scholarly journals Morphological Estimation of Cellularity on Neo-Adjuvant Treated Breast Cancer Histological Images

2020 ◽  
Vol 6 (10) ◽  
pp. 101
Author(s):  
Mauricio Alberto Ortega-Ruiz ◽  
Cefa Karabağ ◽  
Victor García Garduño ◽  
Constantino Carlos Reyes-Aldasoro
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Morphological Features ◽  
Training Data ◽  
Morphological Operations ◽  
Morphological Parameters ◽  
Learning Approaches ◽  
Residual Cancer Burden ◽  
Histological Images ◽  
Treated Breast

This paper describes a methodology that extracts key morphological features from histological breast cancer images in order to automatically assess Tumour Cellularity (TC) in Neo-Adjuvant treatment (NAT) patients. The response to NAT gives information on therapy efficacy and it is measured by the residual cancer burden index, which is composed of two metrics: TC and the assessment of lymph nodes. The data consist of whole slide images (WSIs) of breast tissue stained with Hematoxylin and Eosin (H&E) released in the 2019 SPIE Breast Challenge. The methodology proposed is based on traditional computer vision methods (K-means, watershed segmentation, Otsu’s binarisation, and morphological operations), implementing colour separation, segmentation, and feature extraction. Correlation between morphological features and the residual TC after a NAT treatment was examined. Linear regression and statistical methods were used and twenty-two key morphological parameters from the nuclei, epithelial region, and the full image were extracted. Subsequently, an automated TC assessment that was based on Machine Learning (ML) algorithms was implemented and trained with only selected key parameters. The methodology was validated with the score assigned by two pathologists through the intra-class correlation coefficient (ICC). The selection of key morphological parameters improved the results reported over other ML methodologies and it was very close to deep learning methodologies. These results are encouraging, as a traditionally-trained ML algorithm can be useful when limited training data are available preventing the use of deep learning approaches.

scholarly journals Deep learning identifies morphological features in breast cancer predictive of cancer ERBB2 status and trastuzumab treatment efficacy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dmitrii Bychkov ◽  
Nina Linder ◽  
Aleksei Tiulpin ◽  
Hakan Kücükel ◽  
Mikael Lundin ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Deep Learning ◽  
Gene Amplification ◽  
Characteristic Curve ◽  
Disease Free Survival ◽  
Morphological Features ◽  
Training Data ◽  
Primary Breast Tumor ◽  
Trastuzumab Treatment

AbstractThe treatment of patients with ERBB2 (HER2)-positive breast cancer with anti-ERBB2 therapy is based on the detection of ERBB2 gene amplification or protein overexpression. Machine learning (ML) algorithms can predict the amplification of ERBB2 based on tumor morphological features, but it is not known whether ML-derived features can predict survival and efficacy of anti-ERBB2 treatment. In this study, we trained a deep learning model with digital images of hematoxylin–eosin (H&E)-stained formalin-fixed primary breast tumor tissue sections, weakly supervised by ERBB2 gene amplification status. The gene amplification was determined by chromogenic in situ hybridization (CISH). The training data comprised digitized tissue microarray (TMA) samples from 1,047 patients. The correlation between the deep learning–predicted ERBB2 status, which we call H&E-ERBB2 score, and distant disease-free survival (DDFS) was investigated on a fully independent test set, which included whole-slide tumor images from 712 patients with trastuzumab treatment status available. The area under the receiver operating characteristic curve (AUC) in predicting gene amplification in the test sets was 0.70 (95% CI, 0.63–0.77) on 354 TMA samples and 0.67 (95% CI, 0.62–0.71) on 712 whole-slide images. Among patients with ERBB2-positive cancer treated with trastuzumab, those with a higher than the median morphology–based H&E-ERBB2 score derived from machine learning had more favorable DDFS than those with a lower score (hazard ratio [HR] 0.37; 95% CI, 0.15–0.93; P = 0.034). A high H&E-ERBB2 score was associated with unfavorable survival in patients with ERBB2-negative cancer as determined by CISH. ERBB2-associated morphology correlated with the efficacy of adjuvant anti-ERBB2 treatment and can contribute to treatment-predictive information in breast cancer.

