Application of network link prediction in drug discovery

• Published in: BMC bioinformatics Vol. 22; no. 1; pp. 187 - 21
• Main Authors: Abbas, Khushnood, Abbasi, Alireza, Dong, Shi, Niu, Ling, Yu, Laihang, Chen, Bolun, Cai, Shi-Min, Hasan, Qambar
• Format: Journal Article
• Language: English
• Published: England BioMed Central 12.04.2021; BMC
• Subjects: Algorithms; Biomedical data; Clinical trials; Complex systems; Computer applications; Data-driven drug discovery; Datasets; Deep learning; Disease; Drug Discovery; Drug Interactions; Drug-target prediction; Drugs; Gene expression; Graph representations; Graphical representations; Learning algorithms; Ligands; Machine Learning; Model testing; Network analysis; Network link prediction; Neural networks; Performance evaluation; Pharmaceuticals; Poly-pharmacy; Poly-pharmacy side effects prediction; Predictions; Protein interaction; Proteins; R&D; Research & development; Therapeutic targets; Drug-target prediction; Poly-pharmacy; Network link prediction; Poly-pharmacy side effects prediction; Data-driven drug discovery
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-021-04082-y

Technological and research advances have produced large volumes of biomedical data. When represented as a network (graph), these data become useful for modeling entities and interactions in biological and similar complex systems. In the field of network biology and network medicine, there is a particular interest in predicting results from drug-drug, drug-disease, and protein-protein interactions to advance the speed of drug discovery. Existing data and modern computational methods allow to identify potentially beneficial and harmful interactions, and therefore, narrow drug trials ahead of actual clinical trials. Such automated data-driven investigation relies on machine learning techniques. However, traditional machine learning approaches require extensive preprocessing of the data that makes them impractical for large datasets. This study presents wide range of machine learning methods for predicting outcomes from biomedical interactions and evaluates the performance of the traditional methods with more recent network-based approaches. We applied a wide range of 32 different network-based machine learning models to five commonly available biomedical datasets, and evaluated their performance based on three important evaluations metrics namely AUROC, AUPR, and F1-score. We achieved this by converting link prediction problem as binary classification problem. In order to achieve this we have considered the existing links as positive example and randomly sampled negative examples from non-existant set. After experimental evaluation we found that Prone, ACT and [Formula: see text] are the top 3 best performers on all five datasets. This work presents a comparative evaluation of network-based machine learning algorithms for predicting network links, with applications in the prediction of drug-target and drug-drug interactions, and applied well known network-based machine learning methods. Our work is helpful in guiding researchers in the appropriate selection of machine learning methods for pharmaceutical tasks.