Tuning hyperparameters of machine learning algorithms and deep neural networks using metaheuristics: A bioinformatics study on biomedical and biological cases

Nematzadeh S., Kiani F., Torkamanian-Afshar M., AYDIN N.

COMPUTATIONAL BIOLOGY AND CHEMISTRY, vol.97, 2022 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 97
  • Publication Date: 2022
  • Doi Number: 10.1016/j.compbiolchem.2021.107619
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, Applied Science & Technology Source, BIOSIS, Biotechnology Research Abstracts, Chemical Abstracts Core, Chimica, Compendex, Computer & Applied Sciences, EMBASE, INSPEC, MEDLINE, zbMATH
  • Keywords: Tuning, Hyperparameters, Machine learning, Deep learning, Metaheuristics, Bioinformatics
  • Yıldız Technical University Affiliated: Yes


The performance of a model in machine learning problems highly depends on the dataset and training algorithms. Choosing the right training algorithm can change the tale of a model. While some algorithms have a great performance in some datasets, they may fall into trouble in other datasets. Moreover, by adjusting hyper parameters of an algorithm, which controls the training processes, the performance can be improved. This study contributes a method to tune hyperparameters of machine learning algorithms using Grey Wolf Optimization (GWO) and Genetic algorithm (GA) metaheuristics. Also, 11 different algorithms including Averaged Perceptron, FastTree, FastForest, Light Gradient Boost Machine (LGBM), Limited memory Broyden Fletcher Goldfarb Shanno algorithm Maximum Entropy (LbfgsMxEnt), Linear Support Vector Machine (LinearSVM), and a Deep Neural Network (DNN) including four architectures are employed on 11 datasets in different biological, biomedical, and nature categories such as molecular interactions, cancer, clinical diagnosis, behavior related predictions, RGB images of human skin, and X-rays images of Covid19 and cardiomegaly patients. Our results show that in all trials, the performance of the training phases is improved. Also, GWO demonstrates a better performance with a p-value of 2.6E-5. Moreover, in most experiment cases of this study, the metaheuristic methods demonstrate better performance and faster convergence than Exhaustive Grid Search (EGS). The proposed method just receives a dataset as an input and suggests the best-explored algorithm with related arguments. So, it is appropriate for datasets with unknown distribution, machine learning algorithms with complex behavior, or users who are not experts in analytical statistics and data science algorithms.