Sampled in Pairs and Driven by Text: A New Graph Embedding Framework

In graphs with rich texts, incorporating textual information with structural information would benefit constructing expressive graph embeddings. Among various graph embedding models, random walk (RW)-based is one of the most popular and successful groups. However, it is challenged by two issues when applied on graphs with rich texts: (i) sampling efficiency: deriving from the training objective of RW-based models (e.g., DeepWalk and node2vec), we show that RW-based models are likely to generate large amounts of redundant training samples due to three main drawbacks. (ii) text utilization: these models have difficulty in dealing with zero-shot scenarios where graph embedding models have to infer graph structures directly from texts. To solve these problems, we propose a novel framework, namely Text-driven Graph Embedding with Pairs Sampling (TGE-PS). TGE-PS uses Pairs Sampling (PS) to improve the sampling strategy of RW, being able to reduce ~99% training samples while preserving competitive performance. TGE-PS uses Text-driven Graph Embedding (TGE), an inductive graph embedding approach, to generate node embeddings from texts. Since each node contains rich texts, TGE is able to generate high-quality embeddings and provide reasonable predictions on existence of links to unseen nodes. We evaluate TGE-PS on several real-world datasets, and experiment results demonstrate that TGE-PS produces state-of-the-art results on both traditional and zero-shot link prediction tasks.Comment: Accepted by WWW 2019 (The World Wide Web Conference. ACM, 2019

edge2vec: Representation learning using edge semantics for biomedical knowledge discovery

Representation learning provides new and powerful graph analytical approaches and tools for the highly valued data science challenge of mining knowledge graphs. Since previous graph analytical methods have mostly focused on homogeneous graphs, an important current challenge is extending this methodology for richly heterogeneous graphs and knowledge domains. The biomedical sciences are such a domain, reflecting the complexity of biology, with entities such as genes, proteins, drugs, diseases, and phenotypes, and relationships such as gene co-expression, biochemical regulation, and biomolecular inhibition or activation. Therefore, the semantics of edges and nodes are critical for representation learning and knowledge discovery in real world biomedical problems. In this paper, we propose the edge2vec model, which represents graphs considering edge semantics. An edge-type transition matrix is trained by an Expectation-Maximization approach, and a stochastic gradient descent model is employed to learn node embedding on a heterogeneous graph via the trained transition matrix. edge2vec is validated on three biomedical domain tasks: biomedical entity classification, compound-gene bioactivity prediction, and biomedical information retrieval. Results show that by considering edge-types into node embedding learning in heterogeneous graphs, \textbf{edge2vec}\ significantly outperforms state-of-the-art models on all three tasks. We propose this method for its added value relative to existing graph analytical methodology, and in the real world context of biomedical knowledge discovery applicability.Comment: 10 page

Word-Entity Duet Representations for Document Ranking

This paper presents a word-entity duet framework for utilizing knowledge bases in ad-hoc retrieval. In this work, the query and documents are modeled by word-based representations and entity-based representations. Ranking features are generated by the interactions between the two representations, incorporating information from the word space, the entity space, and the cross-space connections through the knowledge graph. To handle the uncertainties from the automatically constructed entity representations, an attention-based ranking model AttR-Duet is developed. With back-propagation from ranking labels, the model learns simultaneously how to demote noisy entities and how to rank documents with the word-entity duet. Evaluation results on TREC Web Track ad-hoc task demonstrate that all of the four-way interactions in the duet are useful, the attention mechanism successfully steers the model away from noisy entities, and together they significantly outperform both word-based and entity-based learning to rank systems

Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

A Survey on Knowledge Graphs: Representation, Acquisition and Applications

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