Biomedical Knowledge Graphs Construction From Conditional Statements.
Journal:
IEEE/ACM transactions on computational biology and bioinformatics
Published Date:
Jan 1, 2021
Abstract
Conditions play an essential role in biomedical statements. However, existing biomedical knowledge graphs (BioKGs) only focus on factual knowledge, organized as a flat relational network of biomedical concepts. These BioKGs ignore the conditions of the facts being valid, which loses essential contexts for knowledge exploration and inference. We consider both facts and their conditions in biomedical statements and proposed a three-layered information-lossless representation of BioKG. The first layer has biomedical concept nodes, attribute nodes. The second layer represents both biomedical fact and condition tuples by nodes of the relation phrases, connecting to the subject and object in the first layer. The third layer has nodes of statements connecting to a set of fact tuples and/or condition tuples in the second layer. We transform the BioKG construction problem into a sequence labeling problem based on a novel designed tag schema. We design a Multi-Input Multi-Output sequence labeling model (MIMO) that learns from multiple input signals and generates proper number of multiple output sequences for tuple extraction. Experiments on a newly constructed dataset show that MIMO outperforms the existing methods. Further case study demonstrates that the BioKGs constructed provide a good understanding of the biomedical statements.