NASMDR: a framework for miRNA-drug resistance prediction using efficient neural architecture search and graph isomorphism networks

Abstract As a frontier field of individualized therapy, microRNA (miRNA) pharmacogenomics facilitates the understanding of different individual responses to certain drugs and provides a reasonable reference for clinical treatment. However, the known drug resistance-associated miRNAs are not yet suff...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Briefings in bioinformatics 2022-09, Vol.23 (5)
Hauptverfasser: Zheng, Kai, Zhao, Haochen, Zhao, Qichang, Wang, Bin, Gao, Xin, Wang, Jianxin
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext bestellen
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung:Abstract As a frontier field of individualized therapy, microRNA (miRNA) pharmacogenomics facilitates the understanding of different individual responses to certain drugs and provides a reasonable reference for clinical treatment. However, the known drug resistance-associated miRNAs are not yet sufficient to support precision medicine. Although existing methods are effective, they all focus on modelling miRNA-drug resistance interaction graphs, making their performance bounded by the interaction density. In this study, we propose a framework for miRNA-drug resistance prediction through efficient neural architecture search and graph isomorphism networks (NASMDR). NASMDR uses attribute information instead of the commonly used interactive graph information. In the cross-validation experiment, the proposed framework can achieve an AUC of 0.9468 on the ncDR dataset, which is 2.29% higher than the state-of-the-art method. In addition, we propose a novel sequence characterization approach, k-mer Sparse Nonnegative Matrix Factorization (KSNMF). The results show that NASMDR provides novel insights for integrating efficient neural architecture search and graph isomorphic networks into a unified framework to predict drug resistance-related miRNAs. The codes for NASMDR are available at https://github.com/kaizheng-academic/NASMDR.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbac338