Learning compact graph representations via an encoder-decoder network

Abstract

Feature representation learning for classification of multiple graphs is a problem with practical applications in many domains. For instance, in chemoinformatics, the learned feature representations of molecular graphs can be used to classify molecules which exhibit anti-cancer properties. In many previous work, including discriminative subgraph mining and graphlet-based approaches, a graph representation is derived by counting the occurrence of various graph sub-structures. However, these representations fail to capture the co-occurrence patterns that are inherently present among different sub-structures. Recently, various methods (e.g., DeepWalk, node2vec) have been proposed to learn representations for nodes in a graph. These methods use node co-occurrence to learn node embeddings. However, these methods fail to capture the co-occurrence relationship between more complex sub-structures in the graph since they were designed primarily for node representation learning. In this work, we study the problem of learning graph representations that can capture the structural and functional similarity of sub-structures (as evidenced by their co-occurrence relationship) in graphs. This is particularly useful when classifying graphs that have very few sub-structures in common. The proposed method uses an encoder-decoder model to predict the random walk sequence along neighboring regions (or sub-structures) in a graph given a random walk along a particular region. The method is unsupervised and can be used to obtain generic feature representations of graphs making it applicable with various types of graphs. We evaluate the learned representations using several real-world datasets on the binary graph classification task. The proposed model is able to achieve superior results against multiple state-of-the-art techniques.