Predicting the Pathway Involvement of Metabolites Based on Combined Metabolite and Pathway Features

Erik D. Huckvale, Hunter N.B. Moseley

Research output: Contribution to journalArticlepeer-review


A major limitation of most metabolomics datasets is the sparsity of pathway annotations for detected metabolites. It is common for less than half of the identified metabolites in these datasets to have a known metabolic pathway involvement. Trying to address this limitation, machine learning models have been developed to predict the association of a metabolite with a “pathway category”, as defined by a metabolic knowledge base like KEGG. Past models were implemented as a single binary classifier specific to a single pathway category, requiring a set of binary classifiers for generating the predictions for multiple pathway categories. This past approach multiplied the computational resources necessary for training while diluting the positive entries in the gold standard datasets needed for training. To address these limitations, we propose a generalization of the metabolic pathway prediction problem using a single binary classifier that accepts the features both representing a metabolite and representing a pathway category and then predicts whether the given metabolite is involved in the corresponding pathway category. We demonstrate that this metabolite–pathway features pair approach not only outperforms the combined performance of training separate binary classifiers but demonstrates an order of magnitude improvement in robustness: a Matthews correlation coefficient of 0.784 ± 0.013 versus 0.768 ± 0.154.

Original languageEnglish
Article number266
Issue number5
StatePublished - May 2024

Bibliographical note

Publisher Copyright:
© 2024 by the authors.


  • XGBoost
  • binary classification
  • deep learning
  • kyoto encyclopedia of gene and genomes (KEGG)
  • machine learning
  • metabolic pathway
  • metabolism
  • metabolite
  • multilayer perceptron
  • supervised learning

ASJC Scopus subject areas

  • Endocrinology, Diabetes and Metabolism
  • Biochemistry
  • Molecular Biology


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