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"cancer detection": models, code, and papers

AFP-Net: Realtime Anchor-Free Polyp Detection in Colonoscopy

Sep 26, 2019
Dechun Wang, Ning Zhang, Xinzi Sun, Pengfei Zhang, Chenxi Zhang, Yu Cao, Benyuan Liu

Colorectal cancer (CRC) is a common and lethal disease. Globally, CRC is the third most commonly diagnosed cancer in males and the second in females. For colorectal cancer, the best screening test available is the colonoscopy. During a colonoscopic procedure, a tiny camera at the tip of the endoscope generates a video of the internal mucosa of the colon. The video data are displayed on a monitor for the physician to examine the lining of the entire colon and check for colorectal polyps. Detection and removal of colorectal polyps are associated with a reduction in mortality from colorectal cancer. However, the miss rate of polyp detection during colonoscopy procedure is often high even for very experienced physicians. The reason lies in the high variation of polyp in terms of shape, size, textural, color and illumination. Though challenging, with the great advances in object detection techniques, automated polyp detection still demonstrates a great potential in reducing the false negative rate while maintaining a high precision. In this paper, we propose a novel anchor free polyp detector that can localize polyps without using predefined anchor boxes. To further strengthen the model, we leverage a Context Enhancement Module and Cosine Ground truth Projection. Our approach can respond in real time while achieving state-of-the-art performance with 99.36% precision and 96.44% recall.

  
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Breast Cancer Detection Using Convolutional Neural Networks

Mar 19, 2020
Simon Hadush, Yaecob Girmay, Abiot Sinamo, Gebrekirstos Hagos

Breast cancer is prevalent in Ethiopia that accounts 34% among women cancer patients. The diagnosis technique in Ethiopia is manual which was proven to be tedious, subjective, and challenging. Deep learning techniques are revolutionizing the field of medical image analysis and hence in this study, we proposed Convolutional Neural Networks (CNNs) for breast mass detection so as to minimize the overheads of manual analysis. CNN architecture is designed for the feature extraction stage and adapted both the Region Proposal Network (RPN) and Region of Interest (ROI) portion of the faster R-CNN for the automated breast mass abnormality detection. Our model detects mass region and classifies them into benign or malignant abnormality in mammogram(MG) images at once. For the proposed model, MG images were collected from different hospitals, locally.The images were passed through different preprocessing stages such as gaussian filter, median filter, bilateral filters and extracted the region of the breast from the background of the MG image. The performance of the model on test dataset is found to be: detection accuracy 91.86%, sensitivity of 94.67% and AUC-ROC of 92.2%.

  
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New pyramidal hybrid textural and deep features based automatic skin cancer classification model: Ensemble DarkNet and textural feature extractor

Mar 28, 2022
Mehmet Baygin, Turker Tuncer, Sengul Dogan

Background: Skin cancer is one of the widely seen cancer worldwide and automatic classification of skin cancer can be benefited dermatology clinics for an accurate diagnosis. Hence, a machine learning-based automatic skin cancer detection model must be developed. Material and Method: This research interests to overcome automatic skin cancer detection problem. A colored skin cancer image dataset is used. This dataset contains 3297 images with two classes. An automatic multilevel textural and deep features-based model is presented. Multilevel fuse feature generation using discrete wavelet transform (DWT), local phase quantization (LPQ), local binary pattern (LBP), pre-trained DarkNet19, and DarkNet53 are utilized to generate features of the skin cancer images, top 1000 features are selected threshold value-based neighborhood component analysis (NCA). The chosen top 1000 features are classified using the 10-fold cross-validation technique. Results: To obtain results, ten-fold cross-validation is used and 91.54% classification accuracy results are obtained by using the recommended pyramidal hybrid feature generator and NCA selector-based model. Further, various training and testing separation ratios (90:10, 80:20, 70:30, 60:40, 50:50) are used and the maximum classification rate is calculated as 95.74% using the 90:10 separation ratio. Conclusions: The findings and accuracies calculated are denoted that this model can be used in dermatology and pathology clinics to simplify the skin cancer detection process and help physicians.

* 22 pages, 7 figures 
  
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DeepSDCS: Dissecting cancer proliferation heterogeneity in Ki67 digital whole slide images

Jun 28, 2018
Priya Lakshmi Narayanan, Shan E Ahmed Raza, Andrew Dodson, Barry Gusterson, Mitchell Dowsett, Yinyin Yuan

Ki67 is an important biomarker for breast cancer. Classification of positive and negative Ki67 cells in histology slides is a common approach to determine cancer proliferation status. However, there is a lack of generalizable and accurate methods to automate Ki67 scoring in large-scale patient cohorts. In this work, we have employed a novel deep learning technique based on hypercolumn descriptors for cell classification in Ki67 images. Specifically, we developed the Simultaneous Detection and Cell Segmentation (DeepSDCS) network to perform cell segmentation and detection. VGG16 network was used for the training and fine tuning to training data. We extracted the hypercolumn descriptors of each cell to form the vector of activation from specific layers to capture features at different granularity. Features from these layers that correspond to the same pixel were propagated using a stochastic gradient descent optimizer to yield the detection of the nuclei and the final cell segmentations. Subsequently, seeds generated from cell segmentation were propagated to a spatially constrained convolutional neural network for the classification of the cells into stromal, lymphocyte, Ki67-positive cancer cell, and Ki67-negative cancer cell. We validated its accuracy in the context of a large-scale clinical trial of oestrogen-receptor-positive breast cancer. We achieved 99.06% and 89.59% accuracy on two separate test sets of Ki67 stained breast cancer dataset comprising biopsy and whole-slide images.

