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"cancer detection": models, code, and papers

Robust breast cancer detection in mammography and digital breast tomosynthesis using annotation-efficient deep learning approach

Dec 27, 2019
William Lotter, Abdul Rahman Diab, Bryan Haslam, Jiye G. Kim, Giorgia Grisot, Eric Wu, Kevin Wu, Jorge Onieva Onieva, Jerrold L. Boxerman, Meiyun Wang, Mack Bandler, Gopal Vijayaraghavan, A. Gregory Sorensen

Breast cancer remains a global challenge, causing over 1 million deaths globally in 2018. To achieve earlier breast cancer detection, screening x-ray mammography is recommended by health organizations worldwide and has been estimated to decrease breast cancer mortality by 20-40%. Nevertheless, significant false positive and false negative rates, as well as high interpretation costs, leave opportunities for improving quality and access. To address these limitations, there has been much recent interest in applying deep learning to mammography; however, obtaining large amounts of annotated data poses a challenge for training deep learning models for this purpose, as does ensuring generalization beyond the populations represented in the training dataset. Here, we present an annotation-efficient deep learning approach that 1) achieves state-of-the-art performance in mammogram classification, 2) successfully extends to digital breast tomosynthesis (DBT; "3D mammography"), 3) detects cancers in clinically-negative prior mammograms of cancer patients, 4) generalizes well to a population with low screening rates, and 5) outperforms five-out-of-five full-time breast imaging specialists by improving absolute sensitivity by an average of 14%. Our results demonstrate promise towards software that can improve the accuracy of and access to screening mammography worldwide.


Out of distribution detection for skin and malaria images

Nov 02, 2021
Muhammad Zaida, Shafaqat Ali, Mohsen Ali, Sarfaraz Hussein, Asma Saadia, Waqas Sultani

Deep neural networks have shown promising results in disease detection and classification using medical image data. However, they still suffer from the challenges of handling real-world scenarios especially reliably detecting out-of-distribution (OoD) samples. We propose an approach to robustly classify OoD samples in skin and malaria images without the need to access labeled OoD samples during training. Specifically, we use metric learning along with logistic regression to force the deep networks to learn much rich class representative features. To guide the learning process against the OoD examples, we generate ID similar-looking examples by either removing class-specific salient regions in the image or permuting image parts and distancing them away from in-distribution samples. During inference time, the K-reciprocal nearest neighbor is employed to detect out-of-distribution samples. For skin cancer OoD detection, we employ two standard benchmark skin cancer ISIC datasets as ID, and six different datasets with varying difficulty levels were taken as out of distribution. For malaria OoD detection, we use the BBBC041 malaria dataset as ID and five different challenging datasets as out of distribution. We achieved state-of-the-art results, improving 5% and 4% in [email protected]% over the previous state-of-the-art for skin cancer and malaria OoD detection respectively.


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.


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%.


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 

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 

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