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"cancer detection": models, code, and papers

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 
  

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.

  

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 
  

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 
  

An attention-based multi-resolution model for prostate whole slide imageclassification and localization

May 30, 2019
Jiayun Li, Wenyuan Li, Arkadiusz Gertych, Beatrice S. Knudsen, William Speier, Corey W. Arnold

Histology review is often used as the `gold standard' for disease diagnosis. Computer aided diagnosis tools can potentially help improve current pathology workflows by reducing examination time and interobserver variability. Previous work in cancer grading has focused mainly on classifying pre-defined regions of interest (ROIs), or relied on large amounts of fine-grained labels. In this paper, we propose a two-stage attention-based multiple instance learning model for slide-level cancer grading and weakly-supervised ROI detection and demonstrate its use in prostate cancer. Compared with existing Gleason classification models, our model goes a step further by utilizing visualized saliency maps to select informative tiles for fine-grained grade classification. The model was primarily developed on a large-scale whole slide dataset consisting of 3,521 prostate biopsy slides with only slide-level labels from 718 patients. The model achieved state-of-the-art performance for prostate cancer grading with an accuracy of 85.11\% for classifying benign, low-grade (Gleason grade 3+3 or 3+4), and high-grade (Gleason grade 4+3 or higher) slides on an independent test set.

* 8 pages, 4 figures, CVPR 2019 Towards Causal, Explainable and Universal Medical Visual Diagnosis (MVD) Workshop 
  

Eigenspace Method for Spatiotemporal Hotspot Detection

Jun 13, 2014
Hadi Fanaee-T, João Gama

Hotspot detection aims at identifying subgroups in the observations that are unexpected, with respect to the some baseline information. For instance, in disease surveillance, the purpose is to detect sub-regions in spatiotemporal space, where the count of reported diseases (e.g. Cancer) is higher than expected, with respect to the population. The state-of-the-art method for this kind of problem is the Space-Time Scan Statistics (STScan), which exhaustively search the whole space through a sliding window looking for significant spatiotemporal clusters. STScan makes some restrictive assumptions about the distribution of data, the shape of the hotspots and the quality of data, which can be unrealistic for some nontraditional data sources. A novel methodology called EigenSpot is proposed where instead of an exhaustive search over the space, tracks the changes in a space-time correlation structure. Not only does the new approach presents much more computational efficiency, but also makes no assumption about the data distribution, hotspot shape or the data quality. The principal idea is that with the joint combination of abnormal elements in the principal spatial and the temporal singular vectors, the location of hotspots in the spatiotemporal space can be approximated. A comprehensive experimental evaluation, both on simulated and real data sets reveals the effectiveness of the proposed method.

* To appear in Expert Systems Journal 
  

Manifolds for Unsupervised Visual Anomaly Detection

Jun 19, 2020
Louise Naud, Alexander Lavin

Anomalies are by definition rare, thus labeled examples are very limited or nonexistent, and likely do not cover unforeseen scenarios. Unsupervised learning methods that don't necessarily encounter anomalies in training would be immensely useful. Generative vision models can be useful in this regard but do not sufficiently represent normal and abnormal data distributions. To this end, we propose constant curvature manifolds for embedding data distributions in unsupervised visual anomaly detection. Through theoretical and empirical explorations of manifold shapes, we develop a novel hyperspherical Variational Auto-Encoder (VAE) via stereographic projections with a gyroplane layer - a complete equivalent to the Poincar\'e VAE. This approach with manifold projections is beneficial in terms of model generalization and can yield more interpretable representations. We present state-of-the-art results on visual anomaly benchmarks in precision manufacturing and inspection, demonstrating real-world utility in industrial AI scenarios. We further demonstrate the approach on the challenging problem of histopathology: our unsupervised approach effectively detects cancerous brain tissue from noisy whole-slide images, learning a smooth, latent organization of tissue types that provides an interpretable decisions tool for medical professionals.

  

Stacked Hourglass Network with a Multi-level Attention Mechanism: Where to Look for Intervertebral Disc Labeling

Aug 14, 2021
Reza Azad, Lucas Rouhier, Julien Cohen-Adad

Labeling vertebral discs from MRI scans is important for the proper diagnosis of spinal related diseases, including multiple sclerosis, amyotrophic lateral sclerosis, degenerative cervical myelopathy and cancer. Automatic labeling of the vertebral discs in MRI data is a difficult task because of the similarity between discs and bone area, the variability in the geometry of the spine and surrounding tissues across individuals, and the variability across scans (manufacturers, pulse sequence, image contrast, resolution and artefacts). In previous studies, vertebral disc labeling is often done after a disc detection step and mostly fails when the localization algorithm misses discs or has false positive detection. In this work, we aim to mitigate this problem by reformulating the semantic vertebral disc labeling using the pose estimation technique. To do so, we propose a stacked hourglass network with multi-level attention mechanism to jointly learn intervertebral disc position and their skeleton structure. The proposed deep learning model takes into account the strength of semantic segmentation and pose estimation technique to handle the missing area and false positive detection. To further improve the performance of the proposed method, we propose a skeleton-based search space to reduce false positive detection. The proposed method evaluated on spine generic public multi-center dataset and demonstrated better performance comparing to previous work, on both T1w and T2w contrasts. The method is implemented in ivadomed (https://ivadomed.org).

* MICCAI 2021 
  

Producing Histopathology Phantom Images using Generative Adversarial Networks to improve Tumor Detection

May 21, 2022
Vidit Gautam

Advance in medical imaging is an important part in deep learning research. One of the goals of computer vision is development of a holistic, comprehensive model which can identify tumors from histology slides obtained via biopsies. A major problem that stands in the way is lack of data for a few cancer-types. In this paper, we ascertain that data augmentation using GANs can be a viable solution to reduce the unevenness in the distribution of different cancer types in our dataset. Our demonstration showed that a dataset augmented to a 50% increase causes an increase in tumor detection from 80% to 87.5%

  
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