Learning New Tricks from Old Dogs -- Inter-Species, Inter-Tissue Domain Adaptation for Mitotic Figure Assessment

For histopathological tumor assessment, the count of mitotic figures per area is an important part of prognostication. Algorithmic approaches - such as for mitotic figure identification - have significantly improved in recent times, potentially allowing for computer-augmented or fully automatic screening systems in the future. This trend is further supported by whole slide scanning microscopes becoming available in many pathology labs and could soon become a standard imaging tool. For an application in broader fields of such algorithms, the availability of mitotic figure data sets of sufficient size for the respective tissue type and species is an important precondition, that is, however, rarely met. While algorithmic performance climbed steadily for e.g. human mammary carcinoma, thanks to several challenges held in the field, for most tumor types, data sets are not available. In this work, we assess domain transfer of mitotic figure recognition using domain adversarial training on four data sets, two from dogs and two from humans. We were able to show that domain adversarial training considerably improves accuracy when applying mitotic figure classification learned from the canine on the human data sets (up to +12.8% in accuracy) and is thus a helpful method to transfer knowledge from existing data sets to new tissue types and species.Comment: 5 pages, submission to BVM 202

A New Hybrid Breast Cancer Diagnosis Model Using Deep Learning Model and ReliefF

Breast cancer is a dangerous type of cancer usually found in women and is a significant research topic in medical science. In patients who are diagnosed and not treated early, cancer spreads to other organs, making treatment difficult. In breast cancer diagnosis, the accuracy of the pathological diagnosis is of great importance to shorten the decision-making process, minimize unnoticed cancer cells and obtain a faster diagnosis. However, the similarity of images in histopathological breast cancer image analysis is a sensitive and difficult process that requires high competence for field experts. In recent years, researchers have been seeking solutions to this process using machine learning and deep learning methods, which have contributed to significant developments in medical diagnosis and image analysis. In this study, a hybrid DCNN + ReliefF is proposed for the classification of breast cancer histopathological images, utilizing the activation properties of pre-trained deep convolutional neural network (DCNN) models, and the dimension-reduction-based ReliefF feature selective algorithm. The model is based on a fine-tuned transfer-learning technique for fully connected layers. In addition, the models were compared to the k-nearest neighbor (kNN), naive Bayes (NB), and support vector machine (SVM) machine learning approaches. The performance of each feature extractor and classifier combination was analyzed using the sensitivity, precision, F1-Score, and ROC curves. The proposed hybrid model was trained separately at different magnifications using the BreakHis dataset. The results show that the model is an efficient classification model with up to 97.8% (AUC) accuracy. © 2022 Lavoisier. All rights reserved

Evaluation of Machine Learning Models for Breast Cancer Diagnosis Via Histogram of Oriented Gradients Method and Histopathology Images

Breast cancer is the main death rate from malignant growth worldwide and the most frequently diagnosed type of cancer in females. Machine learning systems have been developed to assist in the accurate detection of cancer. There are numerous methods for cancer detection. But histopathological images are thought to be more precise. In this study, we used the HOG features extractor to extract statistical features from histopathology images of invasive ductal carcinoma. We chose the following images at random from the histopathology images: 100, 200, 400, 1000, and 2000. These statistical features were then used to train several algorithms, including the decision tree, quadratic discriminant analysis, extra randomized trees, gradient boosting, gaussian process classifier, naive bayes, nearest centroid, multilayer perceptron, and support vector machine, to identify whether or not the images depict cancerous or noncancerous growth. The algorithms' performance was evaluated depending on the specificity, accuracy, sensitivity, precision, F1_score, and AUC. The algorithms used worked best when the number of images was set to 100. As the number of images went up, their effectiveness went down

Breast cancer diagnosis: a survey of pre-processing, segmentation, feature extraction and classification

Machine learning methods have been an interesting method in the field of medical for many years, and they have achieved successful results in various fields of medical science. This paper examines the effects of using machine learning algorithms in the diagnosis and classification of breast cancer from mammography imaging data. Cancer diagnosis is the identification of images as cancer or non-cancer, and this involves image preprocessing, feature extraction, classification, and performance analysis. This article studied 93 different references mentioned in the previous years in the field of processing and tries to find an effective way to diagnose and classify breast cancer. Based on the results of this research, it can be concluded that most of today’s successful methods focus on the use of deep learning methods. Finding a new method requires an overview of existing methods in the field of deep learning methods in order to make a comparison and case study

