Neuro-symbolic representation learning on biological knowledge graphs
Khan, Mohammed Asif
Kinjo, Akira R
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
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AbstractBiological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge.We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein-protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of SemanticWeb based knowledge bases in biology to use in machine learning and data analytics.https://email@example.com.Supplementary data are available at Bioinformatics online.
CitationAlshahrani M, Khan MA, Maddouri O, Kinjo AR, Queralt-Rosinach N, et al. (2017) Neuro-symbolic representation learning on biological knowledge graphs. Bioinformatics. Available: http://dx.doi.org/10.1093/bioinformatics/btx275.
SponsorsThis work was supported by funding from King Abdullah University of Science and Technology (KAUST).
PublisherOxford University Press (OUP)
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.