Neural forecasting of spatiotemporal time series drives both research and industrial innovation in several relevant application domains. Graph neural networks (GNNs) are often the core component of the forecasting architecture. However, in most spatiotemporal GNNs, the computational complexity scales up to a quadratic factor with the length of the sequence times the number of links in the graph, hence hindering the application of these models to large graphs and long temporal sequences. While methods to improve scalability have been proposed in the context of static graphs, few research efforts have been devoted to the spatiotemporal case. To fill this gap, we propose a scalable architecture that exploits an efficient encoding of both temporal and spatial dynamics. In particular, we use a randomized recurrent neural network to embed the history of the input time series into high-dimensional state representations encompassing multi-scale temporal dynamics. Such representations are then propagated along the spatial dimension using different powers of the graph adjacency matrix to generate node embeddings characterized by a rich pool of spatiotemporal features. The resulting node embeddings can be efficiently pre-computed in an unsupervised manner, before being fed to a feed-forward decoder that learns to map the multi-scale spatiotemporal representations to predictions. The training procedure can then be parallelized node-wise by sampling the node embeddings without breaking any dependency, thus enabling scalability to large networks. Empirical results on relevant datasets show that our approach achieves results competitive with the state of the art, while dramatically reducing the computational burden.
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The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.
Graph Neural Networks (GNNs) have recently become increasingly popular due to their ability to learn complex systems of relations or interactions arising in a broad spectrum of problems ranging from biology and particle physics to social networks and recommendation systems. Despite the plethora of different models for deep learning on graphs, few approaches have been proposed thus far for dealing with graphs that present some sort of dynamic nature (e.g. evolving features or connectivity over time). In this paper, we present Temporal Graph Networks (TGNs), a generic, efficient framework for deep learning on dynamic graphs represented as sequences of timed events. Thanks to a novel combination of memory modules and graph-based operators, TGNs are able to significantly outperform previous approaches being at the same time more computationally efficient. We furthermore show that several previous models for learning on dynamic graphs can be cast as specific instances of our framework. We perform a detailed ablation study of different components of our framework and devise the best configuration that achieves state-of-the-art performance on several transductive and inductive prediction tasks for dynamic graphs.
Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect subgraphs, rendering subgraph prediction tasks challenging to tackle in many impactful applications. Further, subgraph prediction tasks present several unique challenges, because subgraphs can have non-trivial internal topology, but also carry a notion of position and external connectivity information relative to the underlying graph in which they exist. Here, we introduce SUB-GNN, a subgraph neural network to learn disentangled subgraph representations. In particular, we propose a novel subgraph routing mechanism that propagates neural messages between the subgraph's components and randomly sampled anchor patches from the underlying graph, yielding highly accurate subgraph representations. SUB-GNN specifies three channels, each designed to capture a distinct aspect of subgraph structure, and we provide empirical evidence that the channels encode their intended properties. We design a series of new synthetic and real-world subgraph datasets. Empirical results for subgraph classification on eight datasets show that SUB-GNN achieves considerable performance gains, outperforming strong baseline methods, including node-level and graph-level GNNs, by 12.4% over the strongest baseline. SUB-GNN performs exceptionally well on challenging biomedical datasets when subgraphs have complex topology and even comprise multiple disconnected components.
Spectral clustering (SC) is a popular clustering technique to find strongly connected communities on a graph. SC can be used in Graph Neural Networks (GNNs) to implement pooling operations that aggregate nodes belonging to the same cluster. However, the eigendecomposition of the Laplacian is expensive and, since clustering results are graph-specific, pooling methods based on SC must perform a new optimization for each new sample. In this paper, we propose a graph clustering approach that addresses these limitations of SC. We formulate a continuous relaxation of the normalized minCUT problem and train a GNN to compute cluster assignments that minimize this objective. Our GNN-based implementation is differentiable, does not require to compute the spectral decomposition, and learns a clustering function that can be quickly evaluated on out-of-sample graphs. From the proposed clustering method, we design a graph pooling operator that overcomes some important limitations of state-of-the-art graph pooling techniques and achieves the best performance in several supervised and unsupervised tasks.
Graph neural networks (GNNs) have been widely used in representation learning on graphs and achieved state-of-the-art performance in tasks such as node classification and link prediction. However, most existing GNNs are designed to learn node representations on the fixed and homogeneous graphs. The limitations especially become problematic when learning representations on a misspecified graph or a heterogeneous graph that consists of various types of nodes and edges. In this paper, we propose Graph Transformer Networks (GTNs) that are capable of generating new graph structures, which involve identifying useful connections between unconnected nodes on the original graph, while learning effective node representation on the new graphs in an end-to-end fashion. Graph Transformer layer, a core layer of GTNs, learns a soft selection of edge types and composite relations for generating useful multi-hop connections so-called meta-paths. Our experiments show that GTNs learn new graph structures, based on data and tasks without domain knowledge, and yield powerful node representation via convolution on the new graphs. Without domain-specific graph preprocessing, GTNs achieved the best performance in all three benchmark node classification tasks against the state-of-the-art methods that require pre-defined meta-paths from domain knowledge.
