scholarly journals Automatic prediction of tumour malignancy in breast cancer with fractal dimension

2016 ◽  
Vol 3 (12) ◽  
pp. 160558 ◽  
Author(s):  
Alan Chan ◽  
Jack A. Tuszynski
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Fractal Dimension ◽  
Classification Accuracy ◽  
Great Promise ◽  
Support Vector ◽  
Intraobserver Variability ◽  
Training Set ◽  
Manual Examination ◽  
Automatic Algorithm

Breast cancer is one of the most prevalent types of cancer today in women. The main avenue of diagnosis is through manual examination of histopathology tissue slides. Such a process is often subjective and error-ridden, suffering from both inter- and intraobserver variability. Our objective is to develop an automatic algorithm for analysing histopathology slides free of human subjectivity. Here, we calculate the fractal dimension of images of numerous breast cancer slides, at magnifications of 40×, 100×, 200× and 400×. Using machine learning, specifically, the support vector machine (SVM) method, the F1 score for classification accuracy of the 40× slides was found to be 0.979. Multiclass classification on the 40× slides yielded an accuracy of 0.556. A reduction of the size and scope of the SVM training set gave an average F1 score of 0.964. Taken together, these results show great promise in the use of fractal dimension to predict tumour malignancy.

scholarly journals Explainable machine learning can outperform Cox regression predictions and provide insights in breast cancer survival

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arturo Moncada-Torres ◽  
Marissa C. van Maaren ◽  
Mathijs P. Hendriks ◽  
Sabine Siesling ◽  
Gijs Geleijnse
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Explicit Knowledge ◽  
Cox Regression ◽  
Metastatic Breast ◽  
Gradient Boosting ◽  
Support Vector ◽  
Netherlands Cancer Registry ◽  
Extreme Gradient Boosting ◽  
The Impact

AbstractCox Proportional Hazards (CPH) analysis is the standard for survival analysis in oncology. Recently, several machine learning (ML) techniques have been adapted for this task. Although they have shown to yield results at least as good as classical methods, they are often disregarded because of their lack of transparency and little to no explainability, which are key for their adoption in clinical settings. In this paper, we used data from the Netherlands Cancer Registry of 36,658 non-metastatic breast cancer patients to compare the performance of CPH with ML techniques (Random Survival Forests, Survival Support Vector Machines, and Extreme Gradient Boosting [XGB]) in predicting survival using the $$c$$ c -index. We demonstrated that in our dataset, ML-based models can perform at least as good as the classical CPH regression ($$c$$ c -index $$\sim \,0.63$$ ∼ 0.63 ), and in the case of XGB even better ($$c$$ c -index $$\sim 0.73$$ ∼ 0.73 ). Furthermore, we used Shapley Additive Explanation (SHAP) values to explain the models’ predictions. We concluded that the difference in performance can be attributed to XGB’s ability to model nonlinearities and complex interactions. We also investigated the impact of specific features on the models’ predictions as well as their corresponding insights. Lastly, we showed that explainable ML can generate explicit knowledge of how models make their predictions, which is crucial in increasing the trust and adoption of innovative ML techniques in oncology and healthcare overall.

scholarly journals Breast Cancer Type Classification Using Machine Learning

2021 ◽  
Vol 11 (2) ◽  
pp. 61
Author(s):  
Jiande Wu ◽  
Chindo Hicks
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Machine Learning ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Genomic Research ◽  
Support Vector ◽  
Cancer Type ◽  
Classification Models

Background: Breast cancer is a heterogeneous disease defined by molecular types and subtypes. Advances in genomic research have enabled use of precision medicine in clinical management of breast cancer. A critical unmet medical need is distinguishing triple negative breast cancer, the most aggressive and lethal form of breast cancer, from non-triple negative breast cancer. Here we propose use of a machine learning (ML) approach for classification of triple negative breast cancer and non-triple negative breast cancer patients using gene expression data. Methods: We performed analysis of RNA-Sequence data from 110 triple negative and 992 non-triple negative breast cancer tumor samples from The Cancer Genome Atlas to select the features (genes) used in the development and validation of the classification models. We evaluated four different classification models including Support Vector Machines, K-nearest neighbor, Naïve Bayes and Decision tree using features selected at different threshold levels to train the models for classifying the two types of breast cancer. For performance evaluation and validation, the proposed methods were applied to independent gene expression datasets. Results: Among the four ML algorithms evaluated, the Support Vector Machine algorithm was able to classify breast cancer more accurately into triple negative and non-triple negative breast cancer and had less misclassification errors than the other three algorithms evaluated. Conclusions: The prediction results show that ML algorithms are efficient and can be used for classification of breast cancer into triple negative and non-triple negative breast cancer types.

