Please use this identifier to cite or link to this item: https://hdl.handle.net/20.500.11851/8317
Title: A Convolutional Deep Clustering Framework for Gene Expression Time Series
Authors: Özgül, Ozan Frat
Bardak, Batuhan
Tan, Mehmet
Keywords: Time series analysis
Gene expression
Machine learning
Clustering algorithms
Biological system modeling
Trajectory
Biological information theory
Gene expression
clustering
recurrence plots
deep learning
Nf-Kappa-B
Helicobacter-Pylori
Recurrence Plot
Issue Date: 2021
Publisher: Ieee Computer Soc
Abstract: The functional or regulatory processes within the cell are explicitly governed by the expression levels of a subset of its genes. Gene expression time series captures activities of individual genes over time and aids revealing underlying cellular dynamics. An important step in high-throughput gene expression time series experiment is clustering genes based on their temporal expression patterns and is conventionally achieved by unsupervised machine learning techniques. However, most of the clustering techniques either suffer from the short length of gene expression time series or ignore temporal structure of the data. In this work, we propose DeepTrust, a novel deep learning-based framework for gene expression time series clustering which can overcome these issues. DeepTrust initially transforms time series data into images to obtain richer data representations. Afterwards, a deep convolutional clustering algorithm is applied on the constructed images. Analyses on both simulated and biological data sets exhibit the efficiency of this new framework, compared to widely used clustering techniques. We also utilize enrichment analyses to illustrate the biological plausibility of the clusters detected by DeepTrust. Our code and data are available from http://github.com/tanlab/DeepTrust.
URI: https://doi.org/10.1109/TCBB.2020.2988985
https://hdl.handle.net/20.500.11851/8317
ISSN: 1545-5963
1557-9964
Appears in Collections:Bilgisayar Mühendisliği Bölümü / Department of Computer Engineering
PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

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