scholarly journals Comparison of Imputation Methods on Retrospective Breast Cancer Data in Tanzania: A Case Study of Muhimbili and Ocean Road Hospitals

2021 ◽  
Author(s):  
Rahibu A. Abassi ◽  
Amina S. Msengwa ◽  
Rocky R. J. Akarro
Keyword(s):  
Breast Cancer ◽  
Logistic Regression ◽  
Missing Data ◽  
Binary Logistic Regression ◽  
Breast Cancer Dataset ◽  
Cancer Dataset ◽  
Imputation Methods ◽  
Multiple Imputations ◽  
Predictive Mean Matching ◽  
Mean Square Errors

Abstract Background Clinical data are at risk of having missing or incomplete values for several reasons including patients’ failure to attend clinical measurements, wrong interpretations of measurements, and measurement recorder’s defects. Missing data can significantly affect the analysis and results might be doubtful due to bias caused by omission of missed observation during statistical analysis especially if a dataset is considerably small. The objective of this study is to compare several imputation methods in terms of efficiency in filling-in the missing data so as to increase the prediction and classification accuracy in breast cancer dataset. Methods Five imputation methods namely series mean, k-nearest neighbour, hot deck, predictive mean matching, and multiple imputations were applied to replace the missing values to the real breast cancer dataset. The efficiency of imputation methods was compared by using the Root Mean Square Errors and Mean Absolute Errors to obtain a suitable complete dataset. Binary logistic regression and linear discrimination classifiers were applied to the imputed dataset to compare their efficacy on classification and discrimination. Results The evaluation of imputation methods revealed that the predictive mean matching method was better off compared to other imputation methods. In addition, the binary logistic regression and linear discriminant analyses yield almost similar values on overall classification rates, sensitivity and specificity. Conclusion The predictive mean matching imputation showed higher accuracy in estimating and replacing missing/incomplete data values in a real breast cancer dataset under the study. It is a more effective and good method to handle missing data in this scenario. We recommend to replace missing data by using predictive mean matching since it is a plausible approach toward multiple imputations for numerical variables, as it improves estimation and prediction accuracy over the use complete-case analysis especially when percentage of missing data is not very small.

HIOC: a hybrid imputation method to predict missing values in medical datasets

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Pooja Rani ◽  
Rajneesh Kumar ◽  
Anurag Jain
Keyword(s):  
Breast Cancer ◽  
Heart Disease ◽  
Missing Values ◽  
Imputation Method ◽  
Support Vector ◽  
Correct Prediction ◽  
Breast Cancer Dataset ◽  
Cancer Dataset ◽  
Content Type ◽  
Imputation Methods

PurposeDecision support systems developed using machine learning classifiers have become a valuable tool in predicting various diseases. However, the performance of these systems is adversely affected by the missing values in medical datasets. Imputation methods are used to predict these missing values. In this paper, a new imputation method called hybrid imputation optimized by the classifier (HIOC) is proposed to predict missing values efficiently.Design/methodology/approachThe proposed HIOC is developed by using a classifier to combine multivariate imputation by chained equations (MICE), K nearest neighbor (KNN), mean and mode imputation methods in an optimum way. Performance of HIOC has been compared to MICE, KNN, and mean and mode methods. Four classifiers support vector machine (SVM), naive Bayes (NB), random forest (RF) and decision tree (DT) have been used to evaluate the performance of imputation methods.FindingsThe results show that HIOC performed efficiently even with a high rate of missing values. It had reduced root mean square error (RMSE) up to 17.32% in the heart disease dataset and 34.73% in the breast cancer dataset. Correct prediction of missing values improved the accuracy of the classifiers in predicting diseases. It increased classification accuracy up to 18.61% in the heart disease dataset and 6.20% in the breast cancer dataset.Originality/valueThe proposed HIOC is a new hybrid imputation method that can efficiently predict missing values in any medical dataset.

scholarly journals Prediction of benign and malignant breast cancer using data mining techniques

2018 ◽  
Vol 12 (2) ◽  
pp. 119-126 ◽  
Author(s):  
Vikas Chaurasia ◽  
Saurabh Pal ◽  
BB Tiwari
Keyword(s):  
Breast Cancer ◽  
Data Mining ◽  
Low Income ◽  
Prediction Models ◽  
Naive Bayes ◽  
Naïve Bayes ◽  
Low Income Countries ◽  
Breast Cancer Dataset ◽  
Cancer Dataset ◽  
Rbf Network

Breast cancer is the second most leading cancer occurring in women compared to all other cancers. Around 1.1 million cases were recorded in 2004. Observed rates of this cancer increase with industrialization and urbanization and also with facilities for early detection. It remains much more common in high-income countries but is now increasing rapidly in middle- and low-income countries including within Africa, much of Asia, and Latin America. Breast cancer is fatal in under half of all cases and is the leading cause of death from cancer in women, accounting for 16% of all cancer deaths worldwide. The objective of this research paper is to present a report on breast cancer where we took advantage of those available technological advancements to develop prediction models for breast cancer survivability. We used three popular data mining algorithms (Naïve Bayes, RBF Network, J48) to develop the prediction models using a large dataset (683 breast cancer cases). We also used 10-fold cross-validation methods to measure the unbiased estimate of the three prediction models for performance comparison purposes. The results (based on average accuracy Breast Cancer dataset) indicated that the Naïve Bayes is the best predictor with 97.36% accuracy on the holdout sample (this prediction accuracy is better than any reported in the literature), RBF Network came out to be the second with 96.77% accuracy, J48 came out third with 93.41% accuracy.

