Heterogeneous networks contain multiple types of nodes and links, with some link types encapsulating hierarchical structure over entities. Hierarchical relationships can codify information such as subcategories or one entity being subsumed by another and are often used for organizing conceptual knowledge into a tree-structured graph. Hyperbolic embedding models learn node representations in a hyperbolic space suitable for preserving the hierarchical structure. Unfortunately, current hyperbolic embedding models only implicitly capture the hierarchical structure, failing to distinguish between node types, and they only assume a single tree. In practice, many networks contain a mixture of hierarchical and non-hierarchical structures, and the hierarchical relations may be represented as multiple trees with complex structures, such as sharing certain entities. In this work, we propose a new hyperbolic representation learning model that can handle complex hierarchical structures and also learn the representation of both hierarchical and non-hierarchic structures. We evaluate our model on several datasets, including identifying relevant articles for a systematic review, which is an essential tool for evidence-driven medicine and node classification.

There has been rapid growth in biomedical literature, yet capturing the heterogeneity of the bibliographic information of these articles remains relatively understudied. Graph neural networks have gained popularity, however, they may not fully capture the information available in the PubMed database, a biomedical literature repository containing over 33 million articles. We introduce PubMed Graph Benchmark (PGB), a new benchmark dataset for evaluating heterogeneous graph representations. PGB is one of the largest heterogeneous networks to date and aggregates the rich metadata into a unified source including abstract, authors, citations, keywords, and the associated keyword hierarchy. The benchmark contains an evaluation task of 21 systematic review topics, an essential knowledge translation tool.

Over the past few years, knowledge bases (KBs) like DBPedia, Freebase, and YAGO have accumulated a massive amount of knowledge from web data. Despite their seemingly large size, however, individual KBs often lack comprehensive information on any given domain. For example, over 70 percent of people on Freebase lack information on place of birth. For this reason, the complementary nature across different KBs motivates their integration through a process of aligning instances. Meanwhile, since application-level machine systems, such as medical diagnosis, have heavily relied on KBs, it is necessary to provide users with trustworthy reasons why the alignment decisions are made. To address this problem, we propose a new paradigm, explainable instance alignment (XINA), which provides user-understandable explanations for alignment decisions. Specifically, given an alignment candidate, XINA replaces existing scalar representation of an aggregated score, by decision and explanation-vector spaces for machine decision and user understanding, respectively. To validate XINA, we perform extensive experiments on real-world KBs and show that XINA achieves comparable performance with state-of-the-arts, even with far less human effort.

In this extended abstract, we present an instance alignment framework, namely XINA, for KB integration. We then show its effectiveness and efficiency on real-world KBs.