scholarly journals Integrated Analysis of CNV, Gene Expression and Disease State Data in Prostate Cancer

2021 ◽  
Author(s):  
Lin Yuan ◽  
Tao Sun ◽  
Jing Zhao ◽  
Zhen Shen
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Machine Learning ◽  
Logistic Regression ◽  
State Of The Art ◽  
Search Algorithm ◽  
Selection Strategy ◽  
Stability Selection ◽  
Cancer Data ◽  
Path Search

Abstract Background: Copy number variation (CNV) may contribute to development of complex diseases. However, due to the complex mechanism of path association and the lack of sufficient samples, understanding the relationship between CNV and cancer remains a major challenge. The unprecedented abundance of CNV, gene and disease label data provide us with an opportunity to design a new machine learning framework to predict potential disease related CNVs.Results: In this paper, we developed a novel machine learning approach, namely IHI BMLLR (Integrating Heterogeneous Information sources with Biweight Mid correlation and L1 regularized Logistic Regression under stability selection), to predict the CNV disease path associations by using a data set containing CNV, disease state labels and gene data. CNVs, genes, and diseases are connected through edges, and then constitute a biological association network. To construct a biological network, we first used a self adaptive biweight mid correlation (BM) formula to calculate correlation coefficients between CNVs and genes. Then, we used logistic regression with L1 penalty (LLR) function to detect genes related to disease. We added stability selection strategy, which can effectively reduce false positives, when using self adaptive BM and LLR. Finally, a weighted path search algorithm was applied to find top D path associations and important CNVs.Conclusions: Compared with state of the art methods, IHI BMLLR discovers CNVs disease path associations by integrating analysis of CNV, gene expression and disease label data combined with stability selection strategy and weighted path search algorithm, thereby mining more information in the data sets, and improving the accuracy of obtained CNVs. The experimental results on both simulation and prostate cancer data show that IHI BMLLR is significantly better than two state of the art CNV detection methods (i.e., CCRET and DPtest) under false positive control. Furthermore, we applied IHI BMLLR to prostate cancer data and found significant path associations. Three new cancer related genes were discovered in the paths and these genes need to be verified by biological research in the future.

scholarly journals A Novel Computational Framework to Predict Disease-Related Copy Number Variations by Integrating Multiple Data Sources

2021 ◽  
Vol 12 ◽  
Author(s):  
Lin Yuan ◽  
Tao Sun ◽  
Jing Zhao ◽  
Zhen Shen
Keyword(s):  
Prostate Cancer ◽  
Machine Learning ◽  
Logistic Regression ◽  
Copy Number ◽  
Detection Methods ◽  
Biological Research ◽  
Data Set ◽  
Stability Selection ◽  
Cancer Data ◽  
Self Adaptive

Copy number variation (CNV) may contribute to the development of complex diseases. However, due to the complex mechanism of path association and the lack of sufficient samples, understanding the relationship between CNV and cancer remains a major challenge. The unprecedented abundance of CNV, gene, and disease label data provides us with an opportunity to design a new machine learning framework to predict potential disease-related CNVs. In this paper, we developed a novel machine learning approach, namely, IHI-BMLLR (Integrating Heterogeneous Information sources with Biweight Mid-correlation and L1-regularized Logistic Regression under stability selection), to predict the CNV-disease path associations by using a data set containing CNV, disease state labels, and gene data. CNVs, genes, and diseases are connected through edges and then constitute a biological association network. To construct a biological network, we first used a self-adaptive biweight mid-correlation (BM) formula to calculate correlation coefficients between CNVs and genes. Then, we used logistic regression with L1 penalty (LLR) function to detect genes related to disease. We added stability selection strategy, which can effectively reduce false positives, when using self-adaptive BM and LLR. Finally, a weighted path search algorithm was applied to find top D path associations and important CNVs. The experimental results on both simulation and prostate cancer data show that IHI-BMLLR is significantly better than two state-of-the-art CNV detection methods (i.e., CCRET and DPtest) under false-positive control. Furthermore, we applied IHI-BMLLR to prostate cancer data and found significant path associations. Three new cancer-related genes were discovered in the paths, and these genes need to be verified by biological research in the future.

