Integrated Biomarker–Volumetric Profiling Defines Neurodegenerative Subtypes and Predicts Neuroaxonal Injury in Multiple Sclerosis Based on Bayesian and Machine Learning Analyses

Background: The clinical–radiological paradox in multiple sclerosis (MS) underscores the need for biomarkers that better reflect neurodegenerative pathology. Serum neurofilament light chain (sNfL) is a dynamic marker of neuroaxonal injury, while brain volumetry provides structural assessment of disease impact. However, the precise link between sNfL and regional atrophy patterns, as well as their combined utility for patient stratification and prediction, remains underexplored. Objective: This study aimed to establish a multimodal biomarker framework by integrating sNfL with comprehensive volumetric MRI to define neurodegenerative endophenotypes and predict neuroaxonal injury using Bayesian inference and machine learning. Methods: In a cohort of 57 MS patients, sNfL levels were measured using single-molecule array (Simoa) technology. Brain volumes for 42 regions were quantified via automated deep learning segmentation (mdbrain software). We employed (1) Bayesian correlation to quantify evidence for sNfL–volumetric associations; (2) mediation analysis to test whether grey matter atrophy mediates the EDSS–sNfL (Expanded Disability Status Scale) relationship; (3) unsupervised K-means clustering to identify patient subtypes based on combined sNfL–volumetric profiles; and (4) supervised machine learning (Elastic Net and Random Forest regression) to predict sNfL from volumetric features. Results: Bayesian analysis revealed strong evidence linking sNfL to total grey matter volume (r = −0.449, BF10 = 0.022) and lateral ventricular volume (r = 0.349, BF10 = 0.285). Mediation confirmed that grey matter atrophy significantly mediates the relationship between EDSS and sNfL (indirect effect = 0.45, 95% CI [0.20, 0.75]). Unsupervised clustering identified three distinct endophenotypes: “High Neurodegeneration” (elevated sNfL, severe atrophy, high disability), “Moderate Injury,” and “Benign Volumetry” (low sNfL, preserved volumes, mild disability). Supervised models predicted sNfL with high accuracy (R2 = 0.65), identifying total grey matter volume, ventricular volume, and age as top predictors. Conclusions: This integrative multi-method analysis demonstrates that sNfL is robustly associated with global grey matter and ventricular volumes, and that these measures define clinically meaningful neurodegenerative subtypes in MS. Machine learning confirms that a concise set of volumetric features can effectively predict neuroaxonal injury. These findings advance a pathobiology-driven subtyping framework and provide a validated model for using routine MRI volumetry to assess neuroaxonal health, with implications for prognosis and personalised therapeutic strategies.