Graph neural networks have been used for a variety of learning tasks, such as link prediction, node classification, and node clustering. Among them, link prediction is a relatively under-studied graph learning task, with current state-of-the-art models based on one- or two-layer of shallow graph auto-encoder (GAE) architectures. In this paper, we focus on addressing a limitation of current methods for link prediction, which can only use shallow GAEs and variational GAEs, and creating effective methods to deepen (variational) GAE architectures to achieve stable and competitive performance. Our proposed methods innovatively incorporate standard auto-encoders (AEs) into the architectures of GAEs, where standard AEs are leveraged to learn essential, low-dimensional representations via seamlessly integrating the adjacency information and node features, while GAEs further build multi-scaled low-dimensional representations via residual connections to learn a compact overall embedding for link prediction. Empirically, extensive experiments on various benchmarking datasets verify the effectiveness of our methods and demonstrate the competitive performance of our deepened graph models for link prediction. Theoretically, we prove that our deep extensions inclusively express multiple polynomial filters with different orders.
The emergence of Graph Convolutional Network (GCN) has greatly boosted the progress of graph learning. However, two disturbing factors, noise and redundancy in graph data, and lack of interpretation for prediction results, impede further development of GCN. One solution is to recognize a predictive yet compressed subgraph to get rid of the noise and redundancy and obtain the interpretable part of the graph. This setting of subgraph is similar to the information bottleneck (IB) principle, which is less studied on graph-structured data and GCN. Inspired by the IB principle, we propose a novel subgraph information bottleneck (SIB) framework to recognize such subgraphs, named IB-subgraph. However, the intractability of mutual information and the discrete nature of graph data makes the objective of SIB notoriously hard to optimize. To this end, we introduce a bilevel optimization scheme coupled with a mutual information estimator for irregular graphs. Moreover, we propose a continuous relaxation for subgraph selection with a connectivity loss for stabilization. We further theoretically prove the error bound of our estimation scheme for mutual information and the noise-invariant nature of IB-subgraph. Extensive experiments on graph learning and large-scale point cloud tasks demonstrate the superior property of IB-subgraph.
Video anomaly detection has proved to be a challenging task owing to its unsupervised training procedure and high spatio-temporal complexity existing in real-world scenarios. In the absence of anomalous training samples, state-of-the-art methods try to extract features that fully grasp normal behaviors in both space and time domains using different approaches such as autoencoders, or generative adversarial networks. However, these approaches completely ignore or, by using the ability of deep networks in the hierarchical modeling, poorly model the spatio-temporal interactions that exist between objects. To address this issue, we propose a novel yet efficient method named Ano-Graph for learning and modeling the interaction of normal objects. Towards this end, a Spatio-Temporal Graph (STG) is made by considering each node as an object's feature extracted from a real-time off-the-shelf object detector, and edges are made based on their interactions. After that, a self-supervised learning method is employed on the STG in such a way that encapsulates interactions in a semantic space. Our method is data-efficient, significantly more robust against common real-world variations such as illumination, and passes SOTA by a large margin on the challenging datasets ADOC and Street Scene while stays competitive on Avenue, ShanghaiTech, and UCSD.
Though the multiscale graph learning techniques have enabled advanced feature extraction frameworks, the classic ensemble strategy may show inferior performance while encountering the high homogeneity of the learnt representation, which is caused by the nature of existing graph pooling methods. To cope with this issue, we propose a diversified multiscale graph learning model equipped with two core ingredients: a graph self-correction (GSC) mechanism to generate informative embedded graphs, and a diversity boosting regularizer (DBR) to achieve a comprehensive characterization of the input graph. The proposed GSC mechanism compensates the pooled graph with the lost information during the graph pooling process by feeding back the estimated residual graph, which serves as a plug-in component for popular graph pooling methods. Meanwhile, pooling methods enhanced with the GSC procedure encourage the discrepancy of node embeddings, and thus it contributes to the success of ensemble learning strategy. The proposed DBR instead enhances the ensemble diversity at the graph-level embeddings by leveraging the interaction among individual classifiers. Extensive experiments on popular graph classification benchmarks show that the proposed GSC mechanism leads to significant improvements over state-of-the-art graph pooling methods. Moreover, the ensemble multiscale graph learning models achieve superior enhancement by combining both GSC and DBR.