scholarly journals Use of machine learning to identify autism with natural social gaze behavior (Preprint)

2021 ◽  
Author(s):  
Zhong Zhao ◽  
Haiming Tang ◽  
Xiaobin Zhang ◽  
Xingda Qu ◽  
Jianping Lu
Keyword(s):  
Machine Learning ◽  
Eye Tracking ◽  
Classification Accuracy ◽  
Autism Spectrum ◽  
Support Vector ◽  
Gaze Behavior ◽  
Linear Discriminant ◽  
Face To Face ◽  
Area Of Interest ◽  
Social Gaze

BACKGROUND Abnormal gaze behavior is a prominent feature of the autism spectrum disorder (ASD). Previous eye tracking studies had participants watch images (i.e., picture, video and webpage), and the application of machine learning (ML) on these data showed promising results in identify ASD individuals. Given the fact that gaze behavior differs in face-to-face interaction from image viewing tasks, no study has investigated whether natural social gaze behavior could accurately identify ASD. OBJECTIVE The objective of this study was to examine whether and what area of interest (AOI)-based features extracted from the natural social gaze behavior could identify ASD. METHODS Both children with ASD and typical development (TD) were eye-tracked when they were engaged in a face-to-face conversation with an interviewer. Four ML classifiers (support vector machine, SVM; linear discriminant analysis, LDA; decision tree, DT; and random forest, RF) were used to determine the maximum classification accuracy and the corresponding features. RESULTS A maximum classification accuracy of 84.62% were achieved with three classifiers (LDA, DT and RF). Results showed that the mouth, but not the eyes AOI, was a powerful feature in detecting ASD. CONCLUSIONS Natural gaze behavior could be leveraged to identify ASD, suggesting that ASD might be objectively screened with eye tracking technology in everyday social interaction. In addition, the comparison between our and previous findings suggests that eye tracking features that could identify ASD might be culture dependent and context sensitive.

scholarly journals Classifications of Breast Cancer Diagnosis using Machine Learning

2020 ◽  
Vol 14 ◽  
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Random Forest ◽  
Breast Cancer Diagnosis ◽  
Performance Comparison ◽  
Support Vector ◽  
Breast Cancer Dataset ◽  
K Nearest Neighbors ◽  
Cancer Dataset ◽  
Machine Learning Classification

Breast Cancer (BC) is amongst the most common and leading causes of deaths in women throughout the world. Recently, classification and data analysis tools are being widely used in the medical field for diagnosis, prognosis and decision making to help lower down the risks of people dying or suffering from diseases. Advanced machine learning methods have proven to give hope for patients as this has helped the doctors in early detection of diseases like Breast Cancer that can be fatal, in support with providing accurate outcomes. However, the results highly depend on the techniques used for feature selection and classification which will produce a strong machine learning model. In this paper, a performance comparison is conducted using four classifiers which are Multilayer Perceptron (MLP), Support Vector Machine (SVM), K-Nearest Neighbors (KNN) and Random Forest on the Wisconsin Breast Cancer dataset to spot the most effective predictors. The main goal is to apply best machine learning classification methods to predict the Breast Cancer as benign or malignant using terms such as accuracy, f-measure, precision and recall. Experimental results show that Random forest is proven to achieve the highest accuracy of 99.26% on this dataset and features, while SVM and KNN show 97.78% and 97.04% accuracy respectively. MLP shows the least accuracy of 94.07%. All the experiments are conducted using RStudio as the data mining tool platform.

scholarly journals Predicting lung adenocarcinoma disease progression using methylation-correlated blocks and ensemble machine learning classifiers

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10884
Author(s):  
Xin Yu ◽  
Qian Yang ◽  
Dong Wang ◽  
Zhaoyang Li ◽  
Nianhang Chen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Lung Adenocarcinoma ◽  
Cox Regression ◽  
Characteristic Curve ◽  
The Cancer Genome Atlas ◽  
Support Vector ◽  
Survival Prediction ◽  
Ensemble Model ◽  
Training Set ◽  
Cpg Sites

