Chondrogenic Cancer Grading by combining Machine and Deep Learning with Raman Spectra of Histopathological Tissues

Abstract

Raman spectroscopy (RS) turns out to be a promising tool for cancer di- agnosis. In particular, in the last years several studies have demonstrated how the diagnostic performances of Raman Spectroscopy can be significantly improved by employing Machine Learning (ML) algorithms for the interpre- tation of Raman-based data. In line with these findings, in this paper, we demonstrated how RS coupled with ML allowed to accurately distinguish the three grades of Chondrosarcoma and to distinguish Chondrosarcoma and a benign counterpart called Enchondroma. We obtained such results by ana- lyzing a dataset composed of a relatively small number of Raman spectra, collected in a previous study. Such spectra were acquired from micromet- ric tissue sections with a Confocal Raman Microscope. In particular, we tested the classification performances of a Support Vector Machine and a Random Forest Classifier, as representative of Machine Learning, and two versions of the Multi-Layer Perceptron, as representative of Deep Learning (DL). These models showed excellent classification performances, especially those belonging to DL, with accuracy reaching 99.7%. This outcome makes the aforementioned models a promising route for future improvements of di- agnostic devices focused on detecting bone cancerous tissues. In addition, we highlighted how the ML models studied resulted in slightly worse classifi- cation performances in comparison to DL. Alongside the diagnostic purpose, the aforementioned approach allowed to identify characteristic molecules, i. e. amino acids, nucleic acids and bioapatites, relevant for the obtainment of the final diagnostic response, through the analysis of the so-called Per- mutation Feature Importance. Permutation Feature Importance could hence represent a promising parameter for the understanding of the biochemical processes on the basis of the tumor progression. In turn, the spectral bands highlighted by Permutation Feature Importance could represent precious in- dicators in the attempt to restrict the spectral acquisition to specific Raman bands. This last objective could help to reduce the amount of experimental data needed to obtain an accurate final grading outcome, with consequent reduction of the computational cost.