scholarly journals Morphological estimation of Cellularity on Neo-adjuvant treated breast cancer histological images

2020 ◽  
Author(s):  
Mauricio Alberto Ortega-Ruiz ◽  
Cefa Karabağ ◽  
Victor García Garduño ◽  
Constantino Carlos Reyes-Aldasoro
Keyword(s):  
Breast Cancer ◽  
Morphological Analysis ◽  
Tumour Size ◽  
Residual Tumour ◽  
Morphological Parameters ◽  
Watershed Segmentation ◽  
Regression Methods ◽  
Histological Images ◽  
Treated Breast ◽  
Treated Breast Cancer

AbstractThis paper describes a methodology that extracts morphological features from histological breast cancer images stained for Hematoxilyn and Eosin (H&E). Cellularity was estimated and the correlation between features and the residual tumour size cellularity after a Neo-Adjuvant treatment (NAT) was examined. Images from whole slide imaging (WSI) were processed automatically with traditional computer vision methods to extract twenty two morphological parameters from the nuclei, epithelial region and the global image. The methodology was applied to a set of images from breast cancer under NAT. The data came from the BreastPathQ Cancer Cellularity Challenge 2019, and consisted of 2579 patches of 255×255 pixels of H&E histopatological samples from NAT treatment patients. The methodology automatically implements colour separation, segmentation and morphological analysis using traditional algorithms (K-means grouping, watershed segmentation, Otsu’s binarisation). Linear regression methods were applied to determine strongest correlation between the parameters and the cancer cellularity. The morphological parameters showed correlation with the residual tumour cancer cellularity. The strongest correlations corresponded to the stroma concentration value (r = −0.9786) and value from HSV image colour space (r = −0.9728), both from a global image parameters.

scholarly journals A Review of Computer-Aided Expert Systems for Breast Cancer Diagnosis

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2764
Author(s):  
Xin Yu Liew ◽  
Nazia Hameed ◽  
Jeremie Clos
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Deep Learning ◽  
Main Process ◽  
Learning Approaches ◽  
Learning Methods ◽  
Advantages And Disadvantages ◽  
Computer Aided ◽  
Conventional Methods ◽  
The Impact

A computer-aided diagnosis (CAD) expert system is a powerful tool to efficiently assist a pathologist in achieving an early diagnosis of breast cancer. This process identifies the presence of cancer in breast tissue samples and the distinct type of cancer stages. In a standard CAD system, the main process involves image pre-processing, segmentation, feature extraction, feature selection, classification, and performance evaluation. In this review paper, we reviewed the existing state-of-the-art machine learning approaches applied at each stage involving conventional methods and deep learning methods, the comparisons within methods, and we provide technical details with advantages and disadvantages. The aims are to investigate the impact of CAD systems using histopathology images, investigate deep learning methods that outperform conventional methods, and provide a summary for future researchers to analyse and improve the existing techniques used. Lastly, we will discuss the research gaps of existing machine learning approaches for implementation and propose future direction guidelines for upcoming researchers.

scholarly journals Deep Learning of Appearance Affinity for Multi-Object Tracking and Re-Identification: A Comparative View

Electronics ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1757
Author(s):  
María J. Gómez-Silva ◽  
Arturo de la Escalera ◽  
José M. Armingol
Keyword(s):  
Deep Learning ◽  
Object Tracking ◽  
Loss Function ◽  
Neural Model ◽  
Training Data ◽  
Learning Approaches ◽  
The Core ◽  
Triplet Loss ◽  
Affinity Model

