Migrating from partial least squares discriminant analysis to artificial neural networks: a comparison of functionally equivalent visualisation and feature contribution tools using jupyter notebooks

INTRODUCTION: Metabolomics data is commonly modelled multivariately using partial least squares discriminant analysis (PLS-DA). Its success is primarily due to ease of interpretation, through projection to latent structures, and transparent assessment of feature importance using regression coefficients and Variable Importance in Projection scores. In recent years several non-linear machine learning (ML) methods have grown in popularity but with limited uptake essentially due to convoluted optimisation and interpretation. Artificial neural networks (ANNs) are a non-linear projection-based ML method that share a structural equivalence with PLS, and as such should be amenable to equivalent optimisation and interpretation methods. OBJECTIVES: We hypothesise that standardised optimisation, visualisation, evaluation and statistical inference techniques commonly used by metabolomics researchers for PLS-DA can be migrated to a non-linear, single hidden layer, ANN. METHODS: We compared a standardised optimisation, visualisation, evaluation and statistical inference techniques workflow for PLS with the proposed ANN workflow. Both workflows were implemented in the Python programming language. All code and results have been made publicly available as Jupyter notebooks on GitHub. RESULTS: The migration of the PLS workflow to a non-linear, single hidden layer, ANN was successful. There was a similarity in significant metabolites determined using PLS model coefficients and ANN Connection Weight Approach. CONCLUSION: We have shown that it is possible to migrate the standardised PLS-DA workflow to simple non-linear ANNs. This result opens the door for more widespread use and to the investigation of transparent interpretation of more complex ANN architectures. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11306-020-1640-0) contains supplementary material, which is available to authorized users.