Optimization of deep learning methods for visualization of tumor heterogeneity and brain tumor grading through digital pathology

Neuro-oncology Advances
An Hoai TruongMatthew Grech-Sollars

Abstract

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. 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. 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. Our developed visualization method reflects the clinical decision-making process by highlighting t...Continue Reading

References

Oct 27, 2007·Journal of Cardiothoracic Surgery·Andrew M Thomson, William A Wallace
Feb 5, 2008·IEEE Transactions on Neural Networks·Chih-Wei Hsu, Chih-Jen Lin
Jan 1, 1994·IEEE Transactions on Neural Networks·M BianchiniM Maggini
Sep 28, 2013·Nature Genetics·UNKNOWN Cancer Genome Atlas Research NetworkJoshua M Stuart
Oct 15, 2013·Cell·Cameron W BrennanUNKNOWN TCGA Research Network
Nov 26, 2014·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·James P B O'ConnorAlan Jackson
Jun 11, 2015·The New England Journal of Medicine·UNKNOWN Cancer Genome Atlas Research NetworkJianan Zhang
Mar 8, 2016·Handbook of Clinical Neurology·Arie Perry, Pieter Wesseling
Jul 13, 2016·American Journal of Clinical Pathology·William MathiesonGeraldine A Thomas
Jul 10, 2017·Radiological Physics and Technology·Kenji Suzuki
Mar 14, 2018·Proceedings of the National Academy of Sciences of the United States of America·Pooya MobadersanyLee A D Cooper
May 19, 2018·Archives of Pathology & Laboratory Medicine·Sunhee C Lee
Jun 4, 2019·Journal of Clinical Neuroscience : Official Journal of the Neurosurgical Society of Australasia·Justin KerLipo Wang
Sep 25, 2019·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Sebastian R van der VoortMarion Smits

❮ Previous
Next ❯

Software Mentioned

CAM
Grad

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.