Abstract: Computer aided diagnosis (CAD) systems are designed to assist clinicians in various tasks, including highlighting abnormal regions in medical images. Common methods exploit supervised learning using annotated data sets and perform classification at voxel-level. However, many pathologies are characterized by subtle lesions that may be located anywhere in the organ of interest, have various shapes, sizes and textures. Acquiring a data set adequately representing the heterogeneity of such pathologies is therefore a major issue. Moreover, when a lesion is not visually detected on a scan, outlining it accurately is not feasible. Performing supervised learning on such labeled data would not be reliable. In this study, we consider the problem of detecting subtle epilepsy lesions in multiparametric (T1w, FLAIR) MRI exams considered as normal (MRI-negative). We cast this problem as an outlier detection problem and build on a previously proposed approach that consists in learning a oc-SVM model for each voxel in the brain volume using a small number of clinically-guided features. Our goal in this study is to make a step forward by replacing the handcrafted features with automatically learnt representations using neural networks. We propose a novel version of siamese networks trained on patches extracted from healthy patients’ scans only. This network, composed of stacked convolutional autoencoders as subnetworks, is regularized by the reconstruction error of the patches. It is designed to map patches centered at the same spatial localization to ’close’ representations with respect to the chosen metric (i.e. cosine) in a latent space. Finally, the middle layer representations of the subnetworks are fed into oc-SVM models at voxel-level. The model is trained on 75 healthy subjects and validated on 21 patients with confirmed epilepsy lesions (with 18 MR negative patients) and shows a promising performance.
Keywords: Epilepsy, Siamese network, Outlier detection, Anomaly detection, Deep learning
Author Affiliation: Univ Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, UJM-Saint Etienne, CNRS, Inserm, CREATIS UMR 5220, U1206, F-69621, Lyon, France