Special Issue "Deep Learning in Metabolomics"

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Bioinformatics and Data Analysis".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 873

Special Issue Editors

Shenzhen Institute of Agricultural Genomics, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou 518000, China
Interests: deep learning; metabolomics; data analysis; software design; chemometrics
School of Artificial Intelligence and Big Data, Henan University of Technology, Zhengzhou 450001, China
Interests: deep learning; metabolomics; artificial intelligence; big data; chemometrics
Section Editor, Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
Interests: systems biology; translational bioinformatics; biophysical informatics
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Special Issue Information

Dear Colleagues,

Deep learning is a revolutionary technique in artificial intelligence, and has fundamentally changed the machine learning community. Various fields in metabolomics have significantly progressed following the introduction of deep learning, including (but not limited to) metabolic data mining, metabolite identification, biomarker discovery, metabolic network and pathway prediction, and metabolite function prediction. The research paradigm of metabolomics is transforming from experience-driven to data-driven. Such an improvement will provide a less biased and comprehensive view of metabolomics, and lead to a better understanding of the relationship between metabolomics and life activities.

Urgent research targets include improvements in the interpretability and usability of deep learning strategy in metabolomics. For example, designing neural networks with explicit biological meaning specific to metabolomics, designing deep learning algorithms specific to a biological problem, designing software with an integrated interface, and pre-trained model for end-users. This Special Issue will focus on these aims, as well as original research on new deep learning algorithms and applications. We welcome submissions related to biological applications, as well as basic research in computing science within the context of a metabolism problem domain. Insightful reviews and algorithm comparisons are also very welcome.

Dr. Hongchao Ji
Dr. Xiaqiong Fan
Dr. Hunter Moseley
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (1 paper)

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Research

Article
MAD HATTER Correctly Annotates 98% of Small Molecule Tandem Mass Spectra Searching in PubChem
Metabolites 2023, 13(3), 314; https://doi.org/10.3390/metabo13030314 - 21 Feb 2023
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Abstract
Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics usually relies on mass spectrometry, a technology capable of detecting thousands of compounds in a biological sample. Metabolite annotation is executed using tandem mass spectrometry. Spectral library search is far from comprehensive, [...] Read more.
Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics usually relies on mass spectrometry, a technology capable of detecting thousands of compounds in a biological sample. Metabolite annotation is executed using tandem mass spectrometry. Spectral library search is far from comprehensive, and numerous compounds remain unannotated. So-called in silico methods allow us to overcome the restrictions of spectral libraries, by searching in much larger molecular structure databases. Yet, after more than a decade of method development, in silico methods still do not reach the correct annotation rates that users would wish for. Here, we present a novel computational method called Mad Hatter for this task. Mad Hatter combines CSI:FingerID results with information from the searched structure database via a metascore. Compound information includes the melting point, and the number of words in the compound description starting with the letter ‘u’. We then show that Mad Hatter reaches a stunning 97.6% correct annotations when searching PubChem, one of the largest and most comprehensive molecular structure databases. Unfortunately, Mad Hatter is not a real method. Rather, we developed Mad Hatter solely for the purpose of demonstrating common issues in computational method development and evaluation. We explain what evaluation glitches were necessary for Mad Hatter to reach this annotation level, what is wrong with similar metascores in general, and why metascores may screw up not only method evaluations but also the analysis of biological experiments. This paper may serve as an example of problems in the development and evaluation of machine learning models for metabolite annotation. Full article
(This article belongs to the Special Issue Deep Learning in Metabolomics)
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