scholarly journals FRL: An Integrative Feature Selection Algorithm Based on the Fisher Score, Recursive Feature Elimination, and Logistic Regression to Identify Potential Genomic Biomarkers

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Chenyu Ge ◽  
Liqun Luo ◽  
Jialin Zhang ◽  
Xiangbing Meng ◽  
Yun Chen
Keyword(s):  
Logistic Regression ◽  
Feature Selection ◽  
Precision Medicine ◽  
Functional Enrichment ◽  
Recursive Feature Elimination ◽  
Selection Algorithm ◽  
Feature Selection Algorithm ◽  
Fisher Score ◽  
Genomic Biomarkers ◽  
Potential Biomarker

Accurate screening on cancer biomarkers contributes to health assessment, drug screening, and targeted therapy for precision medicine. The rapid development of high-throughput sequencing technology has identified abundant genomic biomarkers, but most of them are limited to single-cancer analysis. Based on the combination of Fisher score, Recursive feature elimination, and Logistic regression (FRL), this paper proposes an integrative feature selection algorithm named FRL to explore potential cancer genomic biomarkers on cancer subsets. Fisher score is initially used to calculate the weights of genes to rapidly reduce the dimension. Recursive feature elimination and Logistic regression are then jointly employed to extract the optimal subset. Compared to the current differential expression analysis tool GEO2R based on the Limma algorithm, FRL has greater classification precision than Limma. Compared with five traditional feature selection algorithms, FRL exhibits excellent performance on accuracy (ACC) and F1-score and greatly improves computational efficiency. On high-noise datasets such as esophageal cancer, the ACC of FRL is 30% superior to the average ACC achieved with other traditional algorithms. As biomarkers found in multiple studies are more reliable and reproducible, and reveal stronger association on potential clinical value than single analysis, through literature review and spatial analyses of gene functional enrichment and functional pathways, we conduct cluster analysis on 10 diverse cancers with high mortality and form a potential biomarker module comprising 19 genes. All genes in this module can serve as potential biomarkers to provide more information on the overall oncogenesis mechanism for the detection of diverse early cancers and assist in targeted anticancer therapies for further developments in precision medicine.

scholarly journals Min-Redundancy and Max-Relevance Multi-view Feature Selection for Predicting Ovarian Cancer Survival using Multi-omics Data

2018 ◽  
Author(s):  
Yasser EL-Manzalawy ◽  
Tsung-Yu Hsieh ◽  
Manu Shivakumar ◽  
Dokyoon Kim ◽  
Vasant Honavar
Keyword(s):  
Ovarian Cancer ◽  
Feature Selection ◽  
Precision Medicine ◽  
Cancer Survival ◽  
Mirna Gene ◽  
Omics Data ◽  
Selection Algorithm ◽  
Feature Selection Algorithm ◽  
Integrative Analyses ◽  
Ovarian Cancer Survival

AbstractBackgroundLarge-scale collaborative precision medicine initiatives (e.g., The Cancer Genome Atlas (TCGA)) are yielding rich multi-omics data. Integrative analyses of the resulting multi-omics data, such as somatic mutation, copy number alteration (CNA), DNA methylation, miRNA, gene expression, and protein expression, offer the tantalizing possibilities of realizing the potential of precision medicine in cancer prevention, diagnosis, and treatment by substantially improving our understanding of underlying mechanisms as well as the discovery of novel biomarkers for different types of cancers. However, such analyses present a number of challenges, including the heterogeneity of data types, and the extreme high-dimensionality of omics data.MethodsIn this study, we propose a novel framework for integrating multi-omics data based on multi-view feature selection, an emerging research problem in machine learning research. We also present a novel multi-view feature selection algorithm, MRMR-mv, which adapts the well-known Min-Redundancy and Maximum-Relevance (MRMR) single-view feature selection algorithm for the multi-view settings.ResultsWe report results of experiments on the task of building a predictive model of cancer survival from an ovarian cancer multi-omics dataset derived from the TCGA database. Our results suggest that multi-view models for predicting ovarian cancer survival outperform both view-specific models (i.e., models trained and tested using one multi-omics data source) and models based on two baseline data fusion methods.ConclusionsOur results demonstrate the potential of multi-view feature selection in integrative analyses and predictive modeling from multi-omics data.