Recognizing the identity of a query individual in a surveillance sequence is the core of Multi-Object Tracking (MOT) and Re-Identification (Re-Id) algorithms. Both tasks can be addressed by measuring the appearance affinity between people observations with a deep neural model. Nevertheless, the differences in their specifications and, consequently, in the characteristics and constraints of the available training data for each one of these tasks, arise from the necessity of employing different learning approaches to attain each one of them. This article offers a comparative view of the Double-Margin-Contrastive and the Triplet loss function, and analyzes the benefits and drawbacks of applying each one of them to learn an Appearance Affinity model for Tracking and Re-Identification. A batch of experiments have been conducted, and their results support the hypothesis concluded from the presented study: Triplet loss function is more effective than the Contrastive one when an Re-Id model is learnt, and, conversely, in the MOT domain, the Contrastive loss can better discriminate between pairs of images rendering the same person or not.

scholarly journals Deep Learning Using Multiple Degrees of Maximum-Intensity Projection for PET/CT Image Classification in Breast Cancer

Tomography ◽  
2022 ◽  
Vol 8 (1) ◽  
pp. 131-141
Author(s):  
Kanae Takahashi ◽  
Tomoyuki Fujioka ◽  
Jun Oyama ◽  
Mio Mori ◽  
Emi Yamaga ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Image Classification ◽  
Test Data ◽  
Characteristic Curve ◽  
Maximum Intensity Projection ◽  
Maximum Intensity ◽  
Training Data ◽  
Ct Image ◽  
Pet Ct

Deep learning (DL) has become a remarkably powerful tool for image processing recently. However, the usefulness of DL in positron emission tomography (PET)/computed tomography (CT) for breast cancer (BC) has been insufficiently studied. This study investigated whether a DL model using images with multiple degrees of PET maximum-intensity projection (MIP) images contributes to increase diagnostic accuracy for PET/CT image classification in BC. We retrospectively gathered 400 images of 200 BC and 200 non-BC patients for training data. For each image, we obtained PET MIP images with four different degrees (0°, 30°, 60°, 90°) and made two DL models using Xception. One DL model diagnosed BC with only 0-degree MIP and the other used four different degrees. After training phases, our DL models analyzed test data including 50 BC and 50 non-BC patients. Five radiologists interpreted these test data. Sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were calculated. Our 4-degree model, 0-degree model, and radiologists had a sensitivity of 96%, 82%, and 80–98% and a specificity of 80%, 88%, and 76–92%, respectively. Our 4-degree model had equal or better diagnostic performance compared with that of the radiologists (AUC = 0.936 and 0.872–0.967, p = 0.036–0.405). A DL model similar to our 4-degree model may lead to help radiologists in their diagnostic work in the future.

scholarly journals Real-Time Automated Classification of Sky Conditions Using Deep Learning and Edge Computing

2021 ◽  
Vol 13 (19) ◽  
pp. 3859
Author(s):  
Joby M. Prince Czarnecki ◽  
Sathishkumar Samiappan ◽  
Meilun Zhou ◽  
Cary Daniel McCraine ◽  
Louis L. Wasson
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Image Quality ◽  
Convolutional Neural Network ◽  
Precision Agriculture ◽  
Edge Computing ◽  
Training Data ◽  
Learning Approaches ◽  
Sky Conditions

The radiometric quality of remotely sensed imagery is crucial for precision agriculture applications because estimations of plant health rely on the underlying quality. Sky conditions, and specifically shadowing from clouds, are critical determinants in the quality of images that can be obtained from low-altitude sensing platforms. In this work, we first compare common deep learning approaches to classify sky conditions with regard to cloud shadows in agricultural fields using a visible spectrum camera. We then develop an artificial-intelligence-based edge computing system to fully automate the classification process. Training data consisting of 100 oblique angle images of the sky were provided to a convolutional neural network and two deep residual neural networks (ResNet18 and ResNet34) to facilitate learning two classes, namely (1) good image quality expected, and (2) degraded image quality expected. The expectation of quality stemmed from the sky condition (i.e., density, coverage, and thickness of clouds) present at the time of the image capture. These networks were tested using a set of 13,000 images. Our results demonstrated that ResNet18 and ResNet34 classifiers produced better classification accuracy when compared to a convolutional neural network classifier. The best overall accuracy was obtained by ResNet34, which was 92% accurate, with a Kappa statistic of 0.77. These results demonstrate a low-cost solution to quality control for future autonomous farming systems that will operate without human intervention and supervision.

