Classification of pathogenic bacteria by Raman spectroscopy combined with variational auto‐encoder and deep learning

• Published in: Journal of biophotonics 2023-04, Vol.16 (4), p.e202200270-n/a
• Main Authors: Liu, Bo, Liu, Kunxiang, Sun, Jide, Shang, Lindong, Yang, Qingxiang, Chen, Xueping, Li, Bei
• Format: Article
• Language: English
• Subjects: Bacteria; Cell culture; Classification; Coders; Deep Learning; long short‐term memory network; pathogenic bacteria; Pathogens; Raman spectra; Raman spectroscopy; Signal-To-Noise Ratio; Spectroscopy; Spectrum analysis; Spectrum Analysis, Raman; Strains (organisms); Training; variational auto‐encoder
• ISSN: 1864-063X; 1864-0648
• DOI: 10.1002/jbio.202200270

Rapid and early identification of pathogens is critical to guide antibiotic therapy. Raman spectroscopy as a noninvasive diagnostic technique provides rapid and accurate detection of pathogens. Raman spectrum of single cells serves as the “fingerprint” of the cell, revealing its metabolic characteristics. Rapid identification of pathogens can be achieved by combining Raman spectroscopy and deep learning. Traditional classification techniques frequently require lots of data for training, which is time costing to collect Raman spectra. For trace samples and strains that are difficult to culture, it is difficult to provide an accurate classification model. In order to reduce the number of samples collected and improve the accuracy of the classification model, a new pathogen detection method integrating Raman spectroscopy, variational auto‐encoder (VAE), and long short‐term memory network (LSTM) is proposed in this paper. We collect the Raman signals of pathogens and input them to VAE for training. VAE will generate a large number of Raman spectral data that cannot be distinguished from the real spectrum, and the signal‐to‐noise ratio is higher than that of the real spectrum. These spectra are input into the LSTM together with the real spectrum for training, and a good classification model is obtained. The results of the experiments reveal that this method not only improves the average accuracy of pathogen classification to 96.9% but also reduces the number of Raman spectra collected from 1000 to 200. With this technology, the number of Raman spectra collected can be greatly reduced, so that strains that are difficult to culture or trace can be rapidly identified. In this work, a pathogen detection method combining Raman spectroscopy, variational auto‐encoder (VAE) and long short‐term memory network is proposed. Experimental results show that this method not only improves the average accuracy of pathogen classification to 96.9%, but also reduces the number of Raman spectra collected from 1000 to 200. Our method can be applied to other spectral techniques (such as mass spectrometry and infrared spectroscopy) and material identification problems with only a slight adjustment.