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Fei, B.

Publications and source records attributed to Fei, B..

4 recordsLinked to original sources
bioRxiv2019

Multidimensional and Multiresolution Ensemble Networks for Brain Tumor Segmentation

In this work, we developed multiple 2D and 3D segmentation models with multiresolution input to segment brain tumor components, and then ensembled them to obtain robust segmentation maps. This reduced overfitting and resulted in a more generalized model. Multiparametric MR images of 335 subjects from BRATS 2019 challenge were used for training the models. Further, we tested a classical machine learning algorithm (xgboost) with features extracted from the segmentation maps to classify subject survival range. Preliminary results on the BRATS 2019 validation dataset demonstrasted this method can achieve excellent performance with DICE scores of 0.898, 0.784, 0.779 for whole tumor, tumor core and enhancing tumor respectively and accuracy 34.5 % for survuval prediction.

neuroscience↗
bioRxiv2019

Fully Automated Brain Tumor Segmentation and Survival Prediction of Gliomas using Deep Learning and MRI

Tumor segmentation of magnetic resonance (MR) images is a critical step in providing objective measures of predicting aggressiveness and response to therapy in gliomas. It has valuable applications in diagnosis, monitoring, and treatment planning of brain tumors. The purpose of this work was to develop a fully automated deep learning method for brain tumor segmentation and survival prediction. Well curated brain tumor cases with multi-parametric MR Images from the BraTS2019 dataset were used. A three-group framework was implemented, with each group consisting of three 3D-Dense-UNets to segment whole tumor (WT), tumor core (TC) and enhancing tumor (ET). This method was implemented to decompose the complex multi-class segmentation problem into individual binary segmentation problems for each sub-component. Each group was trained using different approaches and loss functions. The output segmentations of a particular label from their respective networks from the 3 groups were ensembled and post-processed. For survival analysis, a linear regression model based on imaging texture features and wavelet texture features extracted from each of the segmented components was implemented. The networks were tested on the BraTS2019 validation dataset including 125 cases for the brain tumor segmentation task and 29 cases for the survival prediction task. The segmentation networks achieved average dice scores of 0.901, 0.844 and 0.801 for WT, TC and ET respectively. The survival prediction network achieved an accuracy score of 0.55 and mean squared error (MSE) of 119244. This method could be implemented as a robust tool to assist clinicians in primary brain tumor management and follow-up.

neuroscience↗
bioRxiv2019

Classification of Brain Tumor IDH Status using MRI and Deep Learning

Isocitrate dehydrogenase (IDH) mutation status is an important marker in glioma diagnosis and therapy. We propose a novel automated pipeline for predicting IDH status noninvasively using deep learning and T2-weighted (T2w) MR images with minimal preprocessing (N4 bias correction and normalization to zero mean and unit variance). T2w MRI and genomic data were obtained from The Cancer Imaging Archive dataset (TCIA) for 260 subjects (120 High grade and 140 Low grade gliomas). A fully automated 2D densely connected model was trained to classify IDH mutation status on 208 subjects and tested on another held-out set of 52 subjects, using 5-fold cross validation. Data leakage was avoided by ensuring subject separation during the slice-wise randomization. Mean classification accuracy of 90.5% was achieved for each axial slice in predicting the three classes of no tumor, IDH mutated and IDH wild-type. Test accuracy of 83.8% was achieved in predicting IDH mutation status for individual subjects on the test dataset of 52 subjects. We demonstrate a deep learning method to predict IDH mutation status using T2w MRI alone. Radiologic imaging studies using deep learning methods must address data leakage (subject duplication) in the randomization process to avoid upward bias in the reported classification accuracy.

neuroscience↗