Insights into heart failure metabolite markers through explainable machine learning

Understanding molecular traits through metabolomics offers an avenue to tailor cardiovascular prevention, diagnosis and treatment strategies more effectively. This study focuses on the application of machine learning (ML) and explainable artificial intelligence (XAI) algorithms to detect discriminant molecular signatures in heart failure (HF). We aim to uncover metabolites with significant predictive value by analyzing targeted metabolomics data through ML and XAI algorithms. After quality control, we analyzed 55 metabolites from 124 plasma samples, including 53 HF patients and 71 controls, comparing Ridge Logistic Regression, Support Vector Machine and eXtreme Gradient Boosting models. All achieved high accuracy in predicting group labels: 84.0% [95% CI: 75.3 - 92.7], 85.73 [95% CI: 78.6 - 92.9], and 84.8% [95% CI: 76.1 - 93.5], respectively. Permutation-based variable importance and Local Interpretable Model-agnostic Explanations (LIME) were used for group-level and individual-level explainability, respectively, complemented by H-Friedman statistics for variable interactions, yielding reliable, explainable insights of the ML models. Metabolites well-known for their association with HF, such as glucose and cholesterol, and more recently described, the C18:1 carnitine, were reaffirmed in our analysis. The novel discovery of lignoceric acid (C24:0 fatty acid) as a critical discriminator, was confirmed in a replication cohort, underscoring its potential as a metabolite marker. Furthermore, our study highlights the utility of 2-way variable interaction analysis in unveiling a network of metabolite interactions essential for accurate disease prediction. The results demonstrate our approach's efficacy in identifying key metabolites and their interactions, illustrating the power of ML and XAI in advancing personalized healthcare solutions.