scholarly journals Boosting and lassoing new prostate cancer SNP risk factors and their connection to selenium

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
David E. Booth ◽  
Venugopal Gopalakrishna-Remani ◽  
Matthew L. Cooper ◽  
Fiona R. Green ◽  
Margaret P. Rayman
Keyword(s):  
Prostate Cancer ◽  
Risk Factors ◽  
Logistic Regression ◽  
Variable Selection ◽  
Disease Risk ◽  
Gradient Boosting ◽  
Stepwise Logistic Regression ◽  
Anticancer Effect ◽  
Cancer Data ◽  
Snp Interaction

AbstractWe begin by arguing that the often used algorithm for the discovery and use of disease risk factors, stepwise logistic regression, is unstable. We then argue that there are other algorithms available that are much more stable and reliable (e.g. the lasso and gradient boosting). We then propose a protocol for the discovery and use of risk factors using lasso or boosting variable selection. We then illustrate the use of the protocol with a set of prostate cancer data and show that it recovers known risk factors. Finally, we use the protocol to identify new and important SNP based risk factors for prostate cancer and further seek evidence for or against the hypothesis of an anticancer function for Selenium in prostate cancer. We find that the anticancer effect may depend on the SNP-SNP interaction and, in particular, which alleles are present.

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.  

scholarly journals Predicting the Grade of Prostate Cancer Based on a Biparametric MRI Radiomics Signature

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Li Zhang ◽  
Xia Zhe ◽  
Min Tang ◽  
Jing Zhang ◽  
Jialiang Ren ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Machine Learning ◽  
Logistic Regression ◽  
Learning Algorithm ◽  
Area Under The Curve ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Low Grade ◽  
High Grade ◽  
Random Forest Tree

Purpose. This study aimed to investigate the value of biparametric magnetic resonance imaging (bp-MRI)-based radiomics signatures for the preoperative prediction of prostate cancer (PCa) grade compared with visual assessments by radiologists based on the Prostate Imaging Reporting and Data System Version 2.1 (PI-RADS V2.1) scores of multiparametric MRI (mp-MRI). Methods. This retrospective study included 142 consecutive patients with histologically confirmed PCa who were undergoing mp-MRI before surgery. MRI images were scored and evaluated by two independent radiologists using PI-RADS V2.1. The radiomics workflow was divided into five steps: (a) image selection and segmentation, (b) feature extraction, (c) feature selection, (d) model establishment, and (e) model evaluation. Three machine learning algorithms (random forest tree (RF), logistic regression, and support vector machine (SVM)) were constructed to differentiate high-grade from low-grade PCa. Receiver operating characteristic (ROC) analysis was used to compare the machine learning-based analysis of bp-MRI radiomics models with PI-RADS V2.1. Results. In all, 8 stable radiomics features out of 804 extracted features based on T2-weighted imaging (T2WI) and ADC sequences were selected. Radiomics signatures successfully categorized high-grade and low-grade PCa cases ( P < 0.05 ) in both the training and test datasets. The radiomics model-based RF method (area under the curve, AUC: 0.982; 0.918), logistic regression (AUC: 0.886; 0.886), and SVM (AUC: 0.943; 0.913) in both the training and test cohorts had better diagnostic performance than PI-RADS V2.1 (AUC: 0.767; 0.813) when predicting PCa grade. Conclusions. The results of this clinical study indicate that machine learning-based analysis of bp-MRI radiomic models may be helpful for distinguishing high-grade and low-grade PCa that outperformed the PI-RADS V2.1 scores based on mp-MRI. The machine learning algorithm RF model was slightly better.

scholarly journals A Tweet Sentiment Classification Approach Using a Hybrid Stacked Ensemble Technique

