Biomedical Knowledge Graph
Biomedical knowledge graphs (BioKGs) are structured representations of biomedical data, aiming to integrate diverse information sources for improved knowledge discovery and application. Current research focuses on enhancing BioKG construction and analysis through advanced techniques like graph neural networks (e.g., message-passing models), contrastive learning for improved term representation and clustering, and the integration of large language models (LLMs) to leverage unstructured text data. These advancements are improving tasks such as link prediction, treatment effect estimation, and drug discovery, ultimately accelerating biomedical research and potentially leading to more effective healthcare solutions. The development of comprehensive, easily updatable BioKGs, like Know2BIO, is also a key area of focus.
Papers
LLM-based SPARQL Query Generation from Natural Language over Federated Knowledge Graphs
Vincent Emonet, Jerven Bolleman, Severine Duvaud, Tarcisio Mendes de Farias, Ana Claudia Sima
A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications
Jerven Bolleman, Vincent Emonet, Adrian Altenhoff, Amos Bairoch, Marie-Claude Blatter, Alan Bridge, Severine Duvaud, Elisabeth Gasteiger, Dmitry Kuznetsov, Sebastien Moretti, Pierre-Andre Michel, Anne Morgat, Marco Pagni, Nicole Redaschi, Monique Zahn-Zabal, Tarcisio Mendes de Farias, Ana Claudia Sima