Deep Learning to Classify Bacterial Species in the same Genus

Abstract

Bacterial strains in the same genus share highly similar morphology, gram-staining characteristics, colony sizes, and spatial arrangements. Therefore, identifying them by deep learning can be quite challenging. This study aimed to assess the classification of 7 species of bacteria from 2 genera of Bacillus and Vibrio by using 8 Convolutional Neural Network (CNN) models. We implemented Python programming along with Keras API within the Jupyter Notebook. The models were constructed and evaluated under unbalanced and balanced datasets by augmentation (rotation, flip, etc.). Transfer learning with fine-tuning, and pre-processing of mixup and label smoothing were also applied to reduce overfitting and enhance generalization. Based on the experimental results on private dataset, the results of InceptionResNetV2 emerged as the top-performing model with a notable accuracy of 82.8%, 88.6% precision, 78.4% recall, and 78.0% F1-score when label smoothing was applied at 0.5 on balanced dataset.