Optimization of deep learning methods for visualization of tumor heterogeneity and brain tumor grading through digital patho.pdf (1.12 MB)
Optimization of deep learning methods for visualization of tumor heterogeneity and brain tumor grading through digital pathology
journal contribution
posted on 2023-06-10, 01:53 authored by An Hoai Truong, Viktoriia SharmanskaViktoriia Sharmanska, Clara Limb?ck-Stanic, Matthew Grech-SollarsBackground: Variations in prognosis and treatment options for gliomas are dependent on tumor grading. When tissue is available for analysis, grade is established based on histological criteria. However, histopathological diagnosis is not always reliable or straight-forward due to tumor heterogeneity, sampling error, and subjectivity, and hence there is great interobserver variability in readings. Methods: We trained convolutional neural network models to classify digital whole-slide histopathology images from The Cancer Genome Atlas. We tested a number of optimization parameters. Results: Data augmentation did not improve model training, while a smaller batch size helped to prevent overfitting and led to improved model performance. There was no significant difference in performance between a modular 2-class model and a single 3-class model system. The best models trained achieved a mean accuracy of 73% in classifying glioblastoma from other grades and 53% between WHO grade II and III gliomas. A visualization method was developed to convey the model output in a clinically relevant manner by overlaying color-coded predictions over the original whole-slide image. Conclusions: Our developed visualization method reflects the clinical decision-making process by highlighting the intratumor heterogeneity and may be used in a clinical setting to aid diagnosis. Explainable artificial intelligence techniques may allow further evaluation of the model and underline areas for improvements such as biases. Due to intratumor heterogeneity, data annotation for training was imprecise, and hence performance was lower than expected. The models may be further improved by employing advanced data augmentation strategies and using more precise semiautomatic or manually labeled training data.
History
Publication status
- Published
File Version
- Published version
Journal
Neuro-Oncology AdvancesISSN
2632-2498Publisher
Oxford University PressExternal DOI
Issue
1Volume
2Page range
1-13Event location
EnglandDepartment affiliated with
- Informatics Publications
Full text available
- Yes
Peer reviewed?
- Yes
Legacy Posted Date
2021-11-30First Open Access (FOA) Date
2021-11-30First Compliant Deposit (FCD) Date
2021-11-30Usage metrics
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