Nuclear Morphometry using a Deep Learning-based Algorithm has Prognostic Relevance for Canine Cutaneous Mast Cell Tumors

Variation in nuclear size and shape is an important criterion of malignancy for many tumor types; however, categorical estimates by pathologists have poor reproducibility. Measurements of nuclear characteristics (morphometry) can improve reproducibility, but manual methods are time consuming. In this study, we evaluated fully automated morphometry using a deep learning-based algorithm in 96 canine cutaneous mast cell tumors with information on patient survival. Algorithmic morphometry was compared with karyomegaly estimates by 11 pathologists, manual nuclear morphometry of 12 cells by 9 pathologists, and the mitotic count as a benchmark. The prognostic value of automated morphometry was high with an area under the ROC curve regarding the tumor-specific survival of 0.943 (95% CI: 0.889 - 0.996) for the standard deviation (SD) of nuclear area, which was higher than manual morphometry of all pathologists combined (0.868, 95% CI: 0.737 - 0.991) and the mitotic count (0.885, 95% CI: 0.765 - 1.00). At the proposed thresholds, the hazard ratio for algorithmic morphometry (SD of nuclear area $\geq 9.0 \mu m^2$) was 18.3 (95% CI: 5.0 - 67.1), for manual morphometry (SD of nuclear area $\geq 10.9 \mu m^2$) 9.0 (95% CI: 6.0 - 13.4), for karyomegaly estimates 7.6 (95% CI: 5.7 - 10.1), and for the mitotic count 30.5 (95% CI: 7.8 - 118.0). Inter-rater reproducibility for karyomegaly estimates was fair ($\kappa$ = 0.226) with highly variable sensitivity/specificity values for the individual pathologists. Reproducibility for manual morphometry (SD of nuclear area) was good (ICC = 0.654). This study supports the use of algorithmic morphometry as a prognostic test to overcome the limitations of estimates and manual measurements

Chasing a Better Decision Margin for Discriminative Histopathological Breast Cancer Image Classification

When considering a large dataset of histopathologic breast images captured at various magnification levels, the process of distinguishing between benign and malignant cancer from these images can be time-intensive. The automation of histopathological breast cancer image classification holds significant promise for expediting pathology diagnoses and reducing the analysis time. Convolutional neural networks (CNNs) have recently gained traction for their ability to more accurately classify histopathological breast cancer images. CNNs excel at extracting distinctive features that emphasize semantic information. However, traditional CNNs employing the softmax loss function often struggle to achieve the necessary discriminatory power for this task. To address this challenge, a set of angular margin-based softmax loss functions have emerged, including angular softmax (A-Softmax), large margin cosine loss (CosFace), and additive angular margin (ArcFace), each sharing a common objective: maximizing inter-class variation while minimizing intra-class variation. This study delves into these three loss functions and their potential to extract distinguishing features while expanding the decision boundary between classes. Rigorous experimentation on a well-established histopathological breast cancer image dataset, BreakHis, has been conducted. As per the results, it is evident that CosFace focuses on augmenting the differences between classes, while A-Softmax and ArcFace tend to emphasize augmenting within-class variations. These observations underscore the efficacy of margin penalties on angular softmax losses in enhancing feature discrimination within the embedding space. These loss functions consistently outperform softmax-based techniques, either by widening the gaps among classes or enhancing the compactness of individual classes.This work is partially supported by the project GUI19/027 and by the grant PID2021-126701OB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”

Chasing a Better Decision Margin for Discriminative Histopathological Breast Cancer Image Classification

When considering a large dataset of histopathologic breast images captured at various magnification levels, the process of distinguishing between benign and malignant cancer from these images can be time-intensive. The automation of histopathological breast cancer image classification holds significant promise for expediting pathology diagnoses and reducing the analysis time. Convolutional neural networks (CNNs) have recently gained traction for their ability to more accurately classify histopathological breast cancer images. CNNs excel at extracting distinctive features that emphasize semantic information. However, traditional CNNs employing the softmax loss function often struggle to achieve the necessary discriminatory power for this task. To address this challenge, a set of angular margin-based softmax loss functions have emerged, including angular softmax (A-Softmax), large margin cosine loss (CosFace), and additive angular margin (ArcFace), each sharing a common objective: maximizing inter-class variation while minimizing intra-class variation. This study delves into these three loss functions and their potential to extract distinguishing features while expanding the decision boundary between classes. Rigorous experimentation on a well-established histopathological breast cancer image dataset, BreakHis, has been conducted. As per the results, it is evident that CosFace focuses on augmenting the differences between classes, while A-Softmax and ArcFace tend to emphasize augmenting within-class variations. These observations underscore the efficacy of margin penalties on angular softmax losses in enhancing feature discrimination within the embedding space. These loss functions consistently outperform softmax-based techniques, either by widening the gaps among classes or enhancing the compactness of individual classes

