A Comprehensive Evaluation of Metabolomics Data Preprocessing Methods for Deep Learning

Machine learning has greatly advanced over the past decade, owing to advances in algorithmic innovations, hardware acceleration, and benchmark datasets to train on domains such as computer vision, natural-language processing, and more recently the life sciences. In particular, the subfield of machine learning known as deep learning has found applications in genomics, proteomics, and metabolomics. However, a thorough assessment of how the data preprocessing methods required for the analysis of life science data affect the performance of deep learning is lacking. This work contributes to filling that gap by assessing the impact of commonly used as well as newly developed methods employed in data preprocessing workflows for metabolomics that span from raw data to processed data. The results from these analyses are summarized into a set of best practices that can be used by researchers as a starting point for downstream classification and reconstruction tasks using deep learning.