Recommender system based on Convolutional Recurrent Deep Learning for protein-drug interaction prediction

• Published in: Expert systems with applications 2024-07, Vol.245, p.123090, Article 123090
• Main Authors: Harrouche, Oussama, Yamina, Mohamed Ben Ali
• Format: Article
• Language: English
• Subjects: Bioinformatics; Collaborative filtering; Matrix completion; Neural network; Recommender system
• ISSN: 0957-4174; 1873-6793
• DOI: 10.1016/j.eswa.2023.123090

The tremendous growth the pharmaceutical field witnessed especially concerning drug-development, caused drug-related experiments such as those concerned with estimating their interactions with targets harder to conduct. This issue led researchers to transition from vivo and vitro to selico experimenting methods, which deploy artificial intelligence (AI) techniques such as recommender systems (RS) to solve problems at hand. However, most RSs depend on global features such as indices, which render them incapable of fully understanding the behaviors of individuals. In this paper, we introduce our Convolutional Recurrent Deep Learning model-based RS approach, or ‘RSCRDL’, which tackles the interaction prediction problem from a natural language processing approach’s (NLP) point of view. RSCDRL processes the textual representations of both protein sequences and drugs in order to learn the implicit features of the tokens forming them, rendering it able to process unseen and non-reactive individuals indirectly. We also present a greedier variant of RSCRDL that can exploit additional drugs explicit features for better predictive abilities. Experiments performed on two real-world datasets show significant outperformance achieved by our models over two general-purpose state-of-the-art RSs, while other experiments conducted on orphan protein sequences helped deduce drug candidates that are assumed to be capable of inhibiting their activities.