Applying the knowledge that methyltransferases and demethylases can modify adjacent cytosine-phosphorothioate-guanine (CpG) sites in the same DNA strand, we found that combining multiple CpGs into a single block may improve cancer diagnosis. However, survival prediction remains a challenge. In this study, we developed a pipeline named “stacked ensemble of machine learning models for methylation-correlated blocks” (EnMCB) that combined Cox regression, support vector regression (SVR), and elastic-net models to construct signatures based on DNA methylation-correlated blocks for lung adenocarcinoma (LUAD) survival prediction. We used methylation profiles from the Cancer Genome Atlas (TCGA) as the training set, and profiles from the Gene Expression Omnibus (GEO) as validation and testing sets. First, we partitioned the genome into blocks of tightly co-methylated CpG sites, which we termed methylation-correlated blocks (MCBs). After partitioning and feature selection, we observed different diagnostic capacities for predicting patient survival across the models. We combined the multiple models into a single stacking ensemble model. The stacking ensemble model based on the top-ranked block had the area under the receiver operating characteristic curve of 0.622 in the TCGA training set, 0.773 in the validation set, and 0.698 in the testing set. When stratified by clinicopathological risk factors, the risk score predicted by the top-ranked MCB was an independent prognostic factor. Our results showed that our pipeline was a reliable tool that may facilitate MCB selection and survival prediction.

Effect of GLCM Texture Features on the Medio-Lateral Oblique (MLO) View of Digital Mammograms for Breast Cancer Detection

2020 ◽  
Vol 9 (2) ◽  
pp. 25-44
Author(s):  
Usha N. ◽  
Sriraam N. ◽  
Kavya N. ◽  
Bharathi Hiremath ◽  
Anupama K Pujar ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Classification Accuracy ◽  
Breast Imaging ◽  
Texture Features ◽  
Support Vector ◽  
Risk Of Death ◽  
Automated Method ◽  
Occurrence Matrix ◽  
Aided Diagnosis ◽  
Mammogram Images

Breast cancer is one among the most common cancers in women. The early detection of breast cancer reduces the risk of death. Mammograms are an efficient breast imaging technique for breast cancer screening. Computer aided diagnosis (CAD) systems reduce manual errors and helps radiologists to analyze the mammogram images. The mammogram images are typically in two views, cranial-caudal (CC) and medio lateral oblique (MLO) views. MLO contains pectoral muscles (chest muscles) at the upper right or left corner of the image. In this study, it was removed by using a semi-automated method. All the normal and abnormal images were filtered and enhanced to improve the quality. GLCM (Gray Level Co-occurrence Matrix) texture features were extracted and analyzed by changing the number of features in a feature set. Linear Support Vector Machine (LSVM) was used as classifier. The classification accuracy was improved as the number of features in GLCM feature set increases. Simulation results show an overall classification accuracy of 96.7% with 19 GLCM features using SVM classifiers.

scholarly journals A Novel Method for Sea-Land Clutter Separation Using Regularized Randomized and Kernel Ridge Neural Networks

Sensors ◽  
2020 ◽  
Vol 20 (22) ◽  
pp. 6491
Author(s):  
Le Zhang ◽  
Jeyan Thiyagalingam ◽  
Anke Xue ◽  
Shuwen Xu
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
Classification Accuracy ◽  
Signal Amplitude ◽  
Statistical Characteristics ◽  
Support Vector ◽  
Amplitude Change ◽  
Novel Method

Classification of clutter, especially in the context of shore based radars, plays a crucial role in several applications. However, the task of distinguishing and classifying the sea clutter from land clutter has been historically performed using clutter models and/or coastal maps. In this paper, we propose two machine learning, particularly neural network, based approaches for sea-land clutter separation, namely the regularized randomized neural network (RRNN) and the kernel ridge regression neural network (KRR). We use a number of features, such as energy variation, discrete signal amplitude change frequency, autocorrelation performance, and other statistical characteristics of the respective clutter distributions, to improve the performance of the classification. Our evaluation based on a unique mixed dataset, which is comprised of partially synthetic clutter data for land and real clutter data from sea, offers improved classification accuracy. More specifically, the RRNN and KRR methods offer 98.50% and 98.75% accuracy, outperforming the conventional support vector machine and extreme learning based solutions.