scholarly journals Deep learning-based research on the influence of training data size for breast cancer pathology detection

2019 ◽  
Vol 2019 (23) ◽  
pp. 8729-8732
Author(s):  
Chongyang Cui ◽  
Shangchun Fan ◽  
Han Lei ◽  
Xiaolei Qu ◽  
Dezhi Zheng
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Training Data ◽  
Cancer Pathology ◽  
Breast Cancer Pathology

scholarly journals A general approach for improving deep learning-based medical relation extraction using a pre-trained model and fine-tuning

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Tao Chen ◽  
Mingfen Wu ◽  
Hexi Li
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Relation Extraction ◽  
Training Model ◽  
Biomedical Literature ◽  
Training Data ◽  
Fine Tuning ◽  
Learning Approaches ◽  
Additional Time ◽  
Clinical Records

Abstract The automatic extraction of meaningful relations from biomedical literature or clinical records is crucial in various biomedical applications. Most of the current deep learning approaches for medical relation extraction require large-scale training data to prevent overfitting of the training model. We propose using a pre-trained model and a fine-tuning technique to improve these approaches without additional time-consuming human labeling. Firstly, we show the architecture of Bidirectional Encoder Representations from Transformers (BERT), an approach for pre-training a model on large-scale unstructured text. We then combine BERT with a one-dimensional convolutional neural network (1d-CNN) to fine-tune the pre-trained model for relation extraction. Extensive experiments on three datasets, namely the BioCreative V chemical disease relation corpus, traditional Chinese medicine literature corpus and i2b2 2012 temporal relation challenge corpus, show that the proposed approach achieves state-of-the-art results (giving a relative improvement of 22.2, 7.77, and 38.5% in F1 score, respectively, compared with a traditional 1d-CNN classifier). The source code is available at https://github.com/chentao1999/MedicalRelationExtraction.

scholarly journals BUILDING GENERALIZATION USING DEEP LEARNING

2018 ◽  
Vol XLII-4 ◽  
pp. 565-572 ◽  
Author(s):  
M. Sester ◽  
Y. Feng ◽  
F. Thiemann
Keyword(s):  
Computer Vision ◽  
Deep Learning ◽  
Physical Reality ◽  
Training Data ◽  
Data Sets ◽  
Learning Approaches ◽  
Depth Analysis ◽  
Map Series ◽  
Training Examples ◽  
Future Work

<p><strong>Abstract.</strong> Cartographic generalization is a problem, which poses interesting challenges to automation. Whereas plenty of algorithms have been developed for the different sub-problems of generalization (e.g. simplification, displacement, aggregation), there are still cases, which are not generalized adequately or in a satisfactory way. The main problem is the interplay between different operators. In those cases the benchmark is the human operator, who is able to design an aesthetic and correct representation of the physical reality.</p><p>Deep Learning methods have shown tremendous success for interpretation problems for which algorithmic methods have deficits. A prominent example is the classification and interpretation of images, where deep learning approaches outperform the traditional computer vision methods. In both domains &amp;ndash; computer vision and cartography &amp;ndash; humans are able to produce a solution; a prerequisite for this is, that there is the possibility to generate many training examples for the different cases. Thus, the idea in this paper is to employ Deep Learning for cartographic generalizations tasks, especially for the task of building generalization. An advantage of this task is the fact that many training data sets are available from given map series. The approach is a first attempt using an existing network.</p><p>In the paper, the details of the implementation will be reported, together with an in depth analysis of the results. An outlook on future work will be given.</p>

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