Motivation: Molecular interaction networks summarize complex biological processes as graphs, whose structure is informative of biological function at multiple scales. Simultaneously, omics technologies measure the variation or activity of genes, proteins, or metabolites across individuals or experimental conditions. Integrating the complementary viewpoints of biological networks and omics data is an important task in bioinformatics, but existing methods treat networks as discrete structures, which are intrinsically difficult to integrate with continuous node features or activity measures. Graph neural networks map graph nodes into a low-dimensional vector space representation, and can be trained to preserve both the local graph structure and the similarity between node features. Results: We studied the representation of transcriptional, protein-protein and genetic interaction networks in E. Coli and mouse using graph neural networks. We found that such representations explain a large proportion of variation in gene expression data, and that using gene expression data as node features improves the reconstruction of the graph from the embedding. We further proposed a new end-to-end graph feature auto-encoder which is trained on the feature reconstruction task, and showed that it performs better at predicting unobserved node features than auto-encoders that are trained on the graph reconstruction task before learning to predict node features. When applied to the problem of imputing missing data in single-cell RNAseq data, our graph feature auto-encoder outperformed a state-of-the-art imputation method that does not use protein interaction information, showing the benefit of integrating biological networks and omics data using graph representation learning.
Websites use third-party ads and tracking services to deliver targeted ads and collect information about users that visit them. These services put users' privacy at risk, and that is why users' demand for blocking these services is growing. Most of the blocking solutions rely on crowd-sourced filter lists manually maintained by a large community of users. In this work, we seek to simplify the update of these filter lists by combining different websites through a large-scale graph connecting all resource requests made over a large set of sites. The features of this graph are extracted and used to train a machine learning algorithm with the aim of detecting ads and tracking resources. As our approach combines different information sources, it is more robust toward evasion techniques that use obfuscation or changing the usage patterns. We evaluate our work over the Alexa top-10K websites and find its accuracy to be 96.1% biased and 90.9% unbiased with high precision and recall. It can also block new ads and tracking services, which would necessitate being blocked by further crowd-sourced existing filter lists. Moreover, the approach followed in this paper sheds light on the ecosystem of third-party tracking and advertising.
Graph representation learning has recently been applied to a broad spectrum of problems ranging from computer graphics and chemistry to high energy physics and social media. The popularity of graph neural networks has sparked interest, both in academia and in industry, in developing methods that scale to very large graphs such as Facebook or Twitter social networks. In most of these approaches, the computational cost is alleviated by a sampling strategy retaining a subset of node neighbors or subgraphs at training time. In this paper we propose a new, efficient and scalable graph deep learning architecture which sidesteps the need for graph sampling by using graph convolutional filters of different size that are amenable to efficient precomputation, allowing extremely fast training and inference. Our architecture allows using different local graph operators (e.g. motif-induced adjacency matrices or Personalized Page Rank diffusion matrix) to best suit the task at hand. We conduct extensive experimental evaluation on various open benchmarks and show that our approach is competitive with other state-of-the-art architectures, while requiring a fraction of the training and inference time. Moreover, we obtain state-of-the-art results on ogbn-papers100M, the largest public graph dataset, with over 110 million nodes and 1.5 billion edges.
How to utilize deep learning methods for graph classification tasks has attracted considerable research attention in the past few years. Regarding graph classification tasks, the graphs to be classified may have various graph sizes (i.e., different number of nodes and edges) and have various graph properties (e.g., average node degree, diameter, and clustering coefficient). The diverse property of graphs has imposed significant challenges on existing graph learning techniques since diverse graphs have different best-fit hyperparameters. It is difficult to learn graph features from a set of diverse graphs by a unified graph neural network. This motivates us to use a multiplex structure in a diverse way and utilize a priori properties of graphs to guide the learning. In this paper, we propose MxPool, which concurrently uses multiple graph convolution/pooling networks to build a hierarchical learning structure for graph representation learning tasks. Our experiments on numerous graph classification benchmarks show that our MxPool has superiority over other state-of-the-art graph representation learning methods.
