Deep autoencoder based hybrid dimensionality reduction approach for classification of SERS for melanoma cancer diagnostics

Abstract

Melanoma, a kind of fatal skin cancer, originates in melanin secreting cells of the dermis. Disease identification in the early stages assures a high survival rate for the patient. Most of the existing techniques retard the cancer detection phase. Surface-Enhanced Raman Spectroscopy (SERS) can capture fine details from the specimens that machine learning models can utilize to discriminate between healthy and diseased individuals rapidly. Our research work proposes a deep autoencoder based hybrid dimensionality reduction approach with a machine learning model on SERS spectrums of human skin fibroblast for melanoma cancer diagnostics. SERS measurements of 307 samples in total, belonging to two different classes, such as normal (157 samples) and malignant melanoma (150 samples), are used in this study. The SERS spectra measurements for both the samples lie between 100cm-1 and 4278cm-1. The variations in the intensity of Raman bands between both classes are intrinsically subtle. Neighborhood Component Analysis (NCA) technique has been exerted to transform 2090 dimensional spectral features into 2090 dimensional vectors and then the Deep Autoencoder (DAE) model is used to handle the nonlinearity in the data and produce the latent space, while Linear Discriminant Analysis (LDA) classifier have been employed for discriminating the normal and cancer cells. The k-fold cross-validation technique with a k value of 10 is implemented to assess the metrics of the model. The stated hybrid (NCA and DAE) model with 10-dimension latent space achieves an accuracy of 98%, the sensitivity of 99% and specificity of 97%, respectively. Due to the high-intensity nature of the SERS spectrum, the existing linear dimensionality reduction based discriminating model fails if the class label (Normal or Cancer) gets distributed on the low variance side. The proposed methodology captures both linear and nonlinear underlying structures present in the spectrums, resulting in better classification compared to the standard dimensionality reduction techniques.