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Register a new userDiagnosing Colorectal Polyps in the Wild with Capsule Networks
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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 .
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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.
Lyme disease is one of the most common infectious vector-borne diseases in the world. In the early stage, the disease manifests itself in most cases with erythema migrans (EM) skin lesions. Better diagnosis of these early forms would allow improving the prognosis by preventing the transition to a severe late form thanks to appropriate antibiotic therapy. Recent studies show that convolutional neural networks (CNNs) perform very well to identify skin lesions from the image but, there is not much work for Lyme disease prediction from EM lesion images. The main objective of this study is to extensively analyze the effectiveness of CNNs for diagnosing Lyme disease from images and to find out the best CNN architecture for the purpose. There is no publicly available EM image dataset for Lyme disease prediction mainly because of privacy concerns. In this study, we utilized an EM dataset consisting of images collected from Clermont-Ferrand University Hospital Center (CF-CHU) of France and the internet. CF-CHU collected the images from several hospitals in France. This dataset was labeled by expert dermatologists and infectiologists from CF-CHU. First, we benchmarked this dataset for twenty-three well-known CNN architectures in terms of predictive performance metrics, computational complexity metrics, and statistical significance tests. Second, to improve the performance of the CNNs, we used transfer learning from ImageNet pre-trained models as well as pre-trained the CNNs with the skin lesion dataset Human Against Machine with 10000 training images (HAM1000). In that process, we searched for the best performing number of layers to unfreeze during transfer learning fine-tuning for each of the CNNs. Third, for model explainability, we utilized Gradient-weighted Class Activation Mapping to visualize the regions of input that are significant to the CNNs for making predictions. Fourth, we provided guidelines for model selection based on predictive performance and computational complexity. Our study confirmed the effectiveness and potential of even some lightweight CNNs to be used for Lyme disease pre-scanner mobile applications. We also made all the trained models publicly available at https://dappem.limos.fr/download.html, which can be used by others for transfer learning and building pre-scanners for Lyme disease.
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.
The Medico: Multimedia Task 2020 focuses on developing an efficient and accurate computer-aided diagnosis system for automatic segmentation [3]. We participate in task 1, Polyps segmentation task, which is to develop algorithms for segmenting polyps on a comprehensive dataset. In this task, we propose methods combining Residual module, Inception module, Adaptive Convolutional neural network with U-Net model, and PraNet for semantic segmentation of various types of polyps in endoscopic images. We select 5 runs with different architecture and parameters in our methods. Our methods show potential results in accuracy and efficiency through multiple experiments, and our team is in the Top 3 best results with a Jaccard index of 0.765.
Colorectal cancer is a leading cause of death worldwide. However, early diagnosis dramatically increases the chances of survival, for which it is crucial to identify the tumor in the body. Since its imaging uses high-resolution techniques, annotating the tumor is time-consuming and requires particular expertise. Lately, methods built upon Convolutional Neural Networks(CNNs) have proven to be at par, if not better in many biomedical segmentation tasks. For the task at hand, we propose another CNN-based approach, which uses atrous convolutions and residual connections besides the conventional filters. The training and inference were made using an efficient patch-based approach, which significantly reduced unnecessary computations. The proposed AtResUNet was trained on the DigestPath 2019 Challenge dataset for colorectal cancer segmentation with results having a Dice Coefficient of 0.748.
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