Information ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 374
Author(s):  
Babacar Gaye ◽  
Dezheng Zhang ◽  
Aziguli Wulamu
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Language Processing ◽  
Short Term Memory ◽  
State Of The Art ◽  
Accuracy Score ◽  
Learning Models ◽  
Proposed Model

With the extensive availability of social media platforms, Twitter has become a significant tool for the acquisition of peoples’ views, opinions, attitudes, and emotions towards certain entities. Within this frame of reference, sentiment analysis of tweets has become one of the most fascinating research areas in the field of natural language processing. A variety of techniques have been devised for sentiment analysis, but there is still room for improvement where the accuracy and efficacy of the system are concerned. This study proposes a novel approach that exploits the advantages of the lexical dictionary, machine learning, and deep learning classifiers. We classified the tweets based on the sentiments extracted by TextBlob using a stacked ensemble of three long short-term memory (LSTM) as base classifiers and logistic regression (LR) as a meta classifier. The proposed model proved to be effective and time-saving since it does not require feature extraction, as LSTM extracts features without any human intervention. We also compared our proposed approach with conventional machine learning models such as logistic regression, AdaBoost, and random forest. We also included state-of-the-art deep learning models in comparison with the proposed model. Experiments were conducted on the sentiment140 dataset and were evaluated in terms of accuracy, precision, recall, and F1 Score. Empirical results showed that our proposed approach manifested state-of-the-art results by achieving an accuracy score of 99%.

scholarly journals Predicting Prostate Cancer Upgrading of Biopsy Gleason Grade Group at Radical Prostatectomy Using Machine Learning-assisted Decision-support Models 

2020 ◽  
Author(s):  
Hailang Liu ◽  
Kun Tang ◽  
Ejun Peng ◽  
Liang Wang ◽  
Ding Xia ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Machine Learning ◽  
Logistic Regression ◽  
Radical Prostatectomy ◽  
Predictive Value ◽  
Support Vector ◽  
Gleason Grade ◽  
Good Discrimination ◽  
Grade Group ◽  
Testing Dataset

Abstract Background: This study aimed to develop a machine learning (ML)-assisted model capable of accurately predicting the probability of biopsy Gleason grade group upgrading before making treatment decisions.Methods: We retrospectively collected data from prostate cancer (PCa) patients who underwent systematic biopsy and radical prostatectomy from January 2015 to December 2019 at Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology. The study cohort was divided into training and testing datasets in a 70:30 ratio for further analysis. Four ML-assisted models were developed from 16 clinical features using logistic regression (LR), logistic regression optimized by least absolute shrinkage and selection operator (Lasso) regularization (Lasso-LR), random forest (RF) and support vector machine (SVM). The area under the curve (AUC) was applied to determine the model with the highest discrimination. Calibration plots were used to investigate the extent of over- or underestimation of predicted probabilities relative to the observed probabilities in models. Results: In total, 530 PCa patients were included, with 371 patients in the training dataset and 159 patients in the testing dataset. The Lasso-LR model showed good discrimination with an AUC, accuracy, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of 0.776, 0.712, 0.679, 0.745, 0.730 and 0.695, respectively, followed by SVM (AUC 0.740, 95% confidence interval [CI]: 0.690–0.790), LR (AUC 0.725, 95% CI: 0.674–0.776) and RF (AUC 0.666, 95% CI: 0.618–0.714). Validation of the model showed that the Lasso-LR model had the best discriminative power (AUC 0.735, 95% CI: 0.656–0.813), followed by SVM (AUC 0.723, 95% CI: 0.644–0.802), LR (AUC 0.697, 95% CI: 0.615–0.778) and RF (AUC 0.607, 95% CI: 0.531–0.684) in the testing dataset. Both the Lasso-LR and SVM models were well-calibrated. Conclusion: The Lasso-LR model had good discrimination in the prediction of patients at high risk of harboring incorrect Gleason grade group assignment, and the use of this model may be greatly beneficial to urologists in treatment planning, patient selection, and the decision-making process for PCa patients.

