scholarly journals Faculty Opinions recommendation of Clinical-grade computational pathology using weakly supervised deep learning on whole slide images.

2019 ◽  
Author(s):  
Alvis Brazma
Keyword(s):  
Deep Learning ◽  
Clinical Grade ◽  
Weakly Supervised ◽  
Computational Pathology ◽  
Whole Slide Images

scholarly journals Clinical-grade computational pathology using weakly supervised deep learning on whole slide images

2019 ◽  
Vol 25 (8) ◽  
pp. 1301-1309 ◽  
Author(s):  
Gabriele Campanella ◽  
Matthew G. Hanna ◽  
Luke Geneslaw ◽  
Allen Miraflor ◽  
Vitor Werneck Krauss Silva ◽  
...  
Keyword(s):  
Deep Learning ◽  
Clinical Grade ◽  
Weakly Supervised ◽  
Computational Pathology ◽  
Whole Slide Images

scholarly journals Best Paper Selection

2020 ◽  
Vol 29 (01) ◽  
pp. 246-256
Keyword(s):  
Computed Tomography ◽  
Deep Learning ◽  
Low Dose ◽  
Three Dimensional ◽  
Lung Cancer Screening ◽  
Clinical Grade ◽  
Chest Computed Tomography ◽  
Weakly Supervised ◽  
Computational Pathology ◽  
Whole Slide Images

Ardila D, Kiraly AP, Bharadwaj S, Choi B, Reicher JJ, Peng L, Tse D, Etemadi M, Ye W, Corrado G, Naidich DP, Shetty S. End-to-end lung cancer screening with three-dimensional deep learning on low-dose chest computed tomography. Nat Med 2019 May 20;25:954-61 https://www.nature.com/articles/s41591-019-0447-x Campanella G, Hanna MG, Geneslaw L, Miraflor A, Werneck Krauss Silva V, Busam KJ, Brogi E, Reuter VE, Klimstra DS, Fuchs TJ. Clinical-grade computational pathology using weakly supervised deep learning on whole slide images. Nat Med 2019 Jul 15;25:1301-9 https://www.nature.com/articles/s41591-019-0508-1

scholarly journals A deep learning model for breast ductal carcinoma in situ classification in whole slide images

2022 ◽  
Author(s):  
Fahdi Kanavati ◽  
Shin Ichihara ◽  
Masayuki Tsuneki
Keyword(s):  
Deep Learning ◽  
Ductal Carcinoma In Situ ◽  
Carcinoma In Situ ◽  
Ductal Carcinoma ◽  
New Techniques ◽  
Large Numbers ◽  
Computational Pathology ◽  
Deep Learning Model ◽  
Whole Slide Images

The pathological differential diagnosis between breast ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) is of pivotal importance for determining optimum cancer treatment(s) and clinical outcomes. Since conventional diagnosis by pathologists using microscopes is limited in terms of human resources, it is necessary to develop new techniques that can rapidly and accurately diagnose large numbers of histopathological specimens. Computational pathology tools which can assist pathologists in detecting and classifying DCIS and IDC from whole slide images (WSIs) would be of great benefit for routine pathological diagnosis. In this paper, we trained deep learning models capable of classifying biopsy and surgical histopathological WSIs into DCIS, IDC, and benign. We evaluated the models on two independent test sets (n=1,382, n=548), achieving ROC areas under the curves (AUCs) up to 0.960 and 0.977 for DCIS and IDC, respectively.

scholarly journals A deep learning model for gastric diffuse-type adenocarcinoma classification in whole slide images

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Fahdi Kanavati ◽  
Masayuki Tsuneki
Keyword(s):  
Deep Learning ◽  
The Body ◽  
Diffuse Type ◽  
Workflow System ◽  
Gastric Adenocarcinomas ◽  
Intestinal Type Adenocarcinoma ◽  
Roc Area ◽  
Computational Pathology ◽  
Deep Learning Model ◽  
Whole Slide Images

AbstractGastric diffuse-type adenocarcinoma represents a disproportionately high percentage of cases of gastric cancers occurring in the young, and its relative incidence seems to be on the rise. Usually it affects the body of the stomach, and it presents shorter duration and worse prognosis compared with the differentiated (intestinal) type adenocarcinoma. The main difficulty encountered in the differential diagnosis of gastric adenocarcinomas occurs with the diffuse-type. As the cancer cells of diffuse-type adenocarcinoma are often single and inconspicuous in a background desmoplaia and inflammation, it can often be mistaken for a wide variety of non-neoplastic lesions including gastritis or reactive endothelial cells seen in granulation tissue. In this study we trained deep learning models to classify gastric diffuse-type adenocarcinoma from WSIs. We evaluated the models on five test sets obtained from distinct sources, achieving receiver operator curve (ROC) area under the curves (AUCs) in the range of 0.95–0.99. The highly promising results demonstrate the potential of AI-based computational pathology for aiding pathologists in their diagnostic workflow system.

