Deep Learning Methods for Mitosis Detection in Breast Cancer Histopathological Images: A Comprehensive Review

2020 ◽  
pp. 279-306
Author(s):  
Nassima Dif ◽  
Zakaria Elberrichi
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Learning Methods ◽  
Comprehensive Review ◽  
Mitosis Detection ◽  
Histopathological Images

Data Science in Economics: Comprehensive Review of Advanced Machine Learning and Deep Learning Methods

2020 ◽  
Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Puhong Duan ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Data Science ◽  
Learning Methods ◽  
Comprehensive Review

Sequence-Based Deep Learning Frameworks on Enhancer-Promoter Interactions Prediction

2020 ◽  
Vol 26 ◽  
Author(s):  
Xiaoping Min ◽  
Fengqing Lu ◽  
Chunyan Li
Keyword(s):  
Gene Expression ◽  
Deep Learning ◽  
Dna Sequences ◽  
Experimental Methods ◽  
Learning Methods ◽  
Comprehensive Review ◽  
Genomic Features ◽  
Disease Mechanisms ◽  
Evaluation Strategies ◽  
Learning Frameworks

: Enhancer-promoter interactions (EPIs) in the human genome are of great significance to transcriptional regulation which tightly controls gene expression. Identification of EPIs can help us better deciphering gene regulation and understanding disease mechanisms. However, experimental methods to identify EPIs are constrained by the fund, time and manpower while computational methods using DNA sequences and genomic features are viable alternatives. Deep learning methods have shown promising prospects in classification and efforts that have been utilized to identify EPIs. In this survey, we specifically focus on sequence-based deep learning methods and conduct a comprehensive review of the literatures of them. We first briefly introduce existing sequence-based frameworks on EPIs prediction and their technique details. After that, we elaborate on the dataset, pre-processing means and evaluation strategies. Finally, we discuss the challenges these methods are confronted with and suggest several future opportunities.

Diagnosing breast cancer tumors using stacked ensemble model

2021 ◽  
pp. 1-9
Author(s):  
Ahmet Haşim Yurttakal ◽  
Hasan Erbay ◽  
Türkan İkizceli ◽  
Seyhan Karaçavuş ◽  
Cenker Biçer
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Medical Imaging ◽  
Early Stage ◽  
False Negative ◽  
Gradient Boosting ◽  
Physical Sign ◽  
Ensemble Model ◽  
Learning Methods ◽  
Dce Mri

Breast cancer is the most common cancer that progresses from cells in the breast tissue among women. Early-stage detection could reduce death rates significantly, and the detection-stage determines the treatment process. Mammography is utilized to discover breast cancer at an early stage prior to any physical sign. However, mammography might return false-negative, in which case, if it is suspected that lesions might have cancer of chance greater than two percent, a biopsy is recommended. About 30 percent of biopsies result in malignancy that means the rate of unnecessary biopsies is high. So to reduce unnecessary biopsies, recently, due to its excellent capability in soft tissue imaging, Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) has been utilized to detect breast cancer. Nowadays, DCE-MRI is a highly recommended method not only to identify breast cancer but also to monitor its development, and to interpret tumorous regions. However, in addition to being a time-consuming process, the accuracy depends on radiologists’ experience. Radiomic data, on the other hand, are used in medical imaging and have the potential to extract disease characteristics that can not be seen by the naked eye. Radiomics are hard-coded features and provide crucial information about the disease where it is imaged. Conversely, deep learning methods like convolutional neural networks(CNNs) learn features automatically from the dataset. Especially in medical imaging, CNNs’ performance is better than compared to hard-coded features-based methods. However, combining the power of these two types of features increases accuracy significantly, which is especially critical in medicine. Herein, a stacked ensemble of gradient boosting and deep learning models were developed to classify breast tumors using DCE-MRI images. The model makes use of radiomics acquired from pixel information in breast DCE-MRI images. Prior to train the model, radiomics had been applied to the factor analysis to refine the feature set and eliminate unuseful features. The performance metrics, as well as the comparisons to some well-known machine learning methods, state the ensemble model outperforms its counterparts. The ensembled model’s accuracy is 94.87% and its AUC value is 0.9728. The recall and precision are 1.0 and 0.9130, respectively, whereas F1-score is 0.9545.

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 Breast Cancer Multi-classification from Histopathological Images with Structured Deep Learning Model

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Zhongyi Han ◽  
Benzheng Wei ◽  
Yuanjie Zheng ◽  
Yilong Yin ◽  
Kejian Li ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Learning Model ◽  
Histopathological Images ◽  
Multi Classification ◽  
Deep Learning Model

Extracting comprehensive clinical information for breast cancer using deep learning methods

2019 ◽  
Vol 132 ◽  
pp. 103985 ◽  
Author(s):  
Xiaohui Zhang ◽  
Yaoyun Zhang ◽  
Qin Zhang ◽  
Yuankai Ren ◽  
Tinglin Qiu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Clinical Information ◽  
Learning Methods

scholarly journals Deep learning accurately predicts estrogen receptor status in breast cancer metabolomics data

2017 ◽  
Author(s):  
Fadhl M Alakwaa ◽  
Kumardeep Chaudhary ◽  
Lana X Garmire
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Estrogen Receptor ◽  
Deep Learning ◽  
Support Vector ◽  
Integrated Analysis ◽  
Learning Method ◽  
Learning Methods ◽  
Metabolomics Data ◽  
Machine Learning Methods

ABSTRACTMetabolomics holds the promise as a new technology to diagnose highly heterogeneous diseases. Conventionally, metabolomics data analysis for diagnosis is done using various statistical and machine learning based classification methods. However, it remains unknown if deep neural network, a class of increasingly popular machine learning methods, is suitable to classify metabolomics data. Here we use a cohort of 271 breast cancer tissues, 204 positive estrogen receptor (ER+) and 67 negative estrogen receptor (ER-), to test the accuracies of autoencoder, a deep learning (DL) framework, as well as six widely used machine learning models, namely Random Forest (RF), Support Vector Machines (SVM), Recursive Partitioning and Regression Trees (RPART), Linear Discriminant Analysis (LDA), Prediction Analysis for Microarrays (PAM), and Generalized Boosted Models (GBM). DL framework has the highest area under the curve (AUC) of 0.93 in classifying ER+/ER-patients, compared to the other six machine learning algorithms. Furthermore, the biological interpretation of the first hidden layer reveals eight commonly enriched significant metabolomics pathways (adjusted P-value<0.05) that cannot be discovered by other machine learning methods. Among them, protein digestion & absorption and ATP-binding cassette (ABC) transporters pathways are also confirmed in integrated analysis between metabolomics and gene expression data in these samples. In summary, deep learning method shows advantages for metabolomics based breast cancer ER status classification, with both the highest prediction accurcy (AUC=0.93) and better revelation of disease biology. We encourage the adoption of autoencoder based deep learning method in the metabolomics research community for classification.

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