scholarly journals PERFORMANCE ANALYSIS OF BREAST CANCER CLASSIFICATION USING DECISION TREE CLASSIFIERS

2017 ◽  
Vol 9 (2) ◽  
pp. 19 ◽  
Author(s):  
P. Hamsagayathri ◽  
P. Sampath
Keyword(s):  
Breast Cancer ◽  
Decision Tree ◽  
Ductal Carcinoma ◽  
Research Work ◽  
The United States ◽  
Breast Cancer Dataset ◽  
Decision Tree Classifier ◽  
Cancer Dataset ◽  
Term Survival ◽  
Tree Classifier

Breast cancer is one of the dangerous cancers among world’s women above 35 y. The breast is made up of lobules that secrete milk and thin milk ducts to carry milk from lobules to the nipple. Breast cancer mostly occurs either in lobules or in milk ducts. The most common type of breast cancer is ductal carcinoma where it starts from ducts and spreads across the lobules and surrounding tissues. According to the medical survey, each year there are about 125.0 per 100,000 new cases of breast cancer are diagnosed and 21.5 per 100,000 women due to this disease in the United States. Also, 246,660 new cases of women with cancer are estimated for the year 2016. Early diagnosis of breast cancer is a key factor for long-term survival of cancer patients. Classification plays an important role in breast cancer detection and used by researchers to analyse and classify the medical data. In this research work, priority-based decision tree classifier algorithm has been implemented for Wisconsin Breast cancer dataset. This paper analyzes the different decision tree classifier algorithms for Wisconsin original, diagnostic and prognostic dataset using WEKA software. The performance of the classifiers are evaluated against the parameters like accuracy, Kappa statistic, Entropy, RMSE, TP Rate, FP Rate, Precision, Recall, F-Measure, ROC, Specificity, Sensitivity.

scholarly journals A Comparison Study of Goodness of Fit Tests of Logistic Regression in R: Simulation and Application to Breast Cancer Data

2020 ◽  
pp. 50-59
Author(s):  
El-Housainy A. Rady ◽  
Mohamed R. Abonazel ◽  
Mariam H. Metawe’e
Keyword(s):  
Breast Cancer ◽  
Logistic Regression ◽  
Sample Size ◽  
Null Hypothesis ◽  
Goodness Of Fit ◽  
Quadratic Term ◽  
Breast Cancer Dataset ◽  
Cancer Data ◽  
Interaction Term ◽  
Test Package

Goodness of fit (GOF) tests of logistic regression attempt to find out the suitability of the model to the data. The null hypothesis of all GOF tests is the model fit. R as a free software package has many GOF tests in different packages. A Monte Carlo simulation has been conducted to study two situations; the first, studying the ability of each test, under its default settings, to accept the null hypothesis when the model truly fitted. The second, studying the power of these tests when assumptions of sufficient linear combination of the explanatory variables are violated (by omitting linear covariate term, quadratic term, or interaction term). Moreover, checking whether the same test in different R packages had the same results or not. As the sample size supposed to affect simulation results, so the pattern of change of GOF tests results under different sample sizes as well as different model settings was estimated. All tests accept the null hypothesis (more than 95% of simulation trials) when the model truly fitted except modified Hosmer-Lemeshow test in "LogisticDx" package under all different model settings and Osius and Rojek’s (OsRo) test when the true model had an interaction term between binary and categorical covariates. In addition, le Cessie-van Houwelingen-Copas-Hosmer unweighted sum of squares (CHCH) test gave unexpected different results under different packages. Concerning the power study, all tests had a very low power when a departure of missing covariate existed. Generally, stukel’s test (package ’LogisticDX) and CHCH test (package "RMS") reached a power in detecting a missing quadratic term greater than 80% under lower sample size while OsRo test (package ’LogisticDX’) was better in detecting missing interaction term. Beside the simulation study, we evaluated the performance of GOF tests using the breast cancer dataset.

scholarly journals Breast Cancer Prediction using Machine Learning

2019 ◽  
Vol 8 (4) ◽  
pp. 4879-4881
Keyword(s):  
Breast Cancer ◽  
Random Forest ◽  
Data Science ◽  
Breast Cancer Dataset ◽  
Random Forest Algorithm ◽  
Medical Field ◽  
Cancer Dataset ◽  
Cancer Prediction ◽  
Time Consumption ◽  
Simulated Environment

One of the most dreadful disease is breast cancer and it has a potential cause for death in women. Every year, death rate increases drastically due to breast cancer. An effective way to classify data is through classification or data mining. This becomes very handy, especially in the medical field where diagnosis and analysis are done through these techniques. Wisconsin Breast cancer dataset is used to perform a comparison between SVM, Logistic Regression, Naïve Bayes and Random Forest. Evaluating the correctness in classifying data based on accuracy and time consumption is used to determine the efficiency of the algorithms, which is the main objective. Based on the result of performed experiments, the Random Forest algorithm shows the highest accuracy (99.76%) with the least error rate. ANACONDA Data Science Platform is used to execute all the experiments in a simulated environment.