scholarly journals Prediction of Prostate Cancer using Machine Learning Algorithms

2020 ◽  
Vol 8 (5) ◽  
pp. 5353-5362
Keyword(s):  
Prostate Cancer ◽  
Machine Learning ◽  
Logistic Regression ◽  
Random Forest ◽  
Missing Values ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Cancer Disease ◽  
The Individual

Background/Aim: Prostate cancer is regarded as the most prevalent cancer in the word and the main cause of deaths worldwide. The early strategies for estimating the prostate cancer sicknesses helped in settling on choices about the progressions to have happened in high-chance patients which brought about the decrease of their dangers. Methods: In the proposed research, we have considered informational collection from kaggle and we have done pre-processing tasks for missing values .We have three missing data values in compactness attribute and two missing values in fractal dimension were replaced by mean of their column values .The performance of the diagnosis model is obtained by using methods like classification, accuracy, sensitivity and specificity analysis. This paper proposes a prediction model to predict whether a people have a prostate cancer disease or not and to provide an awareness or diagnosis on that. This is done by comparing the accuracies of applying rules to the individual results of Support Vector Machine, Random forest, Naive Bayes classifier and logistic regression on the dataset taken in a region to present an accurate model of predicting prostate cancer disease. Results: The machine learning algorithms under study were able to predict prostate cancer disease in patients with accuracy between 70% and 90%. Conclusions: It was shown that Logistic Regression and Random Forest both has better Accuracy (90%) when compared to different Machine-learning Algorithms.

scholarly journals A Hierarchical Machine Learning Model to Discover Gleason Grade-Specific Biomarkers in Prostate Cancer

Diagnostics ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 219 ◽  
Author(s):  
Osama Hamzeh ◽  
Abedalrhman Alkhateeb ◽  
Julia Zhuoran Zheng ◽  
Srinath Kandalam ◽  
Crystal Leung ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Machine Learning ◽  
Cancer Patients ◽  
Gleason Score ◽  
Class Imbalance ◽  
Gene Expression Omnibus ◽  
Gleason Grade ◽  
Next Generation Sequencing Technology ◽  
Potential Biomarker

(1) Background:One of the most common cancers that affect North American men and men worldwide is prostate cancer. The Gleason score is a pathological grading system to examine the potential aggressiveness of the disease in the prostate tissue. Advancements in computing and next-generation sequencing technology now allow us to study the genomic profiles of patients in association with their different Gleason scores more accurately and effectively. (2) Methods: In this study, we used a novel machine learning method to analyse gene expression of prostate tumours with different Gleason scores, and identify potential genetic biomarkers for each Gleason group. We obtained a publicly-available RNA-Seq dataset of a cohort of 104 prostate cancer patients from the National Center for Biotechnology Information’s (NCBI) Gene Expression Omnibus (GEO) repository, and categorised patients based on their Gleason scores to create a hierarchy of disease progression. A hierarchical model with standard classifiers in different Gleason groups, also known as nodes, was developed to identify and predict nodes based on their mRNA or gene expression. In each node, patient samples were analysed via class imbalance and hybrid feature selection techniques to build the prediction model. The outcome from analysis of each node was a set of genes that could differentiate each Gleason group from the remaining groups. To validate the proposed method, the set of identified genes were used to classify a second dataset of 499 prostate cancer patients collected from cBioportal. (3) Results: The overall accuracy of applying this novel method to the first dataset was 93.3%; the method was further validated to have 87% accuracy using the second dataset. This method also identified genes that were not previously reported as potential biomarkers for specific Gleason groups. In particular, PIAS3 was identified as a potential biomarker for Gleason score 4 + 3 = 7, and UBE2V2 for Gleason score 6. (4) Insight: Previous reports show that the genes predicted by this newly proposed method strongly correlate with prostate cancer development and progression. Furthermore, pathway analysis shows that both PIAS3 and UBE2V2 share similar protein interaction pathways, the JAK/STAT signaling process.

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