Enabling effective and efficient machine learning (ML) over large-scale graph data (e.g., graphs with billions of edges) can have a great impact on both industrial and scientific applications. However, existing efforts to advance large-scale graph ML have been largely limited by the lack of a suitable public benchmark. Here we present OGB Large-Scale Challenge (OGB-LSC), a collection of three real-world datasets for facilitating the advancements in large-scale graph ML. The OGB-LSC datasets are orders of magnitude larger than existing ones, covering three core graph learning tasks -- link prediction, graph regression, and node classification. Furthermore, we provide dedicated baseline experiments, scaling up expressive graph ML models to the massive datasets. We show that expressive models significantly outperform simple scalable baselines, indicating an opportunity for dedicated efforts to further improve graph ML at scale. Moreover, OGB-LSC datasets were deployed at ACM KDD Cup 2021 and attracted more than 500 team registrations globally, during which significant performance improvements were made by a variety of innovative techniques. We summarize the common techniques used by the winning solutions and highlight the current best practices in large-scale graph ML. Finally, we describe how we have updated the datasets after the KDD Cup to further facilitate research advances. The OGB-LSC datasets, baseline code, and all the information about the KDD Cup are available at https://ogb.stanford.edu/docs/lsc/ .
Node classification is an important research topic in graph learning. Graph neural networks (GNNs) have achieved state-of-the-art performance of node classification. However, existing GNNs address the problem where node samples for different classes are balanced; while for many real-world scenarios, some classes may have much fewer instances than others. Directly training a GNN classifier in this case would under-represent samples from those minority classes and result in sub-optimal performance. Therefore, it is very important to develop GNNs for imbalanced node classification. However, the work on this is rather limited. Hence, we seek to extend previous imbalanced learning techniques for i.i.d data to the imbalanced node classification task to facilitate GNN classifiers. In particular, we choose to adopt synthetic minority over-sampling algorithms, as they are found to be the most effective and stable. This task is non-trivial, as previous synthetic minority over-sampling algorithms fail to provide relation information for newly synthesized samples, which is vital for learning on graphs. Moreover, node attributes are high-dimensional. Directly over-sampling in the original input domain could generates out-of-domain samples, which may impair the accuracy of the classifier. We propose a novel framework, GraphSMOTE, in which an embedding space is constructed to encode the similarity among the nodes. New samples are synthesize in this space to assure genuineness. In addition, an edge generator is trained simultaneously to model the relation information, and provide it for those new samples. This framework is general and can be easily extended into different variations. The proposed framework is evaluated using three different datasets, and it outperforms all baselines with a large margin.
Features representation leverages the great power in network analysis tasks. However, most features are discrete which poses tremendous challenges to effective use. Recently, increasing attention has been paid on network feature learning, which could map discrete features to continued space. Unfortunately, current studies fail to fully preserve the structural information in the feature space due to random negative sampling strategy during training. To tackle this problem, we study the problem of feature learning and novelty propose a force-based graph learning model named GForce inspired by the spring-electrical model. GForce assumes that nodes are in attractive forces and repulsive forces, thus leading to the same representation with the original structural information in feature learning. Comprehensive experiments on benchmark datasets demonstrate the effectiveness of the proposed framework. Furthermore, GForce opens up opportunities to use physics models to model node interaction for graph learning.
Graph signal processing (GSP) is a key tool for satisfying the growing demand for information processing over networks. However, the success of GSP in downstream learning and inference tasks is heavily dependent on the prior identification of the relational structures. Graphs are natural descriptors of the relationships between entities of complex environments. The underlying graph is not readily detectable in many cases and one has to infer the topology from the observed signals. Firstly, we address the problem of graph signal classification by proposing a novel framework for discriminative graph learning. To learn discriminative graphs, we invoke the assumption that signals belonging to each class are smooth with respect to the corresponding graph while maintaining non-smoothness with respect to the graphs corresponding to other classes. Secondly, we extend our work to tackle increasingly dynamic environments and real-time topology inference. We develop a proximal gradient (PG) method which can be adapted to situations where the data are acquired on-the-fly. Beyond discrimination, this is the first work that addresses the problem of dynamic graph learning from smooth signals where the sought network alters slowly. The validation of the proposed frameworks is comprehensively investigated using both synthetic and real data.
The growing success of graph signal processing (GSP) approaches relies heavily on prior identification of a graph over which network data admit certain regularity. However, adaptation to increasingly dynamic environments as well as demands for real-time processing of streaming data pose major challenges to this end. In this context, we develop novel algorithms for online network topology inference given streaming observations assumed to be smooth on the sought graph. Unlike existing batch algorithms, our goal is to track the (possibly) time-varying network topology while maintaining the memory and computational costs in check by processing graph signals sequentially-in-time. To recover the graph in an online fashion, we leverage proximal gradient (PG) methods to solve a judicious smoothness-regularized, time-varying optimization problem. Under mild technical conditions, we establish that the online graph learning algorithm converges to within a neighborhood of (i.e., it tracks) the optimal time-varying batch solution. Computer simulations using both synthetic and real financial market data illustrate the effectiveness of the proposed algorithm in adapting to streaming signals to track slowly-varying network connectivity.
