title: Convolutional neural networks for vibrational spectroscopic data analysis.
abstract: In this work we show that convolutional neural networks (CNNs) can be efficiently used to classify vibrational spectroscopic data and identify important spectral regions. CNNs are the current state-of-the-art in image classification and speech recognition and can learn interpretable representations of the data. These characteristics make CNNs a good candidate for reducing the need for preprocessing and for highlighting important spectral regions, both of which are crucial steps in the analysis of vibrational spectroscopic data. Chemometric analysis of vibrational spectroscopic data often relies on preprocessing methods involving baseline correction, scatter correction and noise removal, which are applied to the spectra prior to model building. Preprocessing is a critical step because even in simple problems using 'reasonable' preprocessing methods may decrease the performance of the final model. We develop a new CNN based method and provide an accompanying publicly available software. It is based on a simple CNN architecture with a single convolutional layer (a so-called shallow CNN). Our method outperforms standard classification algorithms used in chemometrics (e.g. PLS) in terms of accuracy when applied to non-preprocessed test data (86% average accuracy compared to the 62% achieved by PLS), and it achieves better performance even on preprocessed test data (96% average accuracy compared to the 89% achieved by PLS). For interpretability purposes, our method includes a procedure for finding important spectral regions, thereby facilitating qualitative interpretation of results.
authors.affiliation: Radboud University Nijmegen, Institute for Computing and Information Science, The Netherlands. Electronic address: j.acquarelli@cs.ru.nl.
authors.forename: Jacopo
authors.initials: J
authors.lastname: Acquarelli
authors.affiliation: Radboud University Nijmegen, Institute for Computing and Information Science, The Netherlands.
authors.forename: Twan
authors.initials: T
authors.lastname: van Laarhoven
authors.affiliation: Radboud University Nijmegen, Institute for Molecules and Materials, The Netherlands.
authors.forename: Jan
authors.initials: J
authors.lastname: Gerretzen
authors.affiliation: Radboud University Nijmegen, Institute for Molecules and Materials, The Netherlands; Center for Mathematical Sciences, Merck, Sharp & Dohme, Oss, The Netherlands.
authors.forename: Thanh N
authors.initials: TN
authors.lastname: Tran
authors.affiliation: Radboud University Nijmegen, Institute for Molecules and Materials, The Netherlands.
authors.forename: Lutgarde M C
authors.initials: LMC
authors.lastname: Buydens
authors.affiliation: Radboud University Nijmegen, Institute for Computing and Information Science, The Netherlands. Electronic address: elenam@cs.ru.nl.
authors.forename: Elena
authors.initials: E
authors.lastname: Marchiori
keywords: Convolutional neural networks; Preprocessing; Vibrational spectroscopy