Abstract PO-008: Federated learning on whole slide images using weakly supervised computational pathology

2021 ◽  
Author(s):  
Ming Yang Lu ◽  
Dehan Kong ◽  
Jana Lipkova ◽  
Richard J. Chen ◽  
Rajendra Singh ◽  
...  
Keyword(s):  
Weakly Supervised ◽  
Computational Pathology ◽  
Whole Slide Images

scholarly journals Data-efficient and weakly supervised computational pathology on whole-slide images

2021 ◽  
Author(s):  
Ming Y. Lu ◽  
Drew F. K. Williamson ◽  
Tiffany Y. Chen ◽  
Richard J. Chen ◽  
Matteo Barbieri ◽  
...  
Keyword(s):  
Weakly Supervised ◽  
Computational Pathology ◽  
Whole Slide Images

scholarly journals Predicting gastric cancer outcome from resected lymph node histopathology images using deep learning

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Xiaodong Wang ◽  
Ying Chen ◽  
Yunshu Gao ◽  
Huiqing Zhang ◽  
Zehui Guan ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Deep Learning ◽  
Lymph Node ◽  
Lymph Nodes ◽  
Main Method ◽  
Learning Framework ◽  
Prognostic Assessment ◽  
N Stage ◽  
Cancer Outcome ◽  
Whole Slide Images

AbstractN-staging is a determining factor for prognostic assessment and decision-making for stage-based cancer therapeutic strategies. Visual inspection of whole-slides of intact lymph nodes is currently the main method used by pathologists to calculate the number of metastatic lymph nodes (MLNs). Moreover, even at the same N stage, the outcome of patients varies dramatically. Here, we propose a deep-learning framework for analyzing lymph node whole-slide images (WSIs) to identify lymph nodes and tumor regions, and then to uncover tumor-area-to-MLN-area ratio (T/MLN). After training, our model’s tumor detection performance was comparable to that of experienced pathologists and achieved similar performance on two independent gastric cancer validation cohorts. Further, we demonstrate that T/MLN is an interpretable independent prognostic factor. These findings indicate that deep-learning models could assist not only pathologists in detecting lymph nodes with metastases but also oncologists in exploring new prognostic factors, especially those that are difficult to calculate manually.

scholarly journals Two Ensemble-CNN Approaches for Colorectal Cancer Tissue Type Classification

2021 ◽  
Vol 7 (3) ◽  
pp. 51
Author(s):  
Emanuela Paladini ◽  
Edoardo Vantaggiato ◽  
Fares Bougourzi ◽  
Cosimo Distante ◽  
Abdenour Hadid ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Deep Learning ◽  
Digital Pathology ◽  
Texture Features ◽  
Tissue Type ◽  
Cancer Tissue ◽  
Learning Methods ◽  
Feature Based ◽  
Type Classification ◽  
Whole Slide Images

In recent years, automatic tissue phenotyping has attracted increasing interest in the Digital Pathology (DP) field. For Colorectal Cancer (CRC), tissue phenotyping can diagnose the cancer and differentiate between different cancer grades. The development of Whole Slide Images (WSIs) has provided the required data for creating automatic tissue phenotyping systems. In this paper, we study different hand-crafted feature-based and deep learning methods using two popular multi-classes CRC-tissue-type databases: Kather-CRC-2016 and CRC-TP. For the hand-crafted features, we use two texture descriptors (LPQ and BSIF) and their combination. In addition, two classifiers are used (SVM and NN) to classify the texture features into distinct CRC tissue types. For the deep learning methods, we evaluate four Convolutional Neural Network (CNN) architectures (ResNet-101, ResNeXt-50, Inception-v3, and DenseNet-161). Moreover, we propose two Ensemble CNN approaches: Mean-Ensemble-CNN and NN-Ensemble-CNN. The experimental results show that the proposed approaches outperformed the hand-crafted feature-based methods, CNN architectures and the state-of-the-art methods in both databases.

scholarly journals A deep-learning-based prognostic nomogram integrating microscopic digital pathology and macroscopic magnetic resonance images in nasopharyngeal carcinoma: a multi-cohort study

2020 ◽  
Vol 12 ◽  
pp. 175883592097141
Author(s):  
Fan Zhang ◽  
Lian-Zhen Zhong ◽  
Xun Zhao ◽  
Di Dong ◽  
Ji-Jin Yao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Magnetic Resonance ◽  
Nasopharyngeal Carcinoma ◽  
Treatment Failure ◽  
Digital Pathology ◽  
Imaging Features ◽  
Multi Scale ◽  
External Test ◽  
Whole Slide Images ◽  
Independent Cohort

Background: To explore the prognostic value of radiomics-based and digital pathology-based imaging biomarkers from macroscopic magnetic resonance imaging (MRI) and microscopic whole-slide images for patients with nasopharyngeal carcinoma (NPC). Methods: We recruited 220 NPC patients and divided them into training ( n = 132), internal test ( n = 44), and external test ( n = 44) cohorts. The primary endpoint was failure-free survival (FFS). Radiomic features were extracted from pretreatment MRI and selected and integrated into a radiomic signature. The histopathological signature was extracted from whole-slide images of biopsy specimens using an end-to-end deep-learning method. Incorporating two signatures and independent clinical factors, a multi-scale nomogram was constructed. We also tested the correlation between the key imaging features and genetic alternations in an independent cohort of 16 patients (biological test cohort). Results: Both radiomic and histopathologic signatures presented significant associations with treatment failure in the three cohorts (C-index: 0.689–0.779, all p < 0.050). The multi-scale nomogram showed a consistent significant improvement for predicting treatment failure compared with the clinical model in the training (C-index: 0.817 versus 0.730, p < 0.050), internal test (C-index: 0.828 versus 0.602, p < 0.050) and external test (C-index: 0.834 versus 0.679, p < 0.050) cohorts. Furthermore, patients were stratified successfully into two groups with distinguishable prognosis (log-rank p < 0.0010) using our nomogram. We also found that two texture features were related to the genetic alternations of chromatin remodeling pathways in another independent cohort. Conclusion: The multi-scale imaging features showed a complementary value in prognostic prediction and may improve individualized treatment in NPC.

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