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Currently, viral infection diseases cause high mortality rates all over the world such as Ebola, HIV, H5N1, and COVID-19. Nowadays, gene-based therapeutic or personalized medicines are considered in clinical decisions for treating patients. Furthermore, medicines from natural sources such as plant-derived medicine or herbs are wildly used because of easy accessibility, lessor side effects, safer and cheaper. Therefore, this study aims to identify 1) microRNA-target gene interaction of the genes that involve in anti-virus infection by applying various individual classification techniques and the ensemble technique and 2) the combination of phytochemicals compounds that possibly be potential drugs to treat specific biological pathways related to viral infection using clustering technique named MCODE. Our outcome of the present work is to contribute to the discovery of genetic-based therapy and to identify the phytochemical compounds for increasing the efficacy of the treatment of diseases caused by viruses with minor side effects.