Transparent Exploration of Machine Learning for Biomarker Discovery from Proteomics and Omics Data

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  • Furkan M. Torun
  • Sebastian Virreira Winter
  • Sophia Doll
  • Felix M. Riese
  • Artem Vorobyev
  • Johannes B. Mueller-Reif
  • Philipp E. Geyer
  • Strauss, Maximilian

Biomarkers are of central importance for assessing the health state and to guide medical interventions and their efficacy; still, they are lacking for most diseases. Mass spectrometry (MS)-based proteomics is a powerful technology for biomarker discovery but requires sophisticated bioinformatics to identify robust patterns. Machine learning (ML) has become a promising tool for this purpose. However, it is sometimes applied in an opaque manner and generally requires specialized knowledge. To enable easy access to ML for biomarker discovery without any programming or bioinformatics skills, we developed "OmicLearn"(http://OmicLearn.org), an open-source browser-based ML tool using the latest advances in the Python ML ecosystem. Data matrices from omics experiments are easily uploaded to an online or a locally installed web server. OmicLearn enables rapid exploration of the suitability of various ML algorithms for the experimental data sets. It fosters open science via transparent assessment of state-of-the-art algorithms in a standardized format for proteomics and other omics sciences.

Original languageEnglish
JournalJournal of Proteome Research
Volume22
Issue number2
Pages (from-to)359-367
ISSN1535-3893
DOIs
Publication statusPublished - 2023

Bibliographical note

Publisher Copyright:
© 2022 The Authors. Published by American Chemical Society.

    Research areas

  • diagnostics, machine learning, mass spectrometry, metabolome, omics, proteome, transcriptome

ID: 329284339