Brain Tumor Segmentation and Survival Prediction using Automatic Hard mining in 3D CNN Architecture
This research provides an incremental improvement in brain tumor segmentation and survival prediction for medical professionals, specifically in the context of glioma analysis from MRI scans.
This paper addresses brain tumor segmentation and survival prediction using 3D fully convolutional neural networks with dense and residual connections. The method achieved Dice similarity coefficients of 0.775 for enhancing tumor, 0.815 for tumor core, and 0.85 for whole tumor on the BraTS 2020 test data, representing an approximate 7% increment in DSC for tumor core and active tumor compared to validation. For survival prediction, it achieved 0.452 accuracy on the test dataset.
We utilize 3-D fully convolutional neural networks (CNN) to segment gliomas and its constituents from multimodal Magnetic Resonance Images (MRI). The architecture uses dense connectivity patterns to reduce the number of weights and residual connections and is initialized with weights obtained from training this model with BraTS 2018 dataset. Hard mining is done during training to train for the difficult cases of segmentation tasks by increasing the dice similarity coefficient (DSC) threshold to choose the hard cases as epoch increases. On the BraTS2020 validation data (n = 125), this architecture achieved a tumor core, whole tumor, and active tumor dice of 0.744, 0.876, 0.714,respectively. On the test dataset, we get an increment in DSC of tumor core and active tumor by approximately 7%. In terms of DSC, our network performances on the BraTS 2020 test data are 0.775, 0.815, and 0.85 for enhancing tumor, tumor core, and whole tumor, respectively. Overall survival of a subject is determined using conventional machine learning from rediomics features obtained using a generated segmentation mask. Our approach has achieved 0.448 and 0.452 as the accuracy on the validation and test dataset.