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"cancer detection": models, code, and papers

Predicting clinical significance of BRCA1 and BRCA2 single nucleotide substitution variants with unknown clinical significance using probabilistic neural network and deep neural network-stacked autoencoder

May 06, 2018
Ehsan Rahmatizad KhajePasha, Mahdi Bazarghan, Hamidreza Kheiri Manjili, Ramin Mohammadkhani, Ruhallah Amandi

Non-synonymous single nucleotide polymorphisms (nsSNPs) are single nucleotide substitution occurring in the coding region of a gene and leads to a change in amino-acid sequence of protein. The studies have shown these variations may be associated with disease. Thus, investigating the effects of nsSNPs on protein function will give a greater insight on how nsSNPs can lead into disease. Breast cancer is the most common cancer among women causing highest cancer death every year. BRCA1 and BRCA2 tumor suppressor genes are two main candidates of which, mutations in them can increase the risk of developing breast cancer. For prediction and detection of the cancer one can use experimental or computational methods, but the experimental method is very costly and time consuming in comparison with the computational method. The computer and computational methods have been used for more than 30 years. Here we try to predict the clinical significance of BRCA1 and BRCA2 nsSNPs as well as the unknown clinical significances. Nearly 500 BRCA1 and BRCA2 nsSNPs with known clinical significances retrieved from NCBI database. Based on hydrophobicity or hydrophilicity and their role in proteins' second structure, they are divided into 6 groups, each assigned with scores. The data are prepared in the acceptable form to the automated prediction mechanisms, Probabilistic Neural Network (PNN) and Deep Neural NetworkStacked AutoEncoder (DNN). With Jackknife cross validation we show that the prediction accuracy achieved for BRCA1 and BRCA2 using PNN are 87.97% and 82.17% respectively, while 95.41% and 92.80% accuracies achieved using DNN. The total required processing time for the training and testing the PNN is 0.9 second and DNN requires about 7 hours of training and it can predict instantly. both methods show great improvement in accuracy and speed compared to previous attempts.

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A learning without forgetting approach to incorporate artifact knowledge in polyp localization tasks

Feb 11, 2020
Roger D. Soberanis-Mukul, Maxime Kayser, Anna-Maria Zvereva, Peter Klare, Nassir Navab, Shadi Albarqouni

Colorectal polyps are abnormalities in the colon tissue that can develop into colorectal cancer. The survival rate for patients is higher when the disease is detected at an early stage and polyps can be removed before they develop into malignant tumors. Deep learning methods have become the state of art in automatic polyp detection. However, the performance of current models heavily relies on the size and quality of the training datasets. Endoscopic video sequences tend to be corrupted by different artifacts affecting visibility and hence, the detection rates. In this work, we analyze the effects that artifacts have in the polyp localization problem. For this, we evaluate the RetinaNet architecture, originally defined for object localization. We also define a model inspired by the learning without forgetting framework, which allows us to employ artifact detection knowledge in the polyp localization problem. Finally, we perform several experiments to analyze the influence of the artifacts in the performance of these models. To our best knowledge, this is the first extensive analysis of the influence of artifact in polyp localization and the first work incorporating learning without forgetting ideas for simultaneous artifact and polyp localization tasks.

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A CNN toolbox for skin cancer classification

Aug 21, 2019
Fabrizio Nunnari, Daniel Sonntag

We describe a software toolbox for the configuration of deep neural networks in the domain of skin cancer classification. The implemented software architecture allows developers to quickly set up new convolutional neural network (CNN) architectures and hyper-parameter configurations. At the same time, the user interface, manageable as a simple spreadsheet, allows non-technical users to explore different configuration settings that need to be explored when switching to different data sets. In future versions, meta leaning frameworks can be added, or AutoML systems that continuously improve over time. Preliminary results, conducted with two CNNs in the context melanoma detection on dermoscopic images, quantify the impact of image augmentation, image resolution, and rescaling filter on the overall detection performance and training time.

* DFKI Technical Report 
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Automatic tumour segmentation in H&E-stained whole-slide images of the pancreas

Dec 01, 2021
Pierpaolo Vendittelli, Esther M. M. Smeets, Geert Litjens

Pancreatic cancer will soon be the second leading cause of cancer-related death in Western society. Imaging techniques such as CT, MRI and ultrasound typically help providing the initial diagnosis, but histopathological assessment is still the gold standard for final confirmation of disease presence and prognosis. In recent years machine learning approaches and pathomics pipelines have shown potential in improving diagnostics and prognostics in other cancerous entities, such as breast and prostate cancer. A crucial first step in these pipelines is typically identification and segmentation of the tumour area. Ideally this step is done automatically to prevent time consuming manual annotation. We propose a multi-task convolutional neural network to balance disease detection and segmentation accuracy. We validated our approach on a dataset of 29 patients (for a total of 58 slides) at different resolutions. The best single task segmentation network achieved a median Dice of 0.885 (0.122) IQR at a resolution of 15.56 $\mu$m. Our multi-task network improved on that with a median Dice score of 0.934 (0.077) IQR.

