Evaluation of a deep learning architecture for MR imaging prediction of ATRX in glioma patients

Panagiotis Korfiatis, Timothy L. Kline, Bradley J. Erickson

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations


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.

Original languageEnglish (US)
Title of host publicationMedical Imaging 2018
Subtitle of host publicationComputer-Aided Diagnosis
EditorsKensaku Mori, Nicholas Petrick
ISBN (Electronic)9781510616394
StatePublished - 2018
EventMedical Imaging 2018: Computer-Aided Diagnosis - Houston, United States
Duration: Feb 12 2018Feb 15 2018

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
ISSN (Print)1605-7422


OtherMedical Imaging 2018: Computer-Aided Diagnosis
Country/TerritoryUnited States


  • ATRX imaging biomarkers
  • Deep learning
  • MRI
  • glioma

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Biomaterials
  • Atomic and Molecular Physics, and Optics
  • Radiology Nuclear Medicine and imaging


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