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Subtask-aware Representation Learning for Predicting Antibiotic Resistance Gene Properties via Gating-controlled Mechanism
Journal article   Open access   Peer reviewed

Subtask-aware Representation Learning for Predicting Antibiotic Resistance Gene Properties via Gating-controlled Mechanism

Weizhong Zhao, Junze Wu, Shujie Luo, Xingpeng Jiang, Tingting He and Xiaohua Hu
IEEE journal of biomedical and health informatics, pp 1-13
19 Apr 2024
DOI: https://doi.org/10.1109/JBHI.2024.3390246
PMID: 38640044
Featured in Collection :   UN Sustainable Development Goals @ Drexel
url
https://github.com/David-WZhao/GCM-ARG .View
DataThe data and source codes are available in GitHubOpen Access (License Unspecified),  Open

Abstract

Antibiotic Resistance Gene Gating-controlled Mechanism Multi-task Learning Multitasking Poles and towers Representation learning Subtask-aware Representation Learning Training Amino Acids Antibiotics Immune System
The crisis of antibiotic resistance has become a significant global threat to human health. Understanding properties of antibiotic resistance genes (ARGs) is the first step to mitigate this issue. Although many methods have been proposed for predicting properties of ARGs, most of these methods focus only on predicting antibiotic classes, while ignoring other properties of ARGs, such as resistance mechanisms and transferability. However, acquiring all of these properties of ARGs can help researchers gain a more comprehensive understanding of the essence of antibiotic resistance, which will facilitate the development of antibiotics. In this paper, the task of predicting properties of ARGs is modeled as a multi-task learning problem, and an effective subtask-aware representation learning-based framework is proposed accordingly. More specifically, property-specific expert networks and shared expert networks are utilized respectively to learn subtask-specific features for each subtask and shared features among different subtasks. In addition, a gating-controlled mechanism is employed to dynamically allocate weights to subtask-specific semantics and shared semantics obtained respectively from property-specific expert networks and shared expert networks, thus adjusting distinctive contributions of subtask-specific features and shared features to achieve optimal performance for each subtask simultaneously. Extensive experiments are conducted on publicly available data, and experimental results demonstrate the effectiveness of the proposed framework on the task of ARGs properties prediction. The data and source codes are available in GitHub at https://github.com/David-WZhao/GCM-ARG .

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2 citations in Web of Science
2 citations in Scopus

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UN Sustainable Development Goals (SDGs)

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#3 Good Health and Well-Being

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Collaboration types
Domestic collaboration
International collaboration
Web of Science research areas
Computer Science, Information Systems
Computer Science, Interdisciplinary Applications
Mathematical & Computational Biology
Medical Informatics
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