Generative models of graph structure have applications in biology and social sciences. The state of the art is GraphRNN, which decomposes the graph generation process into a series of sequential steps. While effective for modest sizes, it loses its permutation invariance for larger graphs. Instead, we present a permutation invariant latent-variable generative model relying on graph embeddings to encode structure. Using tools from the random graph literature, our model is highly scalable to large graphs with likelihood evaluation and generation in $O(|V | + |E|)$.
Knowledge graph (KG) embedding encodes the entities and relations from a KG into low-dimensional vector spaces to support various applications such as KG completion, question answering, and recommender systems. In real world, knowledge graphs (KGs) are dynamic and evolve over time with addition or deletion of triples. However, most existing models focus on embedding static KGs while neglecting dynamics. To adapt to the changes in a KG, these models need to be retrained on the whole KG with a high time cost. In this paper, to tackle the aforementioned problem, we propose a new context-aware Dynamic Knowledge Graph Embedding (DKGE) method which supports the embedding learning in an online fashion. DKGE introduces two different representations (i.e., knowledge embedding and contextual element embedding) for each entity and each relation, in the joint modeling of entities and relations as well as their contexts, by employing two attentive graph convolutional networks, a gate strategy, and translation operations. This effectively helps limit the impacts of a KG update in certain regions, not in the entire graph, so that DKGE can rapidly acquire the updated KG embedding by a proposed online learning algorithm. Furthermore, DKGE can also learn KG embedding from scratch. Experiments on the tasks of link prediction and question answering in a dynamic environment demonstrate the effectiveness and efficiency of DKGE.
While a wide range of interpretable generative procedures for graphs exist, matching observed graph topologies with such procedures and choices for its parameters remains an open problem. Devising generative models that closely reproduce real-world graphs requires domain knowledge and time-consuming simulation. While existing deep learning approaches rely on less manual modelling, they offer little interpretability. This work approaches graph generation (decoding) as the inverse of graph compression (encoding). We show that in a disentanglement-focused deep autoencoding framework, specifically Beta-Variational Autoencoders (Beta-VAE), choices of generative procedures and their parameters arise naturally in the latent space. Our model is capable of learning disentangled, interpretable latent variables that represent the generative parameters of procedurally generated random graphs and real-world graphs. The degree of disentanglement is quantitatively measured using the Mutual Information Gap (MIG). When training our Beta-VAE model on ER random graphs, its latent variables have a near one-to-one mapping to the ER random graph parameters n and p. We deploy the model to analyse the correlation between graph topology and node attributes measuring their mutual dependence without handpicking topological properties.
The goal of representation learning of knowledge graph is to encode both entities and relations into a low-dimensional embedding spaces. Many recent works have demonstrated the benefits of knowledge graph embedding on knowledge graph completion task, such as relation extraction. However, we observe that: 1) existing method just take direct relations between entities into consideration and fails to express high-order structural relationship between entities; 2) these methods just leverage relation triples of KGs while ignoring a large number of attribute triples that encoding rich semantic information. To overcome these limitations, this paper propose a novel knowledge graph embedding method, named KANE, which is inspired by the recent developments of graph convolutional networks (GCN). KANE can capture both high-order structural and attribute information of KGs in an efficient, explicit and unified manner under the graph convolutional networks framework. Empirical results on three datasets show that KANE significantly outperforms seven state-of-arts methods. Further analysis verify the efficiency of our method and the benefits brought by the attention mechanism.
Recently, self-supervised learning has proved to be effective to learn representations of events suitable for temporal segmentation in image sequences, where events are understood as sets of temporally adjacent images that are semantically perceived as a whole. However, although this approach does not require expensive manual annotations, it is data hungry and suffers from domain adaptation problems. As an alternative, in this work, we propose a novel approach for learning event representations named Dynamic Graph Embedding (DGE). The assumption underlying our model is that a sequence of images can be represented by a graph that encodes both semantic and temporal similarity. The key novelty of DGE is to learn jointly the graph and its graph embedding. At its core, DGE works by iterating over two steps: 1) updating the graph representing the semantic and temporal similarity of the data based on the current data representation, and 2) updating the data representation to take into account the current data graph structure. The main advantage of DGE over state-of-the-art self-supervised approaches is that it does not require any training set, but instead learns iteratively from the data itself a low-dimensional embedding that reflects their temporal and semantic similarity. Experimental results on two benchmark datasets of real image sequences captured at regular time intervals demonstrate that the proposed DGE leads to event representations effective for temporal segmentation. In particular, it achieves robust temporal segmentation on the EDUBSeg and EDUBSeg-Desc benchmark datasets, outperforming the state of the art. Additional experiments on two Human Motion Segmentation benchmark datasets demonstrate the generalization capabilities of the proposed DGE.
