Brain Tumor Classification from 3D MRI Using Persistent Homology and Betti Features: A Topological Data Analysis Approach on BraTS2020

Abstract

Accurate and interpretable brain tumor classification from medical imaging remains a challenging problem due to the high dimensionality and complex structural patterns present in magnetic resonance imaging (MRI). In this study, we propose a topology-driven framework for brain tumor classification based on Topological Data Analysis (TDA) applied directly to three-dimensional (3D) MRI volumes. Specifically, we analyze 3D Fluid Attenuated Inversion Recovery (FLAIR) images from the BraTS 2020 dataset and extract interpretable topological descriptors using persistent homology. Persistent homology captures intrinsic geometric and structural characteristics of the data through Betti numbers, which describe connected components (Betti-0), loops (Betti-1), and voids (Betti-2). From the 3D MRI volumes, we derive a compact set of 100 topological features that summarize the underlying topology of brain tumor structures. These descriptors represent complex 3D tumor morphology while significantly reducing data dimensionality. Unlike many deep learning approaches that require large-scale training data or complex architectures, the proposed framework relies on computationally efficient topological features extracted directly from the images. These features are used to train classical machine learning classifiers, including Random Forest and XGBoost, for binary classification of high-grade glioma (HGG) and low-grade glioma (LGG). Experimental results on the BraTS 2020 dataset show that the Random Forest classifier combined with selected Betti features achieves an accuracy of 89.19%. These findings highlight the potential of persistent homology as an effective and interpretable approach for analyzing complex 3D medical images and performing brain tumor classification.