Graph representation learning (GRL) is a powerful technique for learning low-dimensional vector representation of high-dimensional and often sparse graphs. Most studies explore the structure and metadata associated with the graph using random walks and employ an unsupervised or semi-supervised learning schemes. Learning in these methods is context-free, resulting in only a single representation per node. Recently studies have argued on the adequacy of a single representation and proposed context-sensitive approaches, which are capable of extracting multiple node representations for different contexts. This proved to be highly effective in applications such as link prediction and ranking. However, most of these methods rely on additional textual features that require complex and expensive RNNs or CNNs to capture high-level features or rely on a community detection algorithm to identify multiple contexts of a node. In this study we show that in-order to extract high-quality context-sensitive node representations it is not needed to rely on supplementary node features, nor to employ computationally heavy and complex models. We propose GOAT, a context-sensitive algorithm inspired by gossip communication and a mutual attention mechanism simply over the structure of the graph. We show the efficacy of GOAT using 6 real-world datasets on link prediction and node clustering tasks and compare it against 12 popular and state-of-the-art (SOTA) baselines. GOAT consistently outperforms them and achieves up to 12% and 19% gain over the best performing methods on link prediction and clustering tasks, respectively.
Graph representation learning is a fundamental task in various applications that strives to learn low-dimensional embeddings for nodes that can preserve graph topology information. However, many existing methods focus on static graphs while ignoring evolving graph patterns. Inspired by the success of graph convolutional networks(GCNs) in static graph embedding, we propose a novel k-core based temporal graph convolutional network, the CTGCN, to learn node representations for dynamic graphs. In contrast to previous dynamic graph embedding methods, CTGCN can preserve both local connective proximity and global structural similarity while simultaneously capturing graph dynamics. In the proposed framework, the traditional graph convolution is generalized into two phases, feature transformation and feature aggregation, which gives the CTGCN more flexibility and enables the CTGCN to learn connective and structural information under the same framework. Experimental results on 7 real-world graphs demonstrate that the CTGCN outperforms existing state-of-the-art graph embedding methods in several tasks, including link prediction and structural role classification. The source code of this work can be obtained from \url{https://github.com/jhljx/CTGCN}.
While the self-attention mechanism has been widely used in a wide variety of tasks, it has the unfortunate property of a quadratic cost with respect to the input length, which makes it difficult to deal with long inputs. In this paper, we present a method for accelerating and structuring self-attentions: Sparse Adaptive Connection (SAC). In SAC, we regard the input sequence as a graph and attention operations are performed between linked nodes. In contrast with previous self-attention models with pre-defined structures (edges), the model learns to construct attention edges to improve task-specific performances. In this way, the model is able to select the most salient nodes and reduce the quadratic complexity regardless of the sequence length. Based on SAC, we show that previous variants of self-attention models are its special cases. Through extensive experiments on neural machine translation, language modeling, graph representation learning and image classification, we demonstrate SAC is competitive with state-of-the-art models while significantly reducing memory cost.
Graph representation learning based on graph neural networks (GNNs) can greatly improve the performance of downstream tasks, such as node and graph classification. However, the general GNN models do not aggregate node information in a hierarchical manner, and can miss key higher-order structural features of many graphs. The hierarchical aggregation also enables the graph representations to be explainable. In addition, supervised graph representation learning requires labeled data, which is expensive and error-prone. To address these issues, we present an unsupervised graph representation learning method, Unsupervised Hierarchical Graph Representation (UHGR), which can generate hierarchical representations of graphs. Our method focuses on maximizing mutual information between "local" and high-level "global" representations, which enables us to learn the node embeddings and graph embeddings without any labeled data. To demonstrate the effectiveness of the proposed method, we perform the node and graph classification using the learned node and graph embeddings. The results show that the proposed method achieves comparable results to state-of-the-art supervised methods on several benchmarks. In addition, our visualization of hierarchical representations indicates that our method can capture meaningful and interpretable clusters.
Graph convolution network (GCN) attracts intensive research interest with broad applications. While existing work mainly focused on designing novel GCN architectures for better performance, few of them studied a practical yet challenging problem: How to learn GCNs from data with extremely limited annotation? In this paper, we propose a new learning method by sampling strategy and model compression to overcome this challenge. Our approach has multifold advantages: 1) the adaptive sampling strategy largely suppresses the GCN training deviation over uniform sampling; 2) compressed GCN-based methods with a smaller scale of parameters need fewer labeled data to train; 3) the smaller scale of training data is beneficial to reduce the human resource cost to label them. We choose six popular GCN baselines and conduct extensive experiments on three real-world datasets. The results show that by applying our method, all GCN baselines cut down the annotation requirement by as much as 90$\%$ and compress the scale of parameters more than 6$\times$ without sacrificing their strong performance. It verifies that the training method could extend the existing semi-supervised GCN-based methods to the scenarios with the extremely small scale of labeled data.