Reduced Deep Convolutional Activation Features (R-DeCAF) in Histopathology Images to Improve the Classification Performance for Breast Cancer Diagnosis

Breast cancer is the second most common cancer among women worldwide. Diagnosis of breast cancer by the pathologists is a time-consuming procedure and subjective. Computer aided diagnosis frameworks are utilized to relieve pathologist workload by classifying the data automatically, in which deep convolutional neural networks (CNNs) are effective solutions. The features extracted from activation layer of pre-trained CNNs are called deep convolutional activation features (DeCAF). In this paper, we have analyzed that all DeCAF features are not necessarily led to a higher accuracy in the classification task and dimension reduction plays an important role. Therefore, different dimension reduction methods are applied to achieve an effective combination of features by capturing the essence of DeCAF features. To this purpose, we have proposed reduced deep convolutional activation features (R-DeCAF). In this framework, pre-trained CNNs such as AlexNet, VGG-16 and VGG-19 are utilized in transfer learning mode as feature extractors. DeCAF features are extracted from the first fully connected layer of the mentioned CNNs and support vector machine has been used for binary classification. Among linear and nonlinear dimensionality reduction algorithms, linear approaches such as principal component analysis (PCA) represent a better combination among deep features and lead to a higher accuracy in the classification task using small number of features considering specific amount of cumulative explained variance (CEV) of features. The proposed method is validated using experimental BreakHis dataset. Comprehensive results show improvement in the classification accuracy up to 4.3% with less computational time. Best achieved accuracy is 91.13% for 400x data with feature vector size (FVS) of 23 and CEV equals to 0.15 using pre-trained AlexNet as feature extractor and PCA as feature reduction algorithm

A review on recent progress in machine learning and deep learning methods for cancer classification on gene expression data

Data-driven model with predictive ability are important to be used in medical and healthcare. However, the most challenging task in predictive modeling is to construct a prediction model, which can be addressed using machine learning (ML) methods. The methods are used to learn and trained the model using a gene expression dataset without being programmed explicitly. Due to the vast amount of gene expression data, this task becomes complex and time consuming. This paper provides a recent review on recent progress in ML and deep learning (DL) for cancer classification, which has received increasing attention in bioinformatics and computational biology. The development of cancer classification methods based on ML and DL is mostly focused on this review. Although many methods have been applied to the cancer classification problem, recent progress shows that most of the successful techniques are those based on supervised and DL methods. In addition, the sources of the healthcare dataset are also described. The development of many machine learning methods for insight analysis in cancer classification has brought a lot of improvement in healthcare. Currently, it seems that there is highly demanded further development of efficient classification methods to address the expansion of healthcare applications

Recent advancement in Disease Diagnostic using machine learning: Systematic survey of decades, comparisons, and challenges

Computer-aided diagnosis (CAD), a vibrant medical imaging research field, is expanding quickly. Because errors in medical diagnostic systems might lead to seriously misleading medical treatments, major efforts have been made in recent years to improve computer-aided diagnostics applications. The use of machine learning in computer-aided diagnosis is crucial. A simple equation may result in a false indication of items like organs. Therefore, learning from examples is a vital component of pattern recognition. Pattern recognition and machine learning in the biomedical area promise to increase the precision of disease detection and diagnosis. They also support the decision-making process's objectivity. Machine learning provides a practical method for creating elegant and autonomous algorithms to analyze high-dimensional and multimodal bio-medical data. This review article examines machine-learning algorithms for detecting diseases, including hepatitis, diabetes, liver disease, dengue fever, and heart disease. It draws attention to the collection of machine learning techniques and algorithms employed in studying conditions and the ensuing decision-making process