Know2BIO: A Comprehensive Dual-View Benchmark for Evolving Biomedical Knowledge Graphs

TL;DR

Know2BIO is a comprehensive, multi-modal benchmark for biomedical knowledge graphs that integrates diverse data sources, supports continuous updates, and facilitates evaluation of representation models in the biomedical domain.

Contribution

It introduces Know2BIO, a large-scale, heterogeneous biomedical knowledge graph benchmark with multi-modal data and automated updating capabilities.

Findings

Effective evaluation of KG representation models demonstrated

Supports multi-modal data integration for biomedical applications

Enables continuous updates to reflect latest scientific knowledge

Abstract

Knowledge graphs (KGs) have emerged as a powerful framework for representing and integrating complex biomedical information. However, assembling KGs from diverse sources remains a significant challenge in several aspects, including entity alignment, scalability, and the need for continuous updates to keep pace with scientific advancements. Moreover, the representative power of KGs is often limited by the scarcity of multi-modal data integration. To overcome these challenges, we propose Know2BIO, a general-purpose heterogeneous KG benchmark for the biomedical domain. Know2BIO integrates data from 30 diverse sources, capturing intricate relationships across 11 biomedical categories. It currently consists of ~219,000 nodes and ~6,200,000 edges. Know2BIO is capable of user-directed automated updating to reflect the latest knowledge in biomedical science. Furthermore, Know2BIO is accompanied by multi-modal data: node features including text descriptions, protein and compound sequences and structures, enabling the utilization of emerging natural language processing methods and multi-modal data integration strategies. We evaluate KG representation models on Know2BIO, demonstrating its effectiveness as a benchmark for KG representation learning in the biomedical field. Data and source code of Know2BIO are available at https://github.com/Yijia-Xiao/Know2BIO/.