Augmenting nutritional metabolomics with a genome-scale metabolic model for assessment of diet intake

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Metabolomics-based diet assessment and diet-specific biomarker metabolites identification are becoming ubiquitous. Existing studies offer a limited understanding of the underlying biochemical dynamics due to a lack of information on the holistic metabolic system changing the metabolite concentrations. Moreover, small cohort sizes of feeding trials inhibit the applicability of automated representation learning-based empirical performance improvement. In this work, we integrate prior knowledge of the human metabolic system, specifically from a genome-scale metabolic model, with metabolomic concentrations to draw novel insights into diet-related metabolism and improve dietary intake assessment. We propose multiple feature design approaches utilizing such integration - including the construction and analysis of a heterogeneous knowledge network. The proposed features offer novel hypotheses for a deeper understanding of the underlying diet-specific metabolism - such as prospective metabolic reactions and metabolic subsystems involved in the biomechanism. Our proposed features also often exceed or match baseline empirical performances of diet assessment, when used alone or together with metabolite concentrations.

Original languageEnglish (US)
Title of host publicationACM-BCB 2023 - 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
PublisherAssociation for Computing Machinery
ISBN (Electronic)9798400701269
DOIs
StatePublished - Sep 3 2023
Event14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2023 - Houston, United States
Duration: Sep 3 2023Sep 6 2023

Publication series

NameACM-BCB 2023 - 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

Conference

Conference14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2023
Country/TerritoryUnited States
CityHouston
Period9/3/239/6/23

Keywords

  • diet assessment
  • knowledge network
  • knowledge-based feature design
  • metabolic model
  • nutritional metabolomics

ASJC Scopus subject areas

  • Computer Science Applications
  • Software
  • Biomedical Engineering
  • Health Informatics

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