Survey of Breast Cancer Detection Using Machine Learning Techniques in Big Data

2019 ◽  
Vol 21 (3) ◽  
pp. 80-92
Author(s):  
Madhuri Gupta ◽  
Bharat Gupta
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Research Work ◽  
Cancer Recurrence ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Common Disease ◽  
Learning Techniques ◽  
Learning Frameworks ◽  
Processing Engine

Cancer is a disease in which cells in body grow and divide beyond the control. Breast cancer is the second most common disease after lung cancer in women. Incredible advances in health sciences and biotechnology have prompted a huge amount of gene expression and clinical data. Machine learning techniques are improving the prior detection of breast cancer from this data. The research work carried out focuses on the application of machine learning methods, data analytic techniques, tools, and frameworks in the field of breast cancer research with respect to cancer survivability, cancer recurrence, cancer prediction and detection. Some of the widely used machine learning techniques used for detection of breast cancer are support vector machine and artificial neural network. Apache Spark data processing engine is found to be compatible with most of the machine learning frameworks.

scholarly journals Detecting conversation topics in primary care office visits from transcripts of patient-provider interactions

2019 ◽  
Vol 26 (12) ◽  
pp. 1493-1504 ◽  
Author(s):  
Jihyun Park ◽  
Dimitrios Kotzias ◽  
Patty Kuo ◽  
Robert L Logan IV ◽  
Kritzia Merced ◽  
...  
Keyword(s):  
Machine Learning ◽  
Primary Care ◽  
Classification Accuracy ◽  
Conditional Random Fields ◽  
Markov Models ◽  
Support Vector ◽  
Office Visits ◽  
Noisy Information ◽  
Gated Recurrent Units ◽  
Sequential Models

Abstract Objective Amid electronic health records, laboratory tests, and other technology, office-based patient and provider communication is still the heart of primary medical care. Patients typically present multiple complaints, requiring physicians to decide how to balance competing demands. How this time is allocated has implications for patient satisfaction, payments, and quality of care. We investigate the effectiveness of machine learning methods for automated annotation of medical topics in patient-provider dialog transcripts. Materials and Methods We used dialog transcripts from 279 primary care visits to predict talk-turn topic labels. Different machine learning models were trained to operate on single or multiple local talk-turns (logistic classifiers, support vector machines, gated recurrent units) as well as sequential models that integrate information across talk-turn sequences (conditional random fields, hidden Markov models, and hierarchical gated recurrent units). Results Evaluation was performed using cross-validation to measure 1) classification accuracy for talk-turns and 2) precision, recall, and F1 scores at the visit level. Experimental results showed that sequential models had higher classification accuracy at the talk-turn level and higher precision at the visit level. Independent models had higher recall scores at the visit level compared with sequential models. Conclusions Incorporating sequential information across talk-turns improves the accuracy of topic prediction in patient-provider dialog by smoothing out noisy information from talk-turns. Although the results are promising, more advanced prediction techniques and larger labeled datasets will likely be required to achieve prediction performance appropriate for real-world clinical applications.

scholarly journals Validation of miRNAs as Breast Cancer Biomarkers with a Machine Learning Approach

Cancers ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 431 ◽  
Author(s):  
Oneeb Rehman ◽  
Hanqi Zhuang ◽  
Ali Muhamed Ali ◽  
Ali Ibrahim ◽  
Zhongwei Li
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Information Gain ◽  
Support Vector ◽  
Learning Approach ◽  
Breast Cancers ◽  
Functional Studies ◽  
Normal Tissues ◽  
Machine Learning Approach ◽  
Chi Squared

Certain small noncoding microRNAs (miRNAs) are differentially expressed in normal tissues and cancers, which makes them great candidates for biomarkers for cancer. Previously, a selected subset of miRNAs has been experimentally verified to be linked to breast cancer. In this paper, we validated the importance of these miRNAs using a machine learning approach on miRNA expression data. We performed feature selection, using Information Gain (IG), Chi-Squared (CHI2) and Least Absolute Shrinkage and Selection Operation (LASSO), on the set of these relevant miRNAs to rank them by importance. We then performed cancer classification using these miRNAs as features using Random Forest (RF) and Support Vector Machine (SVM) classifiers. Our results demonstrated that the miRNAs ranked higher by our analysis had higher classifier performance. Performance becomes lower as the rank of the miRNA decreases, confirming that these miRNAs had different degrees of importance as biomarkers. Furthermore, we discovered that using a minimum of three miRNAs as biomarkers for breast cancers can be as effective as using the entire set of 1800 miRNAs. This work suggests that machine learning is a useful tool for functional studies of miRNAs for cancer detection and diagnosis.

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