs temporal graph construction, creates low-dimensional node embeddings, and trains multi-layer neural network models in an online setting. The training of the neural network models is identified as the main performance bottleneck as it performs repeated matrix operations on many sequentially connected low-dimensional kernels. We propose to unlock fine-grain parallelism in these low-dimensional kernels to boost performance of model training.