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Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images

By Pegah Khosravi, Ehsan Kazemi, Marcin Imielinski, Olivier Elemento, Iman Hajirasouliha

Posted 02 Oct 2017
bioRxiv DOI: 10.1101/197517 (published DOI: 10.1016/j.ebiom.2017.12.026)

Pathological evaluation of tumor tissue is pivotal for diagnosis in cancer patients and automated image analysis approaches have great potential to increase precision of diagnosis and help reduce human error. In this study, we utilize various computational methods based on convolutional neural networks (CNN) and build a stand-alone pipeline to effectively classify different histopathology images across different types of cancer. In particular, we demonstrate the utility of our pipeline to discriminate between two subtypes of lung cancer, four biomarkers of bladder cancer, and five biomarkers of breast cancer. In addition, we apply our pipeline to discriminate among four immunohistochemistry (IHC) staining scores of bladder and breast cancers. Our classification pipeline utilizes a basic architecture of CNN, Google's Inceptions within three training strategies, and an ensemble of two state-of-the-art algorithms, Inception and ResNet. These strategies include training the last layer of Google's Inceptions, training the network from scratch, and fine-tunning the parameters for our data using two pre-trained version of Google's Inception architectures, Inception-V1 and Inception-V3. We demonstrate the power of deep learning approaches for identifying cancer subtypes, and the robustness of Google's Inceptions even in presence of extensive tumor heterogeneity. Our pipeline on average achieved accuracies of 100% , 92%, 95%, and 69% for discrimination of various cancer types, subtypes, biomarkers, and scores, respectively. Our pipeline and related documentation is freely available at https://github.com/ih-lab/CNN_Smoothie

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