Automatic representation learning of key entities in electronic health record (EHR) data is a critical step for healthcare informatics that turns heterogeneous medical records into structured and actionable information. Here we propose ME2Vec, an algorithmic framework for learning low-dimensional vectors of the most common entities in EHR: medical services, doctors, and patients. ME2Vec leverages diverse graph embedding techniques to cater for the unique characteristic of each medical entity. Using real-world clinical data, we demonstrate the efficacy of ME2Vec over competitive baselines on disease diagnosis prediction.
Graph embedding techniques have been increasingly deployed in a multitude of different applications that involve learning on non-Euclidean data. However, existing graph embedding models either fail to incorporate node attribute information during training or suffer from node attribute noise, which compromises the accuracy. Moreover, very few of them scale to large graphs due to their high computational complexity and memory usage. In this paper we propose GraphZoom, a multi-level framework for improving both accuracy and scalability of unsupervised graph embedding algorithms. GraphZoom first performs graph fusion to generate a new graph that effectively encodes the topology of the original graph and the node attribute information. This fused graph is then repeatedly coarsened into much smaller graphs by merging nodes with high spectral similarities. GraphZoom allows any existing embedding methods to be applied to the coarsened graph, before it progressively refine the embeddings obtained at the coarsest level to increasingly finer graphs. We have evaluated our approach on a number of popular graph datasets for both transductive and inductive tasks. Our experiments show that GraphZoom can substantially increase the classification accuracy and significantly accelerate the entire graph embedding process by up to 40.8x, when compared to the state-of-the-art unsupervised embedding methods.
Learning network representations is a fundamental task for many graph applications such as link prediction, node classification, graph clustering, and graph visualization. Many real-world networks are interpreted as dynamic networks and evolve over time. Most existing graph embedding algorithms were developed for static graphs mainly and cannot capture the evolution of a large dynamic network. In this paper, we propose Dynamic joint Variational Graph Autoencoders (Dyn-VGAE) that can learn both local structures and temporal evolutionary patterns in a dynamic network. Dyn-VGAE provides a joint learning framework for computing temporal representations of all graph snapshots simultaneously. Each auto-encoder embeds a graph snapshot based on its local structure and can also learn temporal dependencies by collaborating with other autoencoders. We conduct experimental studies on dynamic real-world graph datasets and the results demonstrate the effectiveness of the proposed method.
The spatial convolution layer which is widely used in the Graph Neural Networks (GNNs) aggregates the feature vector of each node with the feature vectors of its neighboring nodes. The GNN is not aware of the locations of the nodes in the global structure of the graph and when the local structures corresponding to different nodes are similar to each other, the convolution layer maps all those nodes to similar or same feature vectors in the continuous feature space. Therefore, the GNN cannot distinguish two graphs if their difference is not in their local structures. In addition, when the nodes are not labeled/attributed the convolution layers can fail to distinguish even different local structures. In this paper, we propose an effective solution to address this problem of the GNNs. The proposed approach leverages a spatial representation of the graph which makes the neural network aware of the differences between the nodes and also their locations in the graph. The spatial representation which is equivalent to a point-cloud representation of the graph is obtained by a graph embedding method. Using the proposed approach, the local feature extractor of the GNN distinguishes similar local structures in different locations of the graph and the GNN infers the topological structure of the graph from the spatial distribution of the locally extracted feature vectors. Moreover, the spatial representation is utilized to simplify the graph down-sampling problem. A new graph pooling method is proposed and it is shown that the proposed pooling method achieves competitive or better results in comparison with the state-of-the-art methods.
Graph embeddings, a class of dimensionality reduction techniques designed for relational data, have proven useful in exploring and modeling network structure. Most dimensionality reduction methods allow out-of-sample extensions, by which an embedding can be applied to observations not present in the training set. Applied to graphs, the out-of-sample extension problem concerns how to compute the embedding of a vertex that is added to the graph after an embedding has already been computed. In this paper, we consider the out-of-sample extension problem for two graph embedding procedures: the adjacency spectral embedding and the Laplacian spectral embedding. In both cases, we prove that when the underlying graph is generated according to a latent space model called the random dot product graph, which includes the popular stochastic block model as a special case, an out-of-sample extension based on a least-squares objective obeys a central limit theorem about the true latent position of the out-of-sample vertex. In addition, we prove a concentration inequality for the out-of-sample extension of the adjacency spectral embedding based on a maximum-likelihood objective. Our results also yield a convenient framework in which to analyze trade-offs between estimation accuracy and computational expense, which we explore briefly.