Deep Convolutional Neural Networks (DCNNs) is currently the method of choice both for generative, as well as for discriminative learning in computer vision and machine learning. The success of DCNNs can be attributed to the careful selection of their building blocks (e.g., residual blocks, rectifiers, sophisticated normalization schemes, to mention but a few). In this paper, we propose $\Pi$-Nets, a new class of DCNNs. $\Pi$-Nets are polynomial neural networks, i.e., the output is a high-order polynomial of the input. $\Pi$-Nets can be implemented using special kind of skip connections and their parameters can be represented via high-order tensors. We empirically demonstrate that $\Pi$-Nets have better representation power than standard DCNNs and they even produce good results without the use of non-linear activation functions in a large battery of tasks and signals, i.e., images, graphs, and audio. When used in conjunction with activation functions, $\Pi$-Nets produce state-of-the-art results in challenging tasks, such as image generation. Lastly, our framework elucidates why recent generative models, such as StyleGAN, improve upon their predecessors, e.g., ProGAN.
Graph representation learning has attracted much attention in supporting high quality candidate search at scale. Despite its effectiveness in learning embedding vectors for objects in the user-item interaction network, the computational costs to infer users' preferences in continuous embedding space are tremendous. In this work, we investigate the problem of hashing with graph neural networks (GNNs) for high quality retrieval, and propose a simple yet effective discrete representation learning framework to jointly learn continuous and discrete codes. Specifically, a deep hashing with GNNs (HashGNN) is presented, which consists of two components, a GNN encoder for learning node representations, and a hash layer for encoding representations to hash codes. The whole architecture is trained end-to-end by jointly optimizing two losses, i.e., reconstruction loss from reconstructing observed links, and ranking loss from preserving the relative ordering of hash codes. A novel discrete optimization strategy based on straight through estimator (STE) with guidance is proposed. The principal idea is to avoid gradient magnification in back-propagation of STE with continuous embedding guidance, in which we begin from learning an easier network that mimic the continuous embedding and let it evolve during the training until it finally goes back to STE. Comprehensive experiments over three publicly available and one real-world Alibaba company datasets demonstrate that our model not only can achieve comparable performance compared with its continuous counterpart but also runs multiple times faster during inference.
Mobile payment such as Alipay has been widely used in our daily lives. To further promote the mobile payment activities, it is important to run marketing campaigns under a limited budget by providing incentives such as coupons, commissions to merchants. As a result, incentive optimization is the key to maximizing the commercial objective of the marketing campaign. With the analyses of online experiments, we found that the transaction network can subtly describe the similarity of merchants' responses to different incentives, which is of great use in the incentive optimization problem. In this paper, we present a graph representation learning method atop of transaction networks for merchant incentive optimization in mobile payment marketing. With limited samples collected from online experiments, our end-to-end method first learns merchant representations based on an attributed transaction networks, then effectively models the correlations between the commercial objectives each merchant may achieve and the incentives under varying treatments. Thus we are able to model the sensitivity to incentive for each merchant, and spend the most budgets on those merchants that show strong sensitivities in the marketing campaign. Extensive offline and online experimental results at Alipay demonstrate the effectiveness of our proposed approach.
To take full advantage of fast-growing unlabeled networked data, this paper introduces a novel self-supervised strategy for graph representation learning by exploiting natural supervision provided by the data itself. Inspired by human social behavior, we assume that the global context of each node is composed of all nodes in the graph since two arbitrary entities in a connected network could interact with each other via paths of varying length. Based on this, we investigate whether the global context can be a source of free and effective supervisory signals for learning useful node representations. Specifically, we randomly select pairs of nodes in a graph and train a well-designed neural net to predict the contextual position of one node relative to the other. Our underlying hypothesis is that the representations learned from such within-graph context would capture the global topology of the graph and finely characterize the similarity and differentiation between nodes, which is conducive to various downstream learning tasks. Extensive benchmark experiments including node classification, clustering, and link prediction demonstrate that our approach outperforms many state-of-the-art unsupervised methods and sometimes even exceeds the performance of supervised counterparts.
Graph representation learning is a ubiquitous task in machine learning where the goal is to embed each vertex into a low-dimensional vector space. We consider the bipartite graph and formalize its representation learning problem as a statistical estimation problem of parameters in a semiparametric exponential family distribution. The bipartite graph is assumed to be generated by a semiparametric exponential family distribution, whose parametric component is given by the proximity of outputs of two one-layer neural networks, while nonparametric (nuisance) component is the base measure. Neural networks take high-dimensional features as inputs and output embedding vectors. In this setting, the representation learning problem is equivalent to recovering the weight matrices. The main challenges of estimation arise from the nonlinearity of activation functions and the nonparametric nuisance component of the distribution. To overcome these challenges, we propose a pseudo-likelihood objective based on the rank-order decomposition technique and focus on its local geometry. We show that the proposed objective is strongly convex in a neighborhood around the ground truth, so that a gradient descent-based method achieves linear convergence rate. Moreover, we prove that the sample complexity of the problem is linear in dimensions (up to logarithmic factors), which is consistent with parametric Gaussian models. However, our estimator is robust to any model misspecification within the exponential family, which is validated in extensive experiments.
