Deep Learning as an Improved Method of Preprocessing Biomedical Raman Spectroscopy Data

Abstract

Machine learning has had a significant impact on the value of spectroscopy-based characterization tools, particularly in biomedical applications, due to its ability to detect latent patterns within complex spectral data. However, it often requires extensive data preprocessing, including baseline correction and denoising, which can lead to unintentional bias during classification. To address this, we present a deep learning-based signal preprocessing method capable of handling all the defects of raw Raman spectroscopy data without any need of human intervention. To achieve this, a novel deep convolutional neural network (CNN) architecture was trained on randomly generated spectra with various defects. We demonstrate that the proposed network results in faster training and that it can perform complete spectral preprocessing in a single step with more accuracy, speed, and defect tolerance than conventional methods. These improvements make it an ideal candidate for hyperspectral imaging applications in which tens of thousands of raw spectra may need to be processed rapidly. The superiority of this method is demonstrated for simulated Raman spectra, surface-enhanced Raman spectroscopy (SERS) imaging of chemical species, classification of low resolution Raman spectra of human bladder cancer tissue, and finally classification of SERS spectra from human placental extracellular vesicles (EVs). These findings encourage the future use of deep learning as a rapid and unbiased method of preprocessing spectroscopy data and may be particularly useful in biomedical applications involving large data sets from highly heterogeneous samples and signal defects of complex nature.

Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms

“…Pre-processing involves the application of specific methods to eliminate undesired contributions or disturbances that originate from the instrument or the sample. Its primary purpose is to refine the measured data by removing these unwanted effects, thereby isolating and enhancing the pure Raman signal of interest, facilitating more accurate and meaningful analysis [ 279 , 280 , 281 , 282 ]. This pre-processing workflow typically begins with a baseline correction, as the Raman spectra often share the same energy range as fluorescence, causing an overlap.…”