Dataset Information


Model selection for metabolomics: predicting diagnosis of coronary artery disease using automated machine learning.



Selecting the optimal machine learning (ML) model for a given dataset is often challenging. Automated ML (AutoML) has emerged as a powerful tool for enabling the automatic selection of ML methods and parameter settings for the prediction of biomedical endpoints. Here, we apply the tree-based pipeline optimization tool (TPOT) to predict angiographic diagnoses of coronary artery disease (CAD). With TPOT, ML models are represented as expression trees and optimal pipelines discovered using a stochastic search method called genetic programing. We provide some guidelines for TPOT-based ML pipeline selection and optimization-based on various clinical phenotypes and high-throughput metabolic profiles in the Angiography and Genes Study (ANGES).


We analyzed nuclear magnetic resonance-derived lipoprotein and metabolite profiles in the ANGES cohort with a goal to identify the role of non-obstructive CAD patients in CAD diagnostics. We performed a comparative analysis of TPOT-generated ML pipelines with selected ML classifiers, optimized with a grid search approach, applied to two phenotypic CAD profiles. As a result, TPOT-generated ML pipelines that outperformed grid search optimized models across multiple performance metrics including balanced accuracy and area under the precision-recall curve. With the selected models, we demonstrated that the phenotypic profile that distinguishes non-obstructive CAD patients from no CAD patients is associated with higher precision, suggesting a discrepancy in the underlying processes between these phenotypes.

Availability and implementation

TPOT is freely available via http://epistasislab.github.io/tpot/.

Supplementary information

Supplementary data are available at Bioinformatics online.

PROVIDER: S-EPMC7703753 | BioStudies |

REPOSITORIES: biostudies

Similar Datasets

| S-EPMC7416036 | BioStudies
| S-EPMC6956793 | BioStudies
| S-EPMC7658976 | BioStudies
| S-EPMC7442326 | BioStudies
| S-EPMC7849944 | BioStudies
| S-EPMC7316297 | BioStudies
| S-EPMC8414332 | BioStudies
| S-EPMC5306314 | BioStudies
| S-EPMC6069842 | BioStudies
| S-EPMC7992933 | BioStudies