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Register a new userDeep neural networks for automated classification of colorectal polyps on histopathology slides: A multi-institutional evaluation
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Histological classification of colorectal polyps plays a critical role in both screening for colorectal cancer and care of affected patients. An accurate and automated algorithm for the classification of colorectal polyps on digitized histopathology slides could benefit clinicians and patients. Evaluate the performance and assess the generalizability of a deep neural network for colorectal polyp classification on histopathology slide images using a multi-institutional dataset. In this study, we developed a deep neural network for classification of four major colorectal polyp types, tubular adenoma, tubulovillous/villous adenoma, hyperplastic polyp, and sessile serrated adenoma, based on digitized histopathology slides from our institution, Dartmouth-Hitchcock Medical Center (DHMC), in New Hampshire. We evaluated the deep neural network on an internal dataset of 157 histopathology slide images from DHMC, as well as on an external dataset of 238 histopathology slide images from 24 different institutions spanning 13 states in the United States. We measured accuracy, sensitivity, and specificity of our model in this evaluation and compared its performance to local pathologists diagnoses at the point-of-care retrieved from corresponding pathology laboratories. For the internal evaluation, the deep neural network had a mean accuracy of 93.5% (95% CI 89.6%-97.4%), compared with local pathologists accuracy of 91.4% (95% CI 87.0%-95.8%). On the external test set, the deep neural network achieved an accuracy of 87.0% (95% CI 82.7%-91.3%), comparable with local pathologists accuracy of 86.6% (95% CI 82.3%-90.9%). If confirmed in clinical settings, our model could assist pathologists by improving the diagnostic efficiency, reproducibility, and accuracy of colorectal cancer screenings.
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Colorectal cancer, largely arising from precursor lesions called polyps, remains one of the leading causes of cancer-related death worldwide. Current clinical standards require the resection and histopathological analysis of polyps due to test accuracy and sensitivity of optical biopsy methods falling substantially below recommended levels. In this study, we design a novel capsule network architecture (D-Caps) to improve the viability of optical biopsy of colorectal polyps. Our proposed method introduces several technical novelties including a novel capsule architecture with a capsule-average pooling (CAP) method to improve efficiency in large-scale image classification. We demonstrate improved results over the previous state-of-the-art convolutional neural network (CNN) approach by as much as 43%. This work provides an important benchmark on the new Mayo Polyp dataset, a significantly more challenging and larger dataset than previous polyp studies, with results stratified across all available categories, imaging devices and modalities, and focus modes to promote future direction into AI-driven colorectal cancer screening systems. Code is publicly available at https://github.com/lalonderodney/D-Caps .
Renal cell carcinoma (RCC) is the most common renal cancer in adults. The histopathologic classification of RCC is essential for diagnosis, prognosis, and management of patients. Reorganization and classification of complex histologic patterns of RCC on biopsy and surgical resection slides under a microscope remains a heavily specialized, error-prone, and time-consuming task for pathologists. In this study, we developed a deep neural network model that can accurately classify digitized surgical resection slides and biopsy slides into five related classes: clear cell RCC, papillary RCC, chromophobe RCC, renal oncocytoma, and normal. In addition to the whole-slide classification pipeline, we visualized the identified indicative regions and features on slides for classification by reprocessing patch-level classification results to ensure the explainability of our diagnostic model. We evaluated our model on independent test sets of 78 surgical resection whole slides and 79 biopsy slides from our tertiary medical institution, and 69 randomly selected surgical resection slides from The Cancer Genome Atlas (TCGA) database. The average area under the curve (AUC) of our classifier on the internal resection slides, internal biopsy slides, and external TCGA slides is 0.98, 0.98 and 0.99, respectively. Our results suggest that the high generalizability of our approach across different data sources and specimen types. More importantly, our model has the potential to assist pathologists by (1) automatically pre-screening slides to reduce false-negative cases, (2) highlighting regions of importance on digitized slides to accelerate diagnosis, and (3) providing objective and accurate diagnosis as the second opinion.
The performance of deep learning-based methods strongly relies on the number of datasets used for training. Many efforts have been made to increase the data in the medical image analysis field. However, unlike photography images, it is hard to generate centralized databases to collect medical images because of numerous technical, legal, and privacy issues. In this work, we study the use of federated learning between two institutions in a real-world setting to collaboratively train a model without sharing the raw data across national boundaries. We quantitatively compare the segmentation models obtained with federated learning and local training alone. Our experimental results show that federated learning models have higher generalizability than standalone training.
Artificial Intelligence (AI) can potentially support histopathologists in the diagnosis of a broad spectrum of cancer types. In colorectal cancer (CRC), AI can alleviate the laborious task of characterization and reporting on resected biopsies, including polyps, the numbers of which are increasing as a result of CRC population screening programs, ongoing in many countries all around the globe. Here, we present an approach to address two major challenges in automated assessment of CRC histopathology whole-slide images. First, we present an AI-based method to segment multiple tissue compartments in the H&E-stained whole-slide image, which provides a different, more perceptible picture of tissue morphology and composition. We test and compare a panel of state-of-the-art loss functions available for segmentation models, and provide indications about their use in histopathology image segmentation, based on the analysis of a) a multi-centric cohort of CRC cases from five medical centers in the Netherlands and Germany, and b) two publicly available datasets on segmentation in CRC. Second, we use the best performing AI model as the basis for a computer-aided diagnosis system (CAD) that classifies colon biopsies into four main categories that are relevant pathologically. We report the performance of this system on an independent cohort of more than 1,000 patients. The results show the potential of such an AI-based system to assist pathologists in diagnosis of CRC in the context of population screening. We have made the segmentation model available for research use on https://grand-challenge.org/algorithms/colon-tissue-segmentation/.
Microscopic examination of tissues or histopathology is one of the diagnostic procedures for detecting colorectal cancer. The pathologist involved in such an examination usually identifies tissue type based on texture analysis, especially focusing on tumour-stroma ratio. In this work, we automate the task of tissue classification within colorectal cancer histology samples using deep transfer learning. We use discriminative fine-tuning with one-cycle-policy and apply structure-preserving colour normalization to boost our results. We also provide visual explanations of the deep neural networks decision on texture classification. With achieving state-of-the-art test accuracy of 96.2% we also embark on using deployment friendly architecture called SqueezeNet for memory-limited hardware.
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