Prediction of glioma-subtypes: comparison of performance on a DL classifier using bounding box areas versus annotated tumors

Muhaddisa Barat Ali; Irene Yu-Hua Gu; Alice Lidemar; Mitchel S Berger; Georg Widhalm; Asgeir Store Jakola

doi:10.1186/s42490-022-00061-3

Prediction of glioma-subtypes: comparison of performance on a DL classifier using bounding box areas versus annotated tumors

BMC Biomed Eng. 2022 May 19;4(1):4. doi: 10.1186/s42490-022-00061-3.

Authors

Muhaddisa Barat Ali¹, Irene Yu-Hua Gu², Alice Lidemar³, Mitchel S Berger⁴, Georg Widhalm⁵, Asgeir Store Jakola^{3

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Affiliations

¹ Department of Electrical Engineering, Chalmers University of Technology, Gothenburg, Sweden. barat@chalmers.se.
² Department of Electrical Engineering, Chalmers University of Technology, Gothenburg, Sweden.
³ Department of Clinical Neuroscience, University of Gothenburg, Gothenburg, Sweden.
⁴ Department of Neurological Surgery,, University of California San Francisco, San Francisco, USA.
⁵ Department of Neurosurgery, Medical University of Vienna, Vienna, Austria.
⁶ Department of Neurosurgery, Sahlgrenska University Hospital, Gothenberg, Sweden.

Abstract

Background: For brain tumors, identifying the molecular subtypes from magnetic resonance imaging (MRI) is desirable, but remains a challenging task. Recent machine learning and deep learning (DL) approaches may help the classification/prediction of tumor subtypes through MRIs. However, most of these methods require annotated data with ground truth (GT) tumor areas manually drawn by medical experts. The manual annotation is a time consuming process with high demand on medical personnel. As an alternative automatic segmentation is often used. However, it does not guarantee the quality and could lead to improper or failed segmented boundaries due to differences in MRI acquisition parameters across imaging centers, as segmentation is an ill-defined problem. Analogous to visual object tracking and classification, this paper shifts the paradigm by training a classifier using tumor bounding box areas in MR images. The aim of our study is to see whether it is possible to replace GT tumor areas by tumor bounding box areas (e.g. ellipse shaped boxes) for classification without a significant drop in performance.

Method: In patients with diffuse gliomas, training a deep learning classifier for subtype prediction by employing tumor regions of interest (ROIs) using ellipse bounding box versus manual annotated data. Experiments were conducted on two datasets (US and TCGA) consisting of multi-modality MRI scans where the US dataset contained patients with diffuse low-grade gliomas (dLGG) exclusively.

Results: Prediction rates were obtained on 2 test datasets: 69.86% for 1p/19q codeletion status on US dataset and 79.50% for IDH mutation/wild-type on TCGA dataset. Comparisons with that of using annotated GT tumor data for training showed an average of 3.0% degradation (2.92% for 1p/19q codeletion status and 3.23% for IDH genotype).

Conclusion: Using tumor ROIs, i.e., ellipse bounding box tumor areas to replace annotated GT tumor areas for training a deep learning scheme, cause only a modest decline in performance in terms of subtype prediction. With more data that can be made available, this may be a reasonable trade-off where decline in performance may be counteracted with more data.

Keywords: 1p/19q codeletion; Brain tumor; Deep learning; Ellipse bounding box; IDH genotype.

Grants and funding

2017-00944/The Swedish Research Council VR