An Explainable Approach to Parkinson’s Diagnosis Using the Contrastive Explanation Method—CEM

<b>Background/Objectives:</b> Parkinson's disease (PD) is a progressive neurodegenerative disorder that requires early and accurate diagnosis. This study aimed to classify individuals with and without PD using volumetric brain MRI data and to improve model interpretability using explainable artificial intelligence (XAI) techniques. <b>Methods:</b> This retrospective study included 79 participants (39 PD patients, 40 controls) recruited at Inonu University Turgut Ozal Medical Center between 2013 and 2025. A deep neural network (DNN) was developed using a multilayer perceptron architecture with six hidden layers and ReLU activation functions. Seventeen volumetric brain features were used as the input. To ensure robust evaluation and prevent overfitting, a stratified five-fold cross-validation was applied, maintaining class balance in each fold. Model transparency was explored using two complementary XAI techniques: the Contrastive Explanation Method (CEM) and Local Interpretable Model-Agnostic Explanations (LIME). CEM highlights features that support or could alter the current classification, while LIME provides instance-based feature attributions. <b>Results:</b> The DNN model achieved high diagnostic performance with 94.1% accuracy, 98.3% specificity, 90.2% sensitivity, and an AUC of 0.97. The CEM analysis suggested that reduced hippocampal volume was a key contributor to PD classification (-0.156 PP), whereas higher volumes in the brainstem and hippocampus were associated with the control class (+0.035 and +0.150 PP, respectively). The LIME results aligned with these findings, revealing consistent feature importance (mean = 0.1945) and faithfulness (0.0269). Comparative analyses showed different volumetric patterns between groups and confirmed the DNN's superiority over conventional machine learning models such as SVM, logistic regression, KNN, and AdaBoost. <b>Conclusions:</b> This study demonstrates that a deep learning model, enhanced with CEM and LIME, can provide both high diagnostic accuracy and interpretable insights for PD classification, supporting the integration of explainable AI in clinical neuroimaging.