We examine two fundamental tasks associated with graph representation learning: link prediction and semi-supervised node classification. We present a densely connected autoencoder architecture capable of learning a joint representation of both local graph structure and available external node features for the multi-task learning of link prediction and node classification. To the best of our knowledge, this is the first architecture that can be efficiently trained end-to-end in a single learning stage to simultaneously perform link prediction and node classification. We provide comprehensive empirical evaluation of our models on a range of challenging benchmark graph-structured datasets, and demonstrate significant improvement in accuracy over related methods for graph representation learning. Code implementation is available at this https URL
Our work is inspired by recent successful applications of autoencoder architectures for collaborative filtering that outperform popular matrix factorization methods @cite_18 @cite_21 @cite_0 , and is related to Structural Deep Network Embedding (SDNE) @cite_28 for link prediction. Similar to SDNE, our models rely on the autoencoder to learn non-linear node embeddings from local graph neighborhoods. However, our models have several important distinctions: 1) we leverage extensive parameter sharing between the encoder and decoder parts to enhance representation learning; 2) our @math LoNGAE model can optionally concatenate side node features to the adjacency matrix for improved link prediction performance; and 3) the @math LoNGAE model can be trained end-to-end in a single stage for multi-task learning of link prediction and semi-supervised node classification. On the other hand, training SDNE requires multiple steps that are difficult to jointly optimize: i) pre-training via a deep belief network; and ii) utilizing a separate downstream classifier on top of node embeddings for LPNC.
@cite_0 @cite_28 @cite_18 @cite_21
2743992351 2393319904 1720514416 2489745941
Network embedding is an important method to learn low-dimensional representations of vertexes in networks, aiming to capture and preserve the network structure. Almost all the existing network embedding methods adopt shallow models. However, since the underlying network structure is complex, shallow models cannot capture the highly non-linear network structure, resulting in sub-optimal network representations. Therefore, how to find a method that is able to effectively capture the highly non-linear network structure and preserve the global and local structure is an open yet important problem. To solve this problem, in this paper we propose a Structural Deep Network Embedding method, namely SDNE. More specifically, we first propose a semi-supervised deep model, which has multiple layers of non-linear functions, thereby being able to capture the highly non-linear network structure. Then we propose to exploit the first-order and second-order proximity jointly to preserve the network structure. The second-order proximity is used by the unsupervised component to capture the global network structure. While the first-order proximity is used as the supervised information in the supervised component to preserve the local network structure. By jointly optimizing them in the semi-supervised deep model, our method can preserve both the local and global network structure and is robust to sparse networks. Empirically, we conduct the experiments on five real-world networks, including a language network, a citation network and three social networks. The results show that compared to the baselines, our method can reconstruct the original network significantly better and achieves substantial gains in three applications, i.e. multi-label classification, link prediction and visualization. Abstract In this paper, we propose a novel graph-based approach for semi-supervised learning problems, which considers an adaptive adjacency of the examples throughout the unsupervised portion of the training. Adjacency of the examples is inferred using the predictions of a neural network model which is first initialized by a supervised pretraining. These predictions are then updated according to a novel unsupervised objective which regularizes another adjacency, now linking the output nodes. Regularizing the adjacency of the output nodes, inferred from the predictions of the network, creates an easier optimization problem and ultimately provides that the predictions of the network turn into the optimal embedding. Ultimately, the proposed framework provides an effective and scalable graph-based solution which is natural to the operational mechanism of deep neural networks. Our results show comparable performance with state-of-the-art generative approaches for semi-supervised learning on an easier-to-train, low-cost framework. Graphs are a fundamental abstraction for modeling relational data. However, graphs are discrete and combinatorial in nature, and learning representations suitable for machine learning tasks poses statistical and computational challenges. In this work, we propose Graphite an algorithmic framework for unsupervised learning of representations over nodes in a graph using deep latent variable generative models. Our model is based on variational autoencoders (VAE), and differs from existing VAE frameworks for data modalities such as images, speech, and text in the use of graph neural networks for parameterizing both the generative model (i.e., decoder) and inference model (i.e., encoder). The use of graph neural networks directly incorporates inductive biases due to the spatial, local structure of graphs directly in the generative model. Moreover, we draw novel connections between graph neural networks and approximate inference via kernel embeddings of distributions. We demonstrate empirically that Graphite outperforms state-of-the-art approaches for the tasks of density estimation, link prediction, and node classification on synthetic and benchmark datasets. In this paper, we propose a novel representation learning framework, namely HIN2Vec, for heterogeneous information networks (HINs). The core of the proposed framework is a neural network model, also called HIN2Vec, designed