RNCE: network integration with reciprocal neighbors contextual encoding for multi-modal drug community study on cancer targets

Mining drug targets and mechanisms of action (MoA) for novel anticancer drugs from pharmacogenomic data is a path to enhance the drug discovery efficiency. Recent approaches have successfully attempted to discover targets/MoA by characterizing drug similarities and communities with integrative methods on multi-modal or multi-omics drug information. However, the sparse and imbalanced community size structure of the drug network is seldom considered in recent approaches. Consequently, we developed a novel network integration approach accounting for network structure by a Reciprocal nearest Neighbor and Contextual information Encoding (RNCE) approach. In addition, we proposed a tailor-made clustering algorithm to perform drug community detection on drug networks. RNCE and spectral clustering are proved to outperform state-of-the-art approaches in a series of tests, including network similarity tests and community detection tests on two drug databases. The observed improvement of RNCE can contribute to the field of drug discovery and the related multi-modal/multi-omics integrative studies.