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Virtual staining for mitosis detection in Breast Histopathology

Mar 17, 2020
Caner Mercan, Germonda Reijnen-Mooij, David Tellez Martin, Johannes Lotz, Nick Weiss, Marcel van Gerven, Francesco Ciompi

We propose a virtual staining methodology based on Generative Adversarial Networks to map histopathology images of breast cancer tissue from H&E stain to PHH3 and vice versa. We use the resulting synthetic images to build Convolutional Neural Networks (CNN) for automatic detection of mitotic figures, a strong prognostic biomarker used in routine breast cancer diagnosis and grading. We propose several scenarios, in which CNN trained with synthetically generated histopathology images perform on par with or even better than the same baseline model trained with real images. We discuss the potential of this application to scale the number of training samples without the need for manual annotations.

* 5 pages, 4 figures. Accepted for publication at the IEEE International Symposium on Biomedical Imaging (ISBI), 2020 
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Extraction of Skin Lesions from Non-Dermoscopic Images Using Deep Learning

Sep 08, 2016
Mohammad H. Jafari, Ebrahim Nasr-Esfahani, Nader Karimi, S. M. Reza Soroushmehr, Shadrokh Samavi, Kayvan Najarian

Melanoma is amongst most aggressive types of cancer. However, it is highly curable if detected in its early stages. Prescreening of suspicious moles and lesions for malignancy is of great importance. Detection can be done by images captured by standard cameras, which are more preferable due to low cost and availability. One important step in computerized evaluation of skin lesions is accurate detection of lesion region, i.e. segmentation of an image into two regions as lesion and normal skin. Accurate segmentation can be challenging due to burdens such as illumination variation and low contrast between lesion and healthy skin. In this paper, a method based on deep neural networks is proposed for accurate extraction of a lesion region. The input image is preprocessed and then its patches are fed to a convolutional neural network (CNN). Local texture and global structure of the patches are processed in order to assign pixels to lesion or normal classes. A method for effective selection of training patches is used for more accurate detection of a lesion border. The output segmentation mask is refined by some post processing operations. The experimental results of qualitative and quantitative evaluations demonstrate that our method can outperform other state-of-the-art algorithms exist in the literature.

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Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor Infiltrating Lymphocytes in Invasive Breast Cancer

May 29, 2019
Han Le, Rajarsi Gupta, Le Hou, Shahira Abousamra, Danielle Fassler, Tahsin Kurc, Dimitris Samaras, Rebecca Batiste, Tianhao Zhao, Alison L. Van Dyke, Ashish Sharma, Erich Bremer, Jonas S. Almeida, Joel Saltz

Quantitative assessment of Tumor-TIL spatial relationships is increasingly important in both basic science and clinical aspects of breast cancer research. We have developed and evaluated convolutional neural network (CNN) analysis pipelines to generate combined maps of cancer regions and tumor infiltrating lymphocytes (TILs) in routine diagnostic breast cancer whole slide tissue images (WSIs). We produce interactive whole slide maps that provide 1) insight about the structural patterns and spatial distribution of lymphocytic infiltrates and 2) facilitate improved quantification of TILs. We evaluated both tumor and TIL analyses using three CNN networks - Resnet-34, VGG16 and Inception v4, and demonstrated that the results compared favorably to those obtained by what believe are the best published methods. We have produced open-source tools and generated a public dataset consisting of tumor/TIL maps for 1,015 TCGA breast cancer images. We also present a customized web-based interface that enables easy visualization and interactive exploration of high-resolution combined Tumor-TIL maps for 1,015TCGA invasive breast cancer cases that can be downloaded for further downstream analyses.

* Nature Scientific Reports Submission 
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Detecting small polyps using a Dynamic SSD-GAN

Oct 29, 2020
Daniel C. Ohrenstein, Patrick Brandao, Daniel Toth, Laurence Lovat, Danail Stoyanov, Peter Mountney

Endoscopic examinations are used to inspect the throat, stomach and bowel for polyps which could develop into cancer. Machine learning systems can be trained to process colonoscopy images and detect polyps. However, these systems tend to perform poorly on objects which appear visually small in the images. It is shown here that combining the single-shot detector as a region proposal network with an adversarially-trained generator to upsample small region proposals can significantly improve the detection of visually-small polyps. The Dynamic SSD-GAN pipeline introduced in this paper achieved a 12% increase in sensitivity on visually-small polyps compared to a conventional FCN baseline.

* Machine Learning for Health (ML4H) at NeurIPS 2020 - Extended Abstract 
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