Chem2Side : A Deep Learning Model with Ensemble Augmentation (Conventional + Pix2Pix) for COVID-19 Drug Side-Effects Prediction from Chemical Images
(2023) In Information (Switzerland) 14(12).- Abstract
Drug side effects (DSEs) or adverse drug reactions (ADRs) are a major concern in the healthcare industry, accounting for a significant number of annual deaths in Europe alone. Identifying and predicting DSEs early in the drug development process is crucial to mitigate their impact on public health and reduce the time and costs associated with drug development. Objective: In this study, our primary objective is to predict multiple drug side effects using 2D chemical structures, especially for COVID-19, departing from the conventional approach of relying on 1D chemical structures. We aim to develop a novel model for DSE prediction that leverages the CNN-based transfer learning architecture of ResNet152V2. Motivation: The motivation behind... (More)
Drug side effects (DSEs) or adverse drug reactions (ADRs) are a major concern in the healthcare industry, accounting for a significant number of annual deaths in Europe alone. Identifying and predicting DSEs early in the drug development process is crucial to mitigate their impact on public health and reduce the time and costs associated with drug development. Objective: In this study, our primary objective is to predict multiple drug side effects using 2D chemical structures, especially for COVID-19, departing from the conventional approach of relying on 1D chemical structures. We aim to develop a novel model for DSE prediction that leverages the CNN-based transfer learning architecture of ResNet152V2. Motivation: The motivation behind this research stems from the need to enhance the efficiency and accuracy of DSE prediction, enabling the pharmaceutical industry to identify potential drug candidates with fewer adverse effects. By utilizing 2D chemical structures and employing data augmentation techniques, we seek to revolutionize the field of drug side-effect prediction. Novelty: This study introduces several novel aspects. The proposed study is the first of its kind to use 2D chemical structures for predicting drug side effects, departing from the conventional 1D approaches. Secondly, we employ data augmentation with both conventional and diffusion-based models (Pix2Pix), a unique strategy in the field. These innovations set the stage for a more advanced and accurate approach to DSE prediction. Results: Our proposed model, named CHEM2SIDE, achieved an impressive average training accuracy of 0.78. Moreover, the average validation and test accuracy, precision, and recall were all at 0.73. When evaluated for COVID-19 drugs, our model exhibited an accuracy of 0.72, a precision of 0.79, a recall of 0.72, and an F1 score of 0.73. Comparative assessments against established transfer learning and machine learning models (VGG16, MobileNetV2, DenseNet121, and KNN) showcased the exceptional performance of CHEM2SIDE, marking a significant advancement in drug side-effect prediction. Conclusions: Our study introduces a groundbreaking approach to predicting drug side effects by using 2D chemical structures and incorporating data augmentation. The CHEM2SIDE model demonstrates remarkable accuracy and outperforms existing models, offering a promising solution to the challenges posed by DSEs in drug development. This research holds great potential for improving drug safety and reducing the associated time and costs.
(Less)
- author
- Arshed, Muhammad Asad ; Ibrahim, Muhammad ; Mumtaz, Shahzad ; Tanveer, Muhammad and Ahmed, Saeed LU
- organization
- publishing date
- 2023-12
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- chemical structure images, COVID-19, deep learning, drug side effects, image classification, machine learning, medicine, Pix2Pix, stable diffusion, transfer learning
- in
- Information (Switzerland)
- volume
- 14
- issue
- 12
- article number
- 663
- publisher
- MDPI AG
- external identifiers
-
- scopus:85180548868
- ISSN
- 2078-2489
- DOI
- 10.3390/info14120663
- language
- English
- LU publication?
- yes
- additional info
- Publisher Copyright: © 2023 by the authors.
- id
- 0b776bcf-11a7-4483-9af3-da697f6403da
- date added to LUP
- 2024-02-05 15:23:15
- date last changed
- 2024-02-05 15:24:33
@article{0b776bcf-11a7-4483-9af3-da697f6403da,
abstract = {{<p>Drug side effects (DSEs) or adverse drug reactions (ADRs) are a major concern in the healthcare industry, accounting for a significant number of annual deaths in Europe alone. Identifying and predicting DSEs early in the drug development process is crucial to mitigate their impact on public health and reduce the time and costs associated with drug development. Objective: In this study, our primary objective is to predict multiple drug side effects using 2D chemical structures, especially for COVID-19, departing from the conventional approach of relying on 1D chemical structures. We aim to develop a novel model for DSE prediction that leverages the CNN-based transfer learning architecture of ResNet152V2. Motivation: The motivation behind this research stems from the need to enhance the efficiency and accuracy of DSE prediction, enabling the pharmaceutical industry to identify potential drug candidates with fewer adverse effects. By utilizing 2D chemical structures and employing data augmentation techniques, we seek to revolutionize the field of drug side-effect prediction. Novelty: This study introduces several novel aspects. The proposed study is the first of its kind to use 2D chemical structures for predicting drug side effects, departing from the conventional 1D approaches. Secondly, we employ data augmentation with both conventional and diffusion-based models (Pix2Pix), a unique strategy in the field. These innovations set the stage for a more advanced and accurate approach to DSE prediction. Results: Our proposed model, named CHEM2SIDE, achieved an impressive average training accuracy of 0.78. Moreover, the average validation and test accuracy, precision, and recall were all at 0.73. When evaluated for COVID-19 drugs, our model exhibited an accuracy of 0.72, a precision of 0.79, a recall of 0.72, and an F1 score of 0.73. Comparative assessments against established transfer learning and machine learning models (VGG16, MobileNetV2, DenseNet121, and KNN) showcased the exceptional performance of CHEM2SIDE, marking a significant advancement in drug side-effect prediction. Conclusions: Our study introduces a groundbreaking approach to predicting drug side effects by using 2D chemical structures and incorporating data augmentation. The CHEM2SIDE model demonstrates remarkable accuracy and outperforms existing models, offering a promising solution to the challenges posed by DSEs in drug development. This research holds great potential for improving drug safety and reducing the associated time and costs.</p>}},
author = {{Arshed, Muhammad Asad and Ibrahim, Muhammad and Mumtaz, Shahzad and Tanveer, Muhammad and Ahmed, Saeed}},
issn = {{2078-2489}},
keywords = {{chemical structure images; COVID-19; deep learning; drug side effects; image classification; machine learning; medicine; Pix2Pix; stable diffusion; transfer learning}},
language = {{eng}},
number = {{12}},
publisher = {{MDPI AG}},
series = {{Information (Switzerland)}},
title = {{Chem2Side : A Deep Learning Model with Ensemble Augmentation (Conventional + Pix2Pix) for COVID-19 Drug Side-Effects Prediction from Chemical Images}},
url = {{http://dx.doi.org/10.3390/info14120663}},
doi = {{10.3390/info14120663}},
volume = {{14}},
year = {{2023}},
}