* MIDL 2018 Conference 
  
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Decision Support System for Detection and Classification of Skin Cancer using CNN

Dec 09, 2019
Rishu Garg, Saumil Maheshwari, Anupam Shukla

Skin Cancer is one of the most deathful of all the cancers. It is bound to spread to different parts of the body on the off chance that it is not analyzed and treated at the beginning time. It is mostly because of the abnormal growth of skin cells, often develops when the body is exposed to sunlight. The Detection Furthermore, the characterization of skin malignant growth in the beginning time is a costly and challenging procedure. It is classified where it develops and its cell type. High Precision and recall are required for the classification of lesions. The paper aims to use MNIST HAM-10000 dataset containing dermoscopy images. The objective is to propose a system that detects skin cancer and classifies it in different classes by using the Convolution Neural Network. The diagnosing methodology uses Image processing and deep learning model. The dermoscopy image of skin cancer taken, undergone various techniques to remove the noise and picture resolution. The image count is also increased by using various image augmentation techniques. In the end, the Transfer Learning method is used to increase the classification accuracy of the images further. Our CNN model gave a weighted average Precision of 0.88, a weighted Recall average of 0.74, and a weighted f1-score of 0.77. The transfer learning approach applied using ResNet model yielded an accuracy of 90.51%

* 9 pages, 3 figures, 5 tables 
  
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Whole-Slide Mitosis Detection in H&E Breast Histology Using PHH3 as a Reference to Train Distilled Stain-Invariant Convolutional Networks

Aug 17, 2018
David Tellez, Maschenka Balkenhol, Irene Otte-Holler, Rob van de Loo, Rob Vogels, Peter Bult, Carla Wauters, Willem Vreuls, Suzanne Mol, Nico Karssemeijer, Geert Litjens, Jeroen van der Laak, Francesco Ciompi

Manual counting of mitotic tumor cells in tissue sections constitutes one of the strongest prognostic markers for breast cancer. This procedure, however, is time-consuming and error-prone. We developed a method to automatically detect mitotic figures in breast cancer tissue sections based on convolutional neural networks (CNNs). Application of CNNs to hematoxylin and eosin (H&E) stained histological tissue sections is hampered by: (1) noisy and expensive reference standards established by pathologists, (2) lack of generalization due to staining variation across laboratories, and (3) high computational requirements needed to process gigapixel whole-slide images (WSIs). In this paper, we present a method to train and evaluate CNNs to specifically solve these issues in the context of mitosis detection in breast cancer WSIs. First, by combining image analysis of mitotic activity in phosphohistone-H3 (PHH3) restained slides and registration, we built a reference standard for mitosis detection in entire H&E WSIs requiring minimal manual annotation effort. Second, we designed a data augmentation strategy that creates diverse and realistic H&E stain variations by modifying the hematoxylin and eosin color channels directly. Using it during training combined with network ensembling resulted in a stain invariant mitosis detector. Third, we applied knowledge distillation to reduce the computational requirements of the mitosis detection ensemble with a negligible loss of performance. The system was trained in a single-center cohort and evaluated in an independent multicenter cohort from The Cancer Genome Atlas on the three tasks of the Tumor Proliferation Assessment Challenge (TUPAC). We obtained a performance within the top-3 best methods for most of the tasks of the challenge.

* Accepted to appear in IEEE Transactions on Medical Imaging 
  
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Y-Net: A deep Convolutional Neural Network for Polyp Detection

Jun 05, 2018
Ahmed Mohammed, Sule Yildirim, Ivar Farup, Marius Pedersen, Øistein Hovde

Colorectal polyps are important precursors to colon cancer, the third most common cause of cancer mortality for both men and women. It is a disease where early detection is of crucial importance. Colonoscopy is commonly used for early detection of cancer and precancerous pathology. It is a demanding procedure requiring significant amount of time from specialized physicians and nurses, in addition to a significant miss-rates of polyps by specialists. Automated polyp detection in colonoscopy videos has been demonstrated to be a promising way to handle this problem. {However, polyps detection is a challenging problem due to the availability of limited amount of training data and large appearance variations of polyps. To handle this problem, we propose a novel deep learning method Y-Net that consists of two encoder networks with a decoder network. Our proposed Y-Net method} relies on efficient use of pre-trained and un-trained models with novel sum-skip-concatenation operations. Each of the encoders are trained with encoder specific learning rate along the decoder. Compared with the previous methods employing hand-crafted features or 2-D/3-D convolutional neural network, our approach outperforms state-of-the-art methods for polyp detection with 7.3% F1-score and 13% recall improvement.

* 11 Pages, 3 figures 
  
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MITOS-RCNN: A Novel Approach to Mitotic Figure Detection in Breast Cancer Histopathology Images using Region Based Convolutional Neural Networks

Jul 04, 2018
Siddhant Rao

Studies estimate that there will be 266,120 new cases of invasive breast cancer and 40,920 breast cancer induced deaths in the year of 2018 alone. Despite the pervasiveness of this affliction, the current process to obtain an accurate breast cancer prognosis is tedious and time consuming, requiring a trained pathologist to manually examine histopathological images in order to identify the features that characterize various cancer severity levels. We propose MITOS-RCNN: a novel region based convolutional neural network (RCNN) geared for small object detection to accurately grade one of the three factors that characterize tumor belligerence described by the Nottingham Grading System: mitotic count. Other computational approaches to mitotic figure counting and detection do not demonstrate ample recall or precision to be clinically viable. Our models outperformed all previous participants in the ICPR 2012 challenge, the AMIDA 2013 challenge and the MITOS-ATYPIA-14 challenge along with recently published works. Our model achieved an F-measure score of 0.955, a 6.11% improvement in accuracy from the most accurate of the previously proposed models.

* Submitted to Elsevier Medical Image Analysis journal. 17 pages. 3 tables. 4 figures 
  
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