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

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.

Automated summary

Biomarkers are crucial for assessing health and guiding medical interventions, but they are lacking for many diseases. Mass spectrometry-based proteomics and machine learning can be used for biomarker discovery. To make machine learning more accessible for biomarker discovery, OmicLearn was developed as a browser-based open-source tool.