Deep learning optimization for drug-target interaction prediction in COVID-19 using graphic processing unit

Refianto Damai Darmawan, Wisnu Ananta Kusuma, Hendra Rahmawan

Abstract


The exponentially increasing bioinformatics data raised a new problem: the computation time length. The amount of data that needs to be processed is not matched by an increase in hardware performance, so it burdens researchers on computation time, especially on drug-target interaction prediction, where the computational complexity is exponential. One of the focuses of high-performance computing research is the utilization of the graphics processing unit (GPU) to perform multiple computations in parallel. This study aims to see how well the GPU performs when used for deep learning problems to predict drug-target interactions. This study used the gold-standard data in drug-target interaction (DTI) and the coronavirus disease (COVID-19) dataset. The stages of this research are data acquisition, data preprocessing, model building, hyperparameter tuning, performance evaluation and COVID-19 dataset testing. The results of this study indicate that the use of GPU in deep learning models can speed up the training process by 100 times. In addition, the hyperparameter tuning process is also greatly helped by the presence of the GPU because it can make the process up to 55 times faster. When tested using the COVID-19 dataset, the model showed good performance with 76% accuracy, 74% F-measure and a speed-up value of 179.

Keywords


bioinformatics; deep learning; drug-target interaction; graphic processing unit; high performance computing;

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DOI: http://doi.org/10.11591/ijece.v13i3.pp3111-3123

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International Journal of Electrical and Computer Engineering (IJECE)
p-ISSN 2088-8708, e-ISSN 2722-2578