to capture the rich semantics embedded in HINs by exploiting different types of relationships among nodes. Given a set of relationships specified in forms of meta-paths in an HIN, HIN2Vec carries out multiple prediction training tasks jointly based on a target set of relationships to learn latent vectors of nodes and meta-paths in the HIN. In addition to model design, several issues unique to HIN2Vec, including regularization of meta-path vectors, node type selection in negative sampling, and cycles in random walks, are examined. To validate our ideas, we learn latent vectors of nodes using four large-scale real HIN datasets, including Blogcatalog, Yelp, DBLP and U.S. Patents, and use them as features for multi-label node classification and link prediction applications on those networks. Empirical results show that HIN2Vec soundly outperforms the state-of-the-art representation learning models for network data, including DeepWalk, LINE, node2vec, PTE, HINE and ESim, by 6.6 to 23.8 of @math - @math in multi-label node classification and 5 to 70.8 of @math in link prediction. Network embedding leverages the node proximity manifested to learn a low-dimensional node vector representation for each node in the network. The learned embeddings could advance various learning tasks such as node classification, network clustering, and link prediction. Most, if not all, of the existing works, are overwhelmingly performed in the context of plain and static networks. Nonetheless, in reality, network structure often evolves over time with addition deletion of links and nodes. Also, a vast majority of real-world networks are associated with a rich set of node attributes, and their attribute values are also naturally changing, with the emerging of new content patterns and the fading of old content patterns. These changing characteristics motivate us to seek an effective embedding representation to capture network and attribute evolving patterns, which is of fundamental importance for learning in a dynamic environment. To our best knowledge, we are the first to tackle this problem with the following two challenges: (1) the inherently correlated network and node attributes could be noisy and incomplete, it necessitates a robust consensus representation to capture their individual properties and correlations; (2) the embedding learning needs to be performed in an online fashion to adapt to the changes accordingly. In this paper, we tackle this problem by proposing a novel dynamic attributed network embedding framework - DANE. In particular, DANE first provides an offline method for a consensus embedding and then leverages matrix perturbation theory to maintain the freshness of the end embedding results in an online manner. We perform extensive experiments on both synthetic and real attributed networks to corroborate the effectiveness and efficiency of the proposed framework. Link prediction is a fundamental task in such areas as social network analysis, information retrieval, and bioinformatics. Usually link prediction methods use the link structures or node attributes as the sources of information. Recently, the relational topic model (RTM) and its variants have been proposed as hybrid methods that jointly model both sources of information and achieve very promising accuracy. However, the representations (features) learned by them are still not effective enough to represent the nodes (items). To address this problem, we generalize recent advances in deep learning from solely modeling i.i.d. sequences of attributes to jointly modeling graphs and non-i.i.d. sequences of attributes. Specifically, we follow the Bayesian deep learning framework and devise a hierarchical Bayesian model, called relational deep learning (RDL), to jointly model high-dimensional node attributes and link structures with layers of latent variables. Due to the multiple nonlinear transformations in RDL, standard variational inference is not applicable. We propose to utilize the product of Gaussians (PoG) structure in RDL to relate the inferences on different variables and derive a generalized variational inference algorithm for learning the variables and predicting the links. Experiments on three real-world datasets show that RDL works surprisingly well and significantly outperforms the state of the art. Graph embedding is an effective method to represent graph data in a low dimensional space for graph analytics. Most existing embedding algorithms typically focus on preserving the topological structure or minimizing the reconstruction errors of graph data, but they have mostly ignored the data distribution of the latent codes from the graphs, which often results in inferior embedding in real-world graph data. In this paper, we propose a novel adversarial graph embedding framework for graph data. The framework encodes the topological structure and node content in a graph to a compact representation, on which a decoder is trained to reconstruct the graph structure. Furthermore, the latent representation is enforced to match a prior distribution via an adversarial training scheme. To learn a robust embedding, two variants of adversarial approaches, adversarially regularized graph autoencoder (ARGA) and adversarially regularized variational graph autoencoder (ARVGA), are developed. Experimental studies on real-world graphs validate our design and demonstrate that our algorithms outperform baselines by a wide margin in link prediction, graph clustering, and graph visualization tasks. The temporal dynamics of a complex system such as a social network or a communication network can be studied by understanding the patterns of link appearance and disappearance over time. A critical task along this understanding is to predict the link state of the network at a future time given a collection of link states at earlier time points. In existing literature, this task is known as link prediction in dynamic networks. Solving this task is more difficult than its counterpart in static networks because an effective feature representation of node-pair instances for the case of dynamic network is hard to obtain. To overcome this problem, we propose a novel method for metric embedding of node-pair instances of a dynamic