The near-infinite chemical diversity of natural and artificial macromolecules arises from the vast range of possible component monomers, linkages, and polymers topologies. This enormous variety contributes to the ubiquity and indispensability of macromolecules but hinders the development of general machine learning methods with macromolecules as input. To address this, we developed GLAMOUR, a framework for chemistry-informed graph representation of macromolecules that enables quantifying structural similarity, and interpretable supervised learning for macromolecules.
Machine learning on graphs has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To solve this critical challenge, automated machine learning (AutoML) on graphs which combines the strength of graph machine learning and AutoML together, is gaining attention from the research community. Therefore, we comprehensively survey AutoML on graphs in this paper, primarily focusing on hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We further overview libraries related to automated graph machine learning and in-depth discuss AutoGL, the first dedicated open-source library for AutoML on graphs. In the end, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive review of automated machine learning on graphs to the best of our knowledge.
Graph neural networks (GNNs) have attracted tremendous attention from the graph learning community in recent years. It has been widely adopted in various real-world applications from diverse domains, such as social networks and biological graphs. The research and applications of graph deep learning present new challenges, including the sparse nature of graph data, complicated training of GNNs, and non-standard evaluation of graph tasks. To tackle the issues, we present CogDL, a comprehensive library for graph deep learning that allows researchers and practitioners to conduct experiments, compare methods, and build applications with ease and efficiency. In CogDL, we propose a unified design for the training and evaluation of GNN models for various graph tasks, making it unique among existing graph learning libraries. By utilizing this unified trainer, CogDL can optimize the GNN training loop with several training techniques, such as mixed precision training. Moreover, we develop efficient sparse operators for CogDL, enabling it to become the most competitive graph library for efficiency. Another important CogDL feature is its focus on ease of use with the aim of facilitating open and reproducible research of graph learning. We leverage CogDL to report and maintain benchmark results on fundamental graph tasks, which can be reproduced and directly used by the community.
In facial action unit (AU) recognition tasks, regional feature learning and AU relation modeling are two effective aspects which are worth exploring. However, the limited representation capacity of regional features makes it difficult for relation models to embed AU relationship knowledge. In this paper, we propose a novel multi-level adaptive ROI and graph learning (MARGL) framework to tackle this problem. Specifically, an adaptive ROI learning module is designed to automatically adjust the location and size of the predefined AU regions. Meanwhile, besides relationship between AUs, there exists strong relevance between regional features across multiple levels of the backbone network as level-wise features focus on different aspects of representation. In order to incorporate the intra-level AU relation and inter-level AU regional relevance simultaneously, a multi-level AU relation graph is constructed and graph convolution is performed to further enhance AU regional features of each level. Experiments on BP4D and DISFA demonstrate the proposed MARGL significantly outperforms the previous state-of-the-art methods.
We present a new approach, that we call AdaGTCN, for identifying human reader intent from Electroencephalogram~(EEG) and Eye movement~(EM) data in order to help differentiate between normal reading and task-oriented reading. Understanding the physiological aspects of the reading process~(the cognitive load and the reading intent) can help improve the quality of crowd-sourced annotated data. Our method, Adaptive Graph Temporal Convolution Network (AdaGTCN), uses an Adaptive Graph Learning Layer and Deep Neighborhood Graph Convolution Layer for identifying the reading activities using time-locked EEG sequences recorded during word-level eye-movement fixations. Adaptive Graph Learning Layer dynamically learns the spatial correlations between the EEG electrode signals while the Deep Neighborhood Graph Convolution Layer exploits temporal features from a dense graph neighborhood to establish the state of the art in reading task identification over other contemporary approaches. We compare our approach with several baselines to report an improvement of 6.29% on the ZuCo 2.0 dataset, along with extensive ablation experiments
Graph neural networks have been widely used on modeling graph data, achieving impressive results on node classification and link prediction tasks. Yet, obtaining an accurate representation for a graph further requires a pooling function that maps a set of node representations into a compact form. A simple sum or average over all node representations considers all node features equally without consideration of their task relevance, and any structural dependencies among them. Recently proposed hierarchical graph pooling methods, on the other hand, may yield the same representation for two different graphs that are distinguished by the Weisfeiler-Lehman test, as they suboptimally preserve information from the node features. To tackle these limitations of existing graph pooling methods, we first formulate the graph pooling problem as a multiset encoding problem with auxiliary information about the graph structure, and propose a Graph Multiset Transformer (GMT) which is a multi-head attention based global pooling layer that captures the interaction between nodes according to their structural dependencies. We show that GMT satisfies both injectiveness and permutation invariance, such that it is at most as powerful as the Weisfeiler-Lehman graph isomorphism test. Moreover, our methods can be easily extended to the previous node clustering approaches for hierarchical graph pooling. Our experimental results show that GMT significantly outperforms state-of-the-art graph pooling methods on graph classification benchmarks with high memory and time efficiency, and obtains even larger performance gain on graph reconstruction and generation tasks.