Graph representation learning embeds nodes in large graphs as low-dimensional vectors and is of great benefit to many downstream applications. Most embedding frameworks, however, are inherently transductive and unable to generalize to unseen nodes or learn representations across different graphs. Although inductive approaches can generalize to unseen nodes, they neglect different contexts of nodes and cannot learn node embeddings dually. In this paper, we present a context-aware unsupervised dual encoding framework, \textbf{CADE}, to generate representations of nodes by combining real-time neighborhoods with neighbor-attentioned representation, and preserving extra memory of known nodes. We exhibit that our approach is effective by comparing to state-of-the-art methods.
Graph convolutional networks (GCNs) are a widely used method for graph representation learning. We investigate the power of GCNs, as a function of their number of layers, to distinguish between different random graph models on the basis of the embeddings of their sample graphs. In particular, the graph models that we consider arise from graphons, which are the most general possible parameterizations of infinite exchangeable graph models and which are the central objects of study in the theory of dense graph limits. We exhibit an infinite class of graphons that are well-separated in terms of cut distance and are indistinguishable by a GCN with nonlinear activation functions coming from a certain broad class if its depth is at least logarithmic in the size of the sample graph. These results theoretically match empirical observations of several prior works. Finally, we show a converse result that for pairs of graphons satisfying a degree profile separation property, a very simple GCN architecture suffices for distinguishability. To prove our results, we exploit a connection to random walks on graphs.
The viral spread of fake news has caused great social harm, making fake news detection an urgent task. Current fake news detection methods rely heavily on text information by learning the extracted news content or writing style of internal knowledge. However, deliberate rumors can mask writing style, bypassing language models and invalidating simple text-based models. In fact, news articles and other related components (such as news creators and news topics) can be modeled as a heterogeneous information network (HIN for short). In this paper, we propose a novel fake news detection framework, namely Hierarchical Graph Attention Network(HGAT), which uses a novel hierarchical attention mechanism to perform node representation learning in HIN, and then detects fake news by classifying news article nodes. Experiments on two real-world fake news datasets show that HGAT can outperform text-based models and other network-based models. In addition, the experiment proved the expandability and generalizability of our for graph representation learning and other node classification related applications in heterogeneous graphs.
Recent advancements in graph representation learning have led to the emergence of condensed encodings that capture the main properties of a graph. However, even though these abstract representations are powerful for downstream tasks, they are not equally suitable for visualisation purposes. In this work, we merge Mapper, an algorithm from the field of Topological Data Analysis (TDA), with the expressive power of Graph Neural Networks (GNNs) to produce hierarchical, topologically-grounded visualisations of graphs. These visualisations do not only help discern the structure of complex graphs but also provide a means of understanding the models applied to them for solving various tasks. We further demonstrate the suitability of Mapper as a topological framework for graph pooling by mathematically proving an equivalence with Min-Cut and Diff Pool. Building upon this framework, we introduce a novel pooling algorithm based on PageRank, which obtains competitive results with state of the art methods on graph classification benchmarks.
The richness in the content of various information networks such as social networks and communication networks provides the unprecedented potential for learning high-quality expressive representations without external supervision. This paper investigates how to preserve and extract the abundant information from graph-structured data into embedding space in an unsupervised manner. To this end, we propose a novel concept, Graphical Mutual Information (GMI), to measure the correlation between input graphs and high-level hidden representations. GMI generalizes the idea of conventional mutual information computations from vector space to the graph domain where measuring mutual information from two aspects of node features and topological structure is indispensable. GMI exhibits several benefits: First, it is invariant to the isomorphic transformation of input graphs---an inevitable constraint in many existing graph representation learning algorithms; Besides, it can be efficiently estimated and maximized by current mutual information estimation methods such as MINE; Finally, our theoretical analysis confirms its correctness and rationality. With the aid of GMI, we develop an unsupervised learning model trained by maximizing GMI between the input and output of a graph neural encoder. Considerable experiments on transductive as well as inductive node classification and link prediction demonstrate that our method outperforms state-of-the-art unsupervised counterparts, and even sometimes exceeds the performance of supervised ones.
Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.