CRISP: a deep learning architecture for GC × GC-TOFMS contour ROI identification, simulation and analysis in imaging metabolomics
2
Issued Date
2022-03-10
Resource Type
eISSN
14774054
Scopus ID
2-s2.0-85127523691
Pubmed ID
35022651
Journal Title
Briefings in bioinformatics
Volume
23
Issue
2
Rights Holder(s)
SCOPUS
Bibliographic Citation
Briefings in bioinformatics Vol.23 No.2 (2022)
Suggested Citation
Mathema V.B., Duangkumpha K., Wanichthanarak K., Jariyasopit N., Dhakal E., Sathirapongsasuti N., Kitiyakara C., Sirivatanauksorn Y., Khoomrung S. CRISP: a deep learning architecture for GC × GC-TOFMS contour ROI identification, simulation and analysis in imaging metabolomics. Briefings in bioinformatics Vol.23 No.2 (2022). doi:10.1093/bib/bbab550 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/106806
Title
CRISP: a deep learning architecture for GC × GC-TOFMS contour ROI identification, simulation and analysis in imaging metabolomics
Corresponding Author(s)
Other Contributor(s)
Abstract
Two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) provides a large amount of molecular information from biological samples. However, the lack of a comprehensive compound library or customizable bioinformatics tool is currently a challenge in GC × GC-TOFMS data analysis. We present an open-source deep learning (DL) software called contour regions of interest (ROI) identification, simulation and untargeted metabolomics profiler (CRISP). CRISP integrates multiple customizable deep neural network architectures for assisting the semi-automated identification of ROIs, contour synthesis, resolution enhancement and classification of GC × GC-TOFMS-based contour images. The approach includes the novel aggregate feature representative contour (AFRC) construction and stacked ROIs. This generates an unbiased contour image dataset that enhances the contrasting characteristics between different test groups and can be suitable for small sample sizes. The utility of the generative models and the accuracy and efficacy of the platform were demonstrated using a dataset of GC × GC-TOFMS contour images from patients with late-stage diabetic nephropathy and healthy control groups. CRISP successfully constructed AFRC images and identified over five ROIs to create a deepstacked dataset. The high fidelity, 512 × 512-pixels generative model was trained as a generator with a Fréchet inception distance of <47.00. The trained classifier achieved an AUROC of >0.96 and a classification accuracy of >95.00% for datasets with and without column bleed. Overall, CRISP demonstrates good potential as a DL-based approach for the rapid analysis of 4-D GC × GC-TOFMS untargeted metabolite profiles by directly implementing contour images. CRISP is available at https://github.com/vivekmathema/GCxGC-CRISP.