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 Identification of Bio-Markers for Breast Cancer Detection through Data Mining Methods

2019 ◽  
Vol 8 (2S3) ◽  
pp. 763-769
Keyword(s):  
Breast Cancer ◽  
Support Vector Machine ◽  
Logistic Regression ◽  
Feature Selection ◽  
Discriminant Analysis ◽  
Classification Tree ◽  
Partial Least Square ◽  
Diagnostic Methods ◽  
Support Vector ◽  
Breast Cancer Dataset

Worldwide, breast cancer is the leading type of cancer in women accounting for 25% of all cases. Survival rates in the developed countries are comparatively higher with that of developing countries. This had led to the importance of computer aided diagnostic methods for early detection of breast cancer disease. This eventually reduces the death rate. This paper intents the scope of the biomarker that can be used to predict the breast cancer from the anthropometric data. This experimental study aims at computing and comparing various classification models (Binary Logistic Regression, Ball Vector Machine (BVM), C4.5, Partial Least Square (PLS) for Classification, Classification Tree, Cost sensitive Classification Tree, Cost sensitive Decision Tree, Support Vector Machine for Classification, Core Vector Machine, ID3, K-Nearest Neighbor, Linear Discriminant Analysis (LDA), Log-Reg TRIRLS, Multi Layer Perceptron (MLP), Multinomial Logistic Regression (MLR), Naïve Bayes (NB), PLS for Discriminant Analysis, PLS for LDA, Random Tree (RT), Support Vector Machine SVM) for the UCI Coimbra breast cancer dataset. The feature selection algorithms (Backward Logit, Fisher Filtering, Forward Logit, ReleifF, Step disc) are worked out to find out the minimum attributes that can achieve a better accuracy. To ascertain the accuracy results, the Jack-knife cross validation method for the algorithms is conducted and validated. The Core vector machine classification algorithm outperforms the other nineteen algorithms with an accuracy of 82.76%, sensitivity of 76.92% and specificity of 87.50% for the selected three attributes, Age, Glucose and Resistin using ReleifF feature selection algorithm.

Comparative Analysis of Supervised Algorithms With Hyperparameter Tuning on Breast Cancer Dataset

2021 ◽  
Author(s):  
Yagya Buttan ◽  
Alka Chaudhary ◽  
Komal Saxena ◽  
Samriddh Kohli ◽  
Ajay Rana
Keyword(s):  
Breast Cancer ◽  
Comparative Analysis ◽  
Breast Cancer Dataset ◽  
Cancer Dataset

scholarly journals Predicting Breast Cancer Using Logistic Regression and Multi-Class Classifiers

2018 ◽  
Vol 7 (4.20) ◽  
pp. 22 ◽  
Author(s):  
Jabeen Sultana ◽  
Abdul Khader Jilani ◽  
. .
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Logistic Regression ◽  
Regression Method ◽  
Breast Cancer Dataset ◽  
Breast Cancer Data ◽  
Data Set ◽  
Cancer Data ◽  
Logistic Regression Method ◽  
Simple Logistic

The primary identification and prediction of type of the cancer ought to develop a compulsion in cancer study, in order to assist and supervise the patients. The significance of classifying cancer patients into high or low risk clusters needs commanded many investigation teams, from the biomedical and the bioinformatics area, to learn and analyze the application of machine learning (ML) approaches. Logistic Regression method and Multi-classifiers has been proposed to predict the breast cancer. To produce deep predictions in a new environment on the breast cancer data. This paper explores the different data mining approaches using Classification which can be applied on Breast Cancer data to build deep predictions. Besides this, this study predicts the best Model yielding high performance by evaluating dataset on various classifiers. In this paper Breast cancer dataset is collected from the UCI machine learning repository has 569 instances with 31 attributes. Data set is pre-processed first and fed to various classifiers like Simple Logistic-regression method, IBK, K-star, Multi-Layer Perceptron (MLP), Random Forest, Decision table, Decision Trees (DT), PART, Multi-Class Classifiers and REP Tree.  10-fold cross validation is applied, training is performed so that new Models are developed and tested. The results obtained are evaluated on various parameters like Accuracy, RMSE Error, Sensitivity, Specificity, F-Measure, ROC Curve Area and Kappa statistic and time taken to build the model. Result analysis reveals that among all the classifiers Simple Logistic Regression yields the deep predictions and obtains the best model yielding high and accurate results followed by other methods IBK: Nearest Neighbor Classifier, K-Star: instance-based Classifier, MLP- Neural network. Other Methods obtained less accuracy in comparison with Logistic regression method.  

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