Supervised Biomedical Semantic Similarity

Semantic similarity between concepts in knowledge graphs is essential for several bioinformatics applications, including the prediction of protein-protein interactions and the discovery of associations between diseases and genes. Although knowledge graphs describe entities in terms of several perspectives (or semantic aspects), state-of-the-art semantic similarity measures are general-purpose. This can represent a challenge since different use cases for the application of semantic similarity may need different similarity perspectives and ultimately depend on expert knowledge for manual fine-tuning. We present a new approach that uses supervised machine learning to tailor aspect-oriented semantic similarity measures to fit a particular view on biological similarity or relatedness. We implement and evaluate it using different combinations of representative semantic similarity measures and machine learning methods with four biological similarity views: protein-protein interaction, protein function similarity, protein sequence similarity and phenotype-based gene similarity. The results demonstrate that our approach outperforms non-supervised methods, producing semantic similarity models that fit different biological perspectives significantly better than the commonly used manual combinations of semantic aspects.