Graph node embedding aims at learning a vector representation for all nodes given a graph. It is a central problem in many machine learning tasks (e.g., node classification, recommendation, community detection). The key problem in graph node embedding lies in how to define the dependence to neighbors. Existing approaches specify (either explicitly or implicitly) certain dependencies on neighbors, which may lead to loss of subtle but important structural information within the graph and other dependencies among neighbors. This intrigues us to ask the question: can we design a model to give the maximal flexibility of dependencies to each node's neighborhood. In this paper, we propose a novel graph node embedding (named PINE) via a novel notion of partial permutation invariant set function, to capture any possible dependence. Our method 1) can learn an arbitrary form of the representation function from the neighborhood, withour losing any potential dependence structures, and 2) is applicable to both homogeneous and heterogeneous graph embedding, the latter of which is challenged by the diversity of node types. Furthermore, we provide theoretical guarantee for the representation capability of our method for general homogeneous and heterogeneous graphs. Empirical evaluation results on benchmark data sets show that our proposed PINE method outperforms the state-of-the-art approaches on producing node vectors for various learning tasks of both homogeneous and heterogeneous graphs.
The transformer self-attention network has been extensively used in research domains such as computer vision, image processing, and natural language processing. But it has not been actively used in graph neural networks (GNNs) where constructing an advanced aggregation function is essential. To this end, we present U2GNN, an effective GNN model leveraging a transformer self-attention mechanism followed by a recurrent transition, to induce a powerful aggregation function to learn graph representations. Experimental results show that the proposed U2GNN achieves state-of-the-art accuracies on well-known benchmark datasets for graph classification. Our code is available at: https://github.com/daiquocnguyen/Graph-Transformer
Learning powerful data embeddings has become a center piece in machine learning, especially in natural language processing and computer vision domains. The crux of these embeddings is that they are pretrained on huge corpus of data in a unsupervised fashion, sometimes aided with transfer learning. However currently in the graph learning domain, embeddings learned through existing graph neural networks (GNNs) are task dependent and thus cannot be shared across different datasets. In this paper, we present a first powerful and theoretically guaranteed graph neural network that is designed to learn task-independent graph embeddings, thereafter referred to as deep universal graph embedding (DUGNN). Our DUGNN model incorporates a novel graph neural network (as a universal graph encoder) and leverages rich Graph Kernels (as a multi-task graph decoder) for both unsupervised learning and (task-specific) adaptive supervised learning. By learning task-independent graph embeddings across diverse datasets, DUGNN also reaps the benefits of transfer learning. Through extensive experiments and ablation studies, we show that the proposed DUGNN model consistently outperforms both the existing state-of-art GNN models and Graph Kernels by an increased accuracy of 3% - 8% on graph classification benchmark datasets.
Scene graphs have become an important form of structured knowledge for tasks such as for image generation, visual relation detection, visual question answering, and image retrieval. While visualizing and interpreting word embeddings is well understood, scene graph embeddings have not been fully explored. In this work, we train scene graph embeddings in a layout generation task with different forms of supervision, specifically introducing triplet super-vision and data augmentation. We see a significant performance increase in both metrics that measure the goodness of layout prediction, mean intersection-over-union (mIoU)(52.3% vs. 49.2%) and relation score (61.7% vs. 54.1%),after the addition of triplet supervision and data augmentation. To understand how these different methods affect the scene graph representation, we apply several new visualization and evaluation methods to explore the evolution of the scene graph embedding. We find that triplet supervision significantly improves the embedding separability, which is highly correlated with the performance of the layout prediction model.