Graph convolutional networks have been successfully applied in various graph-based tasks. In a typical graph convolutional layer, node features are updated by aggregating neighborhood information. Repeatedly applying graph convolutions can cause the oversmoothing issue, i.e., node features at deep layers converge to similar values. Previous studies have suggested that oversmoothing is one of the major issues that restrict the performance of graph convolutional networks. In this paper, we propose a stochastic regularization method to tackle the oversmoothing problem. In the proposed method, we stochastically scale features and gradients (SSFG) by a factor sampled from a probability distribution in the training procedure. By explicitly applying a scaling factor to break feature convergence, the oversmoothing issue is alleviated. We show that applying stochastic scaling at the gradient level is complementary to that applied at the feature level to improve the overall performance. Our method does not increase the number of trainable parameters. When used together with ReLU, our SSFG can be seen as a stochastic ReLU activation function. We experimentally validate our SSFG regularization method on three commonly used types of graph networks. Extensive experimental results on seven benchmark datasets for four graph-based tasks demonstrate that our SSFG regularization is effective in improving the overall performance of the baseline graph networks.
Link prediction is an important learning task for graph-structured data. In this paper, we propose a novel topological approach to characterize interactions between two nodes. Our topological feature, based on the extended persistent homology, encodes rich structural information regarding the multi-hop paths connecting nodes. Based on this feature, we propose a graph neural network method that outperforms state-of-the-arts on different benchmarks. As another contribution, we propose a novel algorithm to more efficiently compute the extended persistence diagrams for graphs. This algorithm can be generally applied to accelerate many other topological methods for graph learning tasks.
Graph Neural Networks have shown excellent performance on semi-supervised classification tasks. However, they assume access to a graph that may not be often available in practice. In the absence of any graph, constructing k-Nearest Neighbor (kNN) graphs from the given data have shown to give improvements when used with GNNs over other semi-supervised methods. This paper proposes a semi-supervised graph learning method for cases when there are no graphs available. This method learns a graph as a convex combination of the unsupervised kNN graph and a supervised label-affinity graph. The label-affinity graph directly captures all the nodes' label-affinity with the labeled nodes, i.e., how likely a node has the same label as the labeled nodes. This affinity measure contrasts with the kNN graph where the metric measures closeness in the feature space. Our experiments suggest that this approach gives close to or better performance (up to 1.5%), while being simpler and faster (up to 70x) to train, than state-of-the-art graph learning methods. We also conduct several experiments to highlight the importance of individual components and contrast them with state-of-the-art methods.
We consider two popular Graph Representation Learning (GRL) methods: message passing for node classification and network embedding for link prediction. For each, we pick a popular model that we: (i) linearize and (ii) and switch its training objective to Frobenius norm error minimization. These simplifications can cast the training into finding the optimal parameters in closed-form. We program in TensorFlow a functional form of Truncated Singular Value Decomposition (SVD), such that, we could decompose a dense matrix $\mathbf{M}$, without explicitly computing $\mathbf{M}$. We achieve competitive performance on popular GRL tasks while providing orders of magnitude speedup. We open-source our code at http://github.com/samihaija/tf-fsvd
We propose CRaWl, a novel neural network architecture for graph learning. Like graph neural networks, CRaWl layers update node features on a graph and thus can freely be combined or interleaved with GNN layers. Yet CRaWl operates fundamentally different from message passing graph neural networks. CRaWl layers extract and aggregate information on subgraphs appearing along random walks through a graph using 1D Convolutions. Thereby it detects long range interactions and computes non-local features. As the theoretical basis for our approach, we prove a theorem stating that the expressiveness of CRaWl is incomparable with that of the Weisfeiler Leman algorithm and hence with graph neural networks. That is, there are functions expressible by CRaWl, but not by GNNs and vice versa. This result extends to higher levels of the Weisfeiler Leman hierarchy and thus to higher-order GNNs. Empirically, we show that CRaWl matches state-of-the-art GNN architectures across a multitude of benchmark datasets for classification and regression on graphs.