Explainable AI-Assisted Label-Free Raman Biosensing Reveals Therapy-Associated Spectral Signatures in Melanoma Tumors

Abstract

Sensitive detection of treatment-associated Raman spectral alterations in tumor tissues remains challenging, particularly when such changes are not readily apparent from conventional morphological evaluation. Here, we developed a label-free Raman biosensing strategy combined with explainable machine learning to characterise treatment-associated spectral signatures in melanoma tumours. A B16-F10 melanoma-bearing mouse model was used to compare untreated and PBS-treated controls with cohorts receiving immune checkpoint blockade, anti-angiogenic intervention, or combination therapy. Raman spectra were acquired from multiple spatial regions of melanoma tissues and analyzed using nonlinear dimensionality reduction, supervised classification, and SHAP-based feature interpretation. Although cohort-averaged spectra showed substantial overlap, multivariate analysis revealed treatment-dependent spectral organization, with the combination-treatment cohort showing the most compact and distinguishable spectral profile. Supervised models, including convolutional neural networks, support vector machines, and k-nearest neighbors, further supported the reproducibility of treatment-associated Raman signatures when evaluated using mouse-level validation strategies. SHAP analysis identified discriminative Raman features mainly located within lipid, phospholipid, ester, protein, and collagen-associated vibrational domains, suggesting potential contributions from metabolic- and extracellular-matrix-related biochemical components to treatment-associated spectral discrimination. These findings indicate that Raman spectroscopy integrated with explainable machine learning provides a sensitive, label-free method for distinguishing treatment-associated spectral differences among melanoma tissues. The proposed approach may serve as a complementary spectroscopic tool alongside conventional histological and molecular analyses for investigating treatment-associated tissue-state alterations.