The trends of open science have enabled several open scholarly datasets which include millions of papers and authors. Managing, exploring, and utilizing such large and complicated datasets effectively are challenging. In recent years, the knowledge graph has emerged as a universal data format for representing knowledge about heterogeneous entities and their relationships. The knowledge graph can be modeled by knowledge graph embedding methods, which represent entities and relations as embedding vectors in semantic space, then model the interactions between these embedding vectors. However, the semantic structures in the knowledge graph embedding space are not well-studied, thus knowledge graph embedding methods are usually only used for knowledge graph completion but not data representation and analysis. In this paper, we propose to analyze these semantic structures based on the well-studied word embedding space and use them to support data exploration. We also define the semantic queries, which are algebraic operations between the embedding vectors in the knowledge graph embedding space, to solve queries such as similarity and analogy between the entities on the original datasets. We then design a general framework for data exploration by semantic queries and discuss the solution to some traditional scholarly data exploration tasks. We also propose some new interesting tasks that can be solved based on the uncanny semantic structures of the embedding space.
Knowledge graph embedding has recently become a popular way to model relations and infer missing links. In this paper, we present a group theoretical perspective of knowledge graph embedding, connecting previous methods with different group actions. Furthermore, by utilizing Schur's lemma from group representation theory, we show that the state of the art embedding method RotatE can model relations from any finite Abelian group.
Recently, as the spread of smart devices increases, the amount of data collected through sensors is increasing. A lifelog is a kind of big data to analyze behavior patterns in the daily life of individuals collected from various smart de-vices. However, sensor data is a low-level signal that makes it difficult for hu-mans to recognize the situation directly and cannot express relations clearly. It is also difficult to identify the daily behavior pattern because it records heterogene-ous data by various sensors. In this paper, we propose a method to define a graph structure with node and edge and to extract the daily behavior pattern from the generated lifelog graph. We use the graph convolution method to embeds the lifelog graph and maps it to low dimension. The graph convolution layer im-proves the expressive power of the daily behavior pattern by implanting the life-log graph in the non-Euclidean space and learns the patterns of graphs. Experi-mental results show that the proposed method automatically extracts meaningful user patterns from UbiqLog dataset. In addition, we confirm the usefulness by comparing our method with existing methods to evaluate performance.
Learning knowledge graph embedding from an existing knowledge graph is very important to knowledge graph completion. For a fact $(h,r,t)$ with the head entity $h$ having a relation $r$ with the tail entity $t$, the current approaches aim to learn low dimensional representations $(\mathbf{h},\mathbf{r},\mathbf{t})$, each of which corresponds to the elements in $(h, r, t)$, respectively. As $(\mathbf{h},\mathbf{r},\mathbf{t})$ is learned from the existing facts within a knowledge graph, these representations can not be used to detect unknown facts (if the entities or relations never occur in the knowledge graph). This paper proposes a new approach called TransW, aiming to go beyond the current work by composing knowledge graph embeddings using word embeddings. Given the fact that an entity or a relation contains one or more words (quite often), it is sensible to learn a mapping function from word embedding spaces to knowledge embedding spaces, which shows how entities are constructed using human words. More importantly, composing knowledge embeddings using word embeddings makes it possible to deal with the emerging new facts (either new entities or relations). Experimental results using three public datasets show the consistency and outperformance of the proposed TransW.
Representation learning on graphs has been gaining attention due to its wide applicability in predicting missing links, and classifying and recommending nodes. Most embedding methods aim to preserve certain properties of the original graph in the low dimensional space. However, real world graphs have a combination of several properties which are difficult to characterize and capture by a single approach. In this work, we introduce the problem of graph representation ensemble learning and provide a first of its kind framework to aggregate multiple graph embedding methods efficiently. We provide analysis of our framework and analyze -- theoretically and empirically -- the dependence between state-of-the-art embedding methods. We test our models on the node classification task on four real world graphs and show that proposed ensemble approaches can outperform the state-of-the-art methods by up to 8% on macro-F1. We further show that the approach is even more beneficial for underrepresented classes providing an improvement of up to 12%.
Graph embedding aims at learning a vector-based representation of vertices that incorporates the structure of the graph. This representation then enables inference of graph properties. Existing graph embedding techniques, however, do not scale well to large graphs. We therefore propose a framework for parallel computation of a graph embedding using a cluster of compute nodes with resource constraints. We show how to distribute any existing embedding technique by first splitting a graph for any given set of constrained compute nodes and then reconciling the embedding spaces derived for these subgraphs. We also propose a new way to evaluate the quality of graph embeddings that is independent of a specific inference task. Based thereon, we give a formal bound on the difference between the embeddings derived by centralised and parallel computation. Experimental results illustrate that our approach for parallel computation scales well, while largely maintaining the embedding quality.