Interpretable Classification of Bacterial Raman Spectra with Knockoff Wavelets

Published in IEEE Journal of Biomedical and Health Informatics, 2021

Recommended citation: Chia, Sesia, Ho, Jeffrey, Dionne, Cand├Ęs, and Howe (2021). "Interpretable Classification of Bacterial Raman Spectra with Knockoff Wavelets." IEEE J. Biomed. Health. Inform. .


Deep neural networks and other machine learning models are widely applied to biomedical signal data because they can detect complex patterns and compute accurate predictions. However, the difficulty of interpreting such models is a limitation, especially for applications involving high-stakes decision, including the identification of bacterial infections. This paper considers fast Raman spectroscopy data and demonstrates that a logistic regression model with carefully selected features achieves accuracy comparable to that of neural networks, while being much simpler and more transparent. Our analysis leverages wavelet features with intuitive chemical interpretations, and performs controlled variable selection with knockoffs to ensure the predictors are relevant and non-redundant. Although we focus on a particular data set, the proposed approach is broadly applicable to other types of signal data for which interpretability may be important.

Download paper here