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"cancer detection": models, code, and papers

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 
  
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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 
  
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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.

  
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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 
  
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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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Weakly Supervised Registration of Prostate MRI and Histopathology Images

Jun 23, 2021
Wei Shao, Indrani Bhattacharya, Simon J. C. Soerensen, Christian A. Kunder, Jeffrey B. Wang, Richard E. Fan, Pejman Ghanouni, James D. Brooks, Geoffrey A. Sonn, Mirabela Rusu

The interpretation of prostate MRI suffers from low agreement across radiologists due to the subtle differences between cancer and normal tissue. Image registration addresses this issue by accurately mapping the ground-truth cancer labels from surgical histopathology images onto MRI. Cancer labels achieved by image registration can be used to improve radiologists' interpretation of MRI by training deep learning models for early detection of prostate cancer. A major limitation of current automated registration approaches is that they require manual prostate segmentations, which is a time-consuming task, prone to errors. This paper presents a weakly supervised approach for affine and deformable registration of MRI and histopathology images without requiring prostate segmentations. We used manual prostate segmentations and mono-modal synthetic image pairs to train our registration networks to align prostate boundaries and local prostate features. Although prostate segmentations were used during the training of the network, such segmentations were not needed when registering unseen images at inference time. We trained and validated our registration network with 135 and 10 patients from an internal cohort, respectively. We tested the performance of our method using 16 patients from the internal cohort and 22 patients from an external cohort. The results show that our weakly supervised method has achieved significantly higher registration accuracy than a state-of-the-art method run without prostate segmentations. Our deep learning framework will ease the registration of MRI and histopathology images by obviating the need for prostate segmentations.

* Accepted to MICCAI 2021 
  
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A translational pathway of deep learning methods in GastroIntestinal Endoscopy

Oct 12, 2020
Sharib Ali, Mariia Dmitrieva, Noha Ghatwary, Sophia Bano, Gorkem Polat, Alptekin Temizel, Adrian Krenzer, Amar Hekalo, Yun Bo Guo, Bogdan Matuszewski, Mourad Gridach, Irina Voiculescu, Vishnusai Yoganand, Arnav Chavan, Aryan Raj, Nhan T. Nguyen, Dat Q. Tran, Le Duy Huynh, Nicolas Boutry, Shahadate Rezvy, Haijian Chen, Yoon Ho Choi, Anand Subramanian, Velmurugan Balasubramanian, Xiaohong W. Gao, Hongyu Hu, Yusheng Liao, Danail Stoyanov, Christian Daul, Stefano Realdon, Renato Cannizzaro, Dominique Lamarque, Terry Tran-Nguyen, Adam Bailey, Barbara Braden, James East, Jens Rittscher

The Endoscopy Computer Vision Challenge (EndoCV) is a crowd-sourcing initiative to address eminent problems in developing reliable computer aided detection and diagnosis endoscopy systems and suggest a pathway for clinical translation of technologies. Whilst endoscopy is a widely used diagnostic and treatment tool for hollow-organs, there are several core challenges often faced by endoscopists, mainly: 1) presence of multi-class artefacts that hinder their visual interpretation, and 2) difficulty in identifying subtle precancerous precursors and cancer abnormalities. Artefacts often affect the robustness of deep learning methods applied to the gastrointestinal tract organs as they can be confused with tissue of interest. EndoCV2020 challenges are designed to address research questions in these remits. In this paper, we present a summary of methods developed by the top 17 teams and provide an objective comparison of state-of-the-art methods and methods designed by the participants for two sub-challenges: i) artefact detection and segmentation (EAD2020), and ii) disease detection and segmentation (EDD2020). Multi-center, multi-organ, multi-class, and multi-modal clinical endoscopy datasets were compiled for both EAD2020 and EDD2020 sub-challenges. An out-of-sample generalisation ability of detection algorithms was also evaluated. Whilst most teams focused on accuracy improvements, only a few methods hold credibility for clinical usability. The best performing teams provided solutions to tackle class imbalance, and variabilities in size, origin, modality and occurrences by exploring data augmentation, data fusion, and optimal class thresholding techniques.

* 30 pages 
  
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Evaluation of Joint Multi-Instance Multi-Label Learning For Breast Cancer Diagnosis

Oct 10, 2015
Baris Gecer, Ozge Yalcinkaya, Onur Tasar, Selim Aksoy

Multi-instance multi-label (MIML) learning is a challenging problem in many aspects. Such learning approaches might be useful for many medical diagnosis applications including breast cancer detection and classification. In this study subset of digiPATH dataset (whole slide digital breast cancer histopathology images) are used for training and evaluation of six state-of-the-art MIML methods. At the end, performance comparison of these approaches are given by means of effective evaluation metrics. It is shown that MIML-kNN achieve the best performance that is %65.3 average precision, where most of other methods attain acceptable results as well.

  
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Preserving Dense Features for Ki67 Nuclei Detection

Nov 10, 2021
Seyed Hossein Mirjahanmardi, Melanie Dawe, Anthony Fyles, Wei Shi, Fei-Fei Liu, Susan Done, April Khademi

Nuclei detection is a key task in Ki67 proliferation index estimation in breast cancer images. Deep learning algorithms have shown strong potential in nuclei detection tasks. However, they face challenges when applied to pathology images with dense medium and overlapping nuclei since fine details are often diluted or completely lost by early maxpooling layers. This paper introduces an optimized UV-Net architecture, specifically developed to recover nuclear details with high-resolution through feature preservation for Ki67 proliferation index computation. UV-Net achieves an average F1-score of 0.83 on held-out test patch data, while other architectures obtain 0.74-0.79. On tissue microarrays (unseen) test data obtained from multiple centers, UV-Net's accuracy exceeds other architectures by a wide margin, including 9-42\% on Ontario Veterinary College, 7-35\% on Protein Atlas and 0.3-3\% on University Health Network.

* Accepted to SPIE Computational Digital Pathology 2022 
  
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Skin cancer reorganization and classification with deep neural network

Mar 01, 2017
Hao Chang

As one kind of skin cancer, melanoma is very dangerous. Dermoscopy based early detection and recarbonization strategy is critical for melanoma therapy. However, well-trained dermatologists dominant the diagnostic accuracy. In order to solve this problem, many effort focus on developing automatic image analysis systems. Here we report a novel strategy based on deep learning technique, and achieve very high skin lesion segmentation and melanoma diagnosis accuracy: 1) we build a segmentation neural network (skin_segnn), which achieved very high lesion boundary detection accuracy; 2) We build another very deep neural network based on Google inception v3 network (skin_recnn) and its well-trained weight. The novel designed transfer learning based deep neural network skin_inceptions_v3_nn helps to achieve a high prediction accuracy.

* 5 pages, 2 figures. ISIC2017 
  
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