Protocol for constructing correlation-based molecular networks from large-scale untargeted metabolomics data

This protocol describes a computational approach for constructing correlation-based molecular networks from untargeted metabolomics data using MetVAE, a variational autoencoder-based framework. Complementing spectral similarity networks, it captures functional relationships reflected in cross-sample correlations. The workflow imports metabolomics features and sample metadata, adjusts for compositionality, missingness, confounding, and high-dimensionality, estimates sparse metabolite correlations, and exports GraphML files for network visualization. In a hepatocellular carcinoma mouse model, it links lipid classes in high-fat-diet animals, suggesting an endogenous "auto-brewery" route to lipotoxic metabolites.