network. The proposed method models the metric embedding task as an optimal coding problem where the objective is to minimize the reconstruction error, and it solves this optimization task using a gradient descent method. We validate the effectiveness of the learned feature representation by utilizing it for link prediction in various real-life dynamic networks. Specifically, we show that our proposed link prediction model, which uses the extracted feature representation for the training instances, outperforms several existing methods that use well-known link prediction features. We propose a new method for embedding graphs while preserving directed edge information. Learning such continuous-space vector representations (or embeddings) of nodes in a graph is an important first step for using network information (from social networks, user-item graphs, knowledge bases, etc.) in many machine learning tasks. Unlike previous work, we (1) explicitly model an edge as a function of node embeddings, and we (2) propose a novel objective, the graph likelihood, which contrasts information from sampled random walks with non-existent edges. Individually, both of these contributions improve the learned representations, especially when there are memory constraints on the total size of the embeddings. When combined, our contributions enable us to significantly improve the state-of-the-art by learning more concise representations that better preserve the graph structure. We evaluate our method on a variety of link-prediction task including social networks, collaboration networks, and protein interactions, showing that our proposed method learn representations with error reductions of up to 76 and 55 , on directed and undirected graphs. In addition, we show that the representations learned by our method are quite space efficient, producing embeddings which have higher structure-preserving accuracy but are 10 times smaller. Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions. Knowledge graphs are graphical representations of large databases of facts, which typically suffer from incompleteness. Inferring missing relations (links) between entities (nodes) is the task of link prediction. A recent state-of-the-art approach to link prediction, ConvE, implements a convolutional neural network to extract features from concatenated subject and relation vectors. Whilst results are impressive, the method is unintuitive and poorly understood. We propose a hypernetwork architecture that generates simplified relation-specific convolutional filters that (i) outperforms ConvE and all previous approaches across standard datasets; and (ii) can be framed as tensor factorization and thus set within a well established family of factorization models for link prediction. We thus demonstrate that convolution simply offers a convenient computational means of introducing sparsity and parameter tying to find an effective trade-off between non-linear expressiveness and the number of parameters to learn. Deep neural networks are widely used for classification. These deep models often suffer from a lack of interpretability -- they are particularly difficult to understand because of their non-linear nature. As a result, neural networks are often treated as "black box" models, and in the past, have been trained purely to optimize the accuracy of predictions. In this work, we create a novel network architecture for deep learning that naturally explains its own reasoning for each prediction. This architecture contains an autoencoder and a special prototype layer, where each unit of that layer stores a weight vector that resembles an encoded training input. The encoder of the autoencoder allows us to do comparisons within the latent space, while the decoder allows us to visualize the learned prototypes. The training objective has four terms: an accuracy term, a term that encourages every prototype to be similar to at least one encoded input, a term that encourages every encoded input to be close to at least one prototype, and a term that encourages faithful reconstruction by the autoencoder. The distances computed in the prototype layer are used as part of the classification process. Since the prototypes are learned during training, the learned network naturally comes with explanations for each prediction, and the explanations are loyal to what the network actually computes. We study the problem of representation learning in heterogeneous networks. Its unique challenges come from the existence of multiple types of nodes and links, which limit the feasibility of the conventional network embedding techniques. We develop two scalable representation learning models, namely metapath2vec and metapath2vec++. The metapath2vec model formalizes meta-path-based random walks to construct the heterogeneous neighborhood of a node and then leverages a heterogeneous skip-gram model to perform node embeddings. The metapath2vec++ model further enables the simultaneous modeling of structural and semantic correlations in heterogeneous networks. Extensive experiments show that metapath2vec and metapath2vec++ are able to not only outperform state-of-the-art embedding models in various heterogeneous network mining tasks, such as node classification, clustering, and similarity search, but also discern the structural and semantic correlations between diverse network objects. Embedding large graphs in low dimensional spaces has recently attracted significant interest due to its wide applications such as graph visualization, link prediction and node classification. Existing methods focus on computing the embedding for static graphs. However, many graphs in practical applications are dynamic and evolve constantly over time. Naively applying existing embedding algorithms to each snapshot of dynamic graphs independently usually leads to unsatisfactory performance in terms of stability, flexibility and efficiency. In this work, we present an efficient algorithm DynGEM based on recent advances in deep autoencoders for graph embeddings, to address this problem. The major advantages of DynGEM include: (1) the embedding is stable over time, (2) it can handle growing dynamic graphs, and (3) it has better running time than using static embedding methods on each snapshot of a dynamic graph. We test DynGEM on a variety of tasks including graph visualization, graph reconstruction, link prediction and anomaly detection (on both synthetic and real datasets). Experimental results demonstrate the superior stability and scalability of our approach. Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs---a limitation that is especially problematic for the task of graph classification, where the goal is to predict the label associated with an entire graph. Here we propose DiffPool, a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DiffPool learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Our experimental results show that combining existing GNN methods with DiffPool yields an average improvement of 5-10 accuracy on graph classification benchmarks, compared to all existing pooling approaches, achieving a new state-of-the-art on four out of five benchmark datasets. Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs---a limitation that is especially problematic for the task of graph classification, where the goal is to predict the label associated with an entire graph. Here we propose DiffPool, a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DiffPool learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Our experimental results show that combining existing GNN methods with DiffPool yields an average improvement of 5-10 accuracy on graph classification benchmarks, compared to all existing pooling approaches, achieving a new state-of-the-art on four out of five benchmark data sets. Neural message passing algorithms for semi-supervised classification on graphs have recently achieved great success. However, for classifying a node these methods only consider nodes that are a few propagation steps away and the size of this utilized neighborhood is hard to extend. In this paper, we use the relationship between graph convolutional networks (GCN) and PageRank to derive an improved propagation scheme based on personalized PageRank. We utilize this propagation procedure to construct a simple model, personalized propagation of neural predictions (PPNP), and its fast approximation, APPNP. Our model's training time is on par or faster and its number of parameters on par or lower than previous models. It leverages a large, adjustable neighborhood for classification and can be easily combined with any neural network. We show that this model outperforms several recently proposed methods for semi-supervised classification in the most thorough study done so far for GCN-like models. Our implementation is available online. We present a deep generative model for learning to predict classes not seen at training time. Unlike most existing methods for this problem, that represent each class as a point (via a semantic embedding), we represent each seen unseen class using a class-specific latent-space distribution, conditioned on class attributes. We use these latent-space distributions as a prior for a supervised variational autoencoder (VAE), which also facilitates learning highly discriminative feature representations for the inputs. The entire framework is learned end-to-end using only the seen-class training data. The model infers corresponding attributes of a test image by maximizing the VAE lower bound; the inferred attributes may be linked to labels not seen when training. We further extend our model to a (1) semi-supervised transductive setting by leveraging unlabeled unseen-class data via an unsupervised learning module, and (2) few-shot learning where we also have a small number of labeled inputs from the unseen classes. We compare our model with several state-of-the-art methods through a comprehensive set of experiments on a variety of benchmark data sets. Unsupervised anomaly detection on multi- or high-dimensional data is of great importance in both fundamental machine learning research and industrial applications, for which density estimation lies at the core. Although previous approaches based on dimensionality reduction followed by density estimation have made fruitful progress, they mainly suffer from decoupled model learning with inconsistent optimization goals and incapability of preserving essential information in the low-dimensional space. In this paper, we present a Deep Autoencoding Gaussian Mixture Model (DAGMM) for unsupervised anomaly detection. Our model utilizes a deep autoencoder to generate a low-dimensional representation and reconstruction error for each input data point, which is further fed into a Gaussian Mixture Model (GMM). Instead of using decoupled two-stage training and the standard Expectation-Maximization (EM) algorithm, DAGMM jointly optimizes the parameters of the deep autoencoder and the mixture model simultaneously in an end-to-end fashion, leveraging a separate estimation network to facilitate the parameter learning of the mixture model. The joint optimization, which well balances autoencoding reconstruction, density estimation of latent representation, and regularization, helps the autoencoder escape from less attractive local optima and further reduce reconstruction errors, avoiding the need of pre-training. Experimental results on several public benchmark datasets show that, DAGMM significantly outperforms state-of-the-art anomaly detection techniques, and achieves up to 14 improvement based on the standard F1 score. Network embedding methods aim at learning low-dimensional latent representation of nodes in a network. These representations can be used as features for a wide range of tasks on graphs such as classification, clustering, link prediction, and visualization. In this survey, we give an overview of network embeddings by summarizing and categorizing recent advancements in this research field. We first discuss the desirable properties of network embeddings and briefly introduce the history of network embedding algorithms. Then, we discuss network embedding methods under different scenarios, such as supervised versus unsupervised learning, learning embeddings for homogeneous networks versus for heterogeneous networks, etc. We further demonstrate the applications of network embeddings, and conclude the survey with future work in this area.