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Current Bioinformatics

Editor-in-Chief

ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

Research Article

Deep Learning Model for Pathogen Classification Using Feature Fusion and Data Augmentation

Author(s): Fareed Ahmad*, Amjad Farooq and Muhammad Usman Ghani Khan

Volume 16, Issue 3, 2021

Published on: 07 July, 2020

Page: [466 - 483] Pages: 18

DOI: 10.2174/1574893615999200707143535

Price: $65

Abstract

Background: Bacterial pathogens are deadly for animals and humans. The ease of their dissemination, coupled with their high capacity for ailments and death in infected individuals, makes them a threat to society.

Objective: Due to the high similarity among genera and species of pathogens, it is sometimes difficult for microbiologists to differentiate between them. Their automatic classification using deeplearning models can help in gaining reliable and accurate outcomes.

Methods: Deep-learning models, namely; AlexNet, GoogleNet, ResNet101, and InceptionV3 are used with numerous variations including training model from scratch, fine-tuning without pre-trained weights, fine-tuning along with freezing weights of initial layers, fine-tuning along with adjusting weights of all layers and augmenting the dataset by random translation and reflection. Moreover, as the dataset is small, fine-tuning and data augmentation strategies are applied to avoid overfitting and produce a generalized model. A merged feature vector is produced using two best-performing models and accuracy is calculated by xgboost algorithm on the feature vector by applying cross-validation.

Results: Fine-tuned models where augmentation is applied produces the best results. Out of these, two-best-performing deep models i.e. (ResNet101, and InceptionV3) selected for feature fusion, produced a similar validation accuracy of 95.83 with a loss of 0.0213 and 0.1066, and testing accuracy of 97.92 and 93.75, respectively. The proposed model used xgboost to attain a classification accuracy of 98.17% by using 35-folds cross-validation.

Conclusion: The automatic classification using these models can help experts in the correct identification of pathogens. Consequently, they can help in controlling epidemics and thereby minimizing the socio-economic impact on the community.

Keywords: Pathogen classification, augmentation, feature fusion, deep learning models, fine-tuning, transfer learning, zoonotic diseases, disease outbreaks.

Graphical Abstract
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