Learning node embeddings that capture a node's position within the broader graph structure is crucial for many prediction tasks on graphs. However, existing Graph Neural Network (GNN) architectures have limited power in capturing the position/location of a given node with respect to all other nodes of the graph. Here we propose Position-aware Graph Neural Networks (P-GNNs), a new class of GNNs for computing position-aware node embeddings. P-GNN first samples sets of anchor nodes, computes the distance of a given target node to each anchor-set,and then learns a non-linear distance-weighted aggregation scheme over the anchor-sets. This way P-GNNs can capture positions/locations of nodes with respect to the anchor nodes. P-GNNs have several advantages: they are inductive, scalable,and can incorporate node feature information. We apply P-GNNs to multiple prediction tasks including link prediction and community detection. We show that P-GNNs consistently outperform state of the art GNNs, with up to 66% improvement in terms of the ROC AUC score.
Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into different categories. With a focus on graph convolutional networks, we review alternative architectures that have recently been developed; these learning paradigms include graph attention networks, graph autoencoders, graph generative networks, and graph spatial-temporal networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes and benchmarks of the existing algorithms on different learning tasks. Finally, we propose potential research directions in this fast-growing field.
Graphs, which describe pairwise relations between objects, are essential representations of many real-world data such as social networks. In recent years, graph neural networks, which extend the neural network models to graph data, have attracted increasing attention. Graph neural networks have been applied to advance many different graph related tasks such as reasoning dynamics of the physical system, graph classification, and node classification. Most of the existing graph neural network models have been designed for static graphs, while many real-world graphs are inherently dynamic. For example, social networks are naturally evolving as new users joining and new relations being created. Current graph neural network models cannot utilize the dynamic information in dynamic graphs. However, the dynamic information has been proven to enhance the performance of many graph analytical tasks such as community detection and link prediction. Hence, it is necessary to design dedicated graph neural networks for dynamic graphs. In this paper, we propose DGNN, a new {\bf D}ynamic {\bf G}raph {\bf N}eural {\bf N}etwork model, which can model the dynamic information as the graph evolving. In particular, the proposed framework can keep updating node information by capturing the sequential information of edges, the time intervals between edges and information propagation coherently. Experimental results on various dynamic graphs demonstrate the effectiveness of the proposed framework.
Graph Neural Networks (GNNs) for representation learning of graphs broadly follow a neighborhood aggregation framework, where the representation vector of a node is computed by recursively aggregating and transforming feature vectors of its neighboring nodes. Many GNN variants have been proposed and have achieved state-of-the-art results on both node and graph classification tasks. However, despite GNNs revolutionizing graph representation learning, there is limited understanding of their representational properties and limitations. Here, we present a theoretical framework for analyzing the expressive power of GNNs in capturing different graph structures. Our results characterize the discriminative power of popular GNN variants, such as Graph Convolutional Networks and GraphSAGE, and show that they cannot learn to distinguish certain simple graph structures. We then develop a simple architecture that is provably the most expressive among the class of GNNs and is as powerful as the Weisfeiler-Lehman graph isomorphism test. We empirically validate our theoretical findings on a number of graph classification benchmarks, and demonstrate that our model achieves state-of-the-art performance.
Traditional methods for link prediction can be categorized into three main types: graph structure feature-based, latent feature-based, and explicit feature-based. Graph structure feature methods leverage some handcrafted node proximity scores, e.g., common neighbors, to estimate the likelihood of links. Latent feature methods rely on factorizing networks' matrix representations to learn an embedding for each node. Explicit feature methods train a machine learning model on two nodes' explicit attributes. Each of the three types of methods has its unique merits. In this paper, we propose SEAL (learning from Subgraphs, Embeddings, and Attributes for Link prediction), a new framework for link prediction which combines the power of all the three types into a single graph neural network (GNN). GNN is a new type of neural network which directly accepts graphs as input and outputs their labels. In SEAL, the input to the GNN is a local subgraph around each target link. We prove theoretically that our local subgraphs also reserve a great deal of high-order graph structure features related to link existence. Another key feature is that our GNN can naturally incorporate latent features and explicit features. It is achieved by concatenating node embeddings (latent features) and node attributes (explicit features) in the node information matrix for each subgraph, thus combining the three types of features to enhance GNN learning. Through extensive experiments, SEAL shows unprecedentedly strong performance against a wide range of baseline methods, including various link prediction heuristics and network embedding methods.
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