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Proceedings Paper

Evaluation of a deep learning architecture for MR imaging prediction of ATRX in glioma patients
Author(s): Panagiotis Korfiatis; Timothy L. Kline; Bradley J. Erickson
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Paper Abstract

Predicting mutation/loss of alpha-thalassemia/mental retardation syndrome X-linked (ATRX) gene utilizing MR imaging is of high importance since it is a predictor of response and prognosis in brain tumors. In this study, we compare a deep neural network approach based on a residual deep neural network (ResNet) architecture and one based on a classical machine learning approach and evaluate their ability in predicting ATRX mutation status without the need for a distinct tumor segmentation step. We found that the ResNet50 (50 layers) architecture, pre trained on ImageNet data was the best performing model, achieving an accuracy of 0.91 for the test set (classification of a slice as no tumor, ATRX mutated, or mutated) in terms of f1 score in a test set of 35 cases. The SVM classifier achieved 0.63 for differentiating the Flair signal abnormality regions from the test patients based on their mutation status. We report a method that alleviates the need for extensive preprocessing and acts as a proof of concept that deep neural network architectures can be used to predict molecular biomarkers from routine medical images.

Paper Details

Date Published: 27 February 2018
PDF: 7 pages
Proc. SPIE 10575, Medical Imaging 2018: Computer-Aided Diagnosis, 105752G (27 February 2018); doi: 10.1117/12.2293538
Show Author Affiliations
Panagiotis Korfiatis, Mayo Clinic (United States)
Timothy L. Kline, Mayo Clinic (United States)
Bradley J. Erickson, Mayo Clinic (United States)

Published in SPIE Proceedings Vol. 10575:
Medical Imaging 2018: Computer-Aided Diagnosis
Nicholas Petrick; Kensaku Mori, Editor(s)

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