A dynamic recursive feature elimination framework (dRFE) to further refine a set of OMIC biomarkers

2021 ◽  
Author(s):  
Yuanyuan Han ◽  
Lan Huang ◽  
Fengfeng Zhou
Keyword(s):  
Experimental Data ◽  
Feature Selection ◽  
The Other ◽  
Supplementary Information ◽  
Recursive Feature Elimination ◽  
Supplementary Data ◽  
Selection Algorithm ◽  
Feature Selection Algorithm ◽  
Class Labels ◽  
Selection Algorithms

Abstract Motivation A feature selection algorithm may select the subset of features with the best associations with the class labels. The recursive feature elimination (RFE) is a heuristic feature screening framework and has been widely used to select the biological OMIC biomarkers. This study proposed a dynamic recursive feature elimination (dRFE) framework with more flexible feature elimination operations. The proposed dRFE was comprehensively compared with 11 existing feature selection algorithms and five classifiers on the eight difficult transcriptome datasets from a previous study, the ten newly collected transcriptome datasets and the five methylome datasets. Results The experimental data suggested that the regular RFE framework did not perform well, and dRFE outperformed the existing feature selection algorithms in most cases. The dRFE-detected features achieved Acc = 1.0000 for the two methylome datasets GSE53045 and GSE66695. The best prediction accuracies of the dRFE-detected features were 0.9259, 0.9424 and 0.8601 for the other three methylome datasets GSE74845, GSE103186 and GSE80970, respectively. Four transcriptome datasets received Acc = 1.0000 using the dRFE-detected features, and the prediction accuracies for the other six newly collected transcriptome datasets were between 0.6301 and 0.9917. Availability and implementation The experiments in this study are implemented and tested using the programming language Python version 3.7.6. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Recursive Feature Elimination with Ridge Regression (L2) Machine Learning Hybrid Feature Selection Algorithm for Diabetic Prediction using Random Forest Classifer.

2021 ◽  
Author(s):  
K venkatachalam ◽  
P Prabhu ◽  
B saravana Balaji ◽  
Mohamed Abouhawwash ◽  
R Rajadevi
Keyword(s):  
Machine Learning ◽  
Feature Selection ◽  
Random Forest ◽  
Ridge Regression ◽  
Feature Selection Method ◽  
Selection Method ◽  
Recursive Feature Elimination ◽  
Selection Algorithm ◽  
Feature Selection Algorithm ◽  
Data Set

Abstract In day today life, diabetes illness is increasing in count due to the body not able to metabolize the glucose level. The prediction of the right diabetes patients is an important research area that many researchers are proposing the techniques to predict this disease through data mining and machine learning methods. In prediction, feature selection is one of the key concept in preprocessing so that the features that are relevant to the disease will be used for prediction. This will improve the prediction accuracy. Selecting right features among the whole feature set is a complicated process and many researchers are concentrating on it to produce the predictive model with high accuracy. In this proposed work, the wrapper based feature selection method called Recursive Feature Elimination (RFE) is combined with Ridge regression (L2) to form a hybrid L2 regulated feature selection algorithm to overcome the overfilling problem of the data set. Over fitting is the major problem in feature selection which means that the new data are not fit to the model since the training data is small. Ridge regression is mainly used to overcome the overfitting problem. Once the features are selected using the proposed feature selection method, random forest classifier is used to classify the data based on the selected features. The proposed work is experimented in PIDD data set and the evaluated results are compared with the existing algorithms to prove the accuracy effect of the proposed algorithm. From the results obtained by proposed algorithm, the accuracy of predicting the diabetes disease is high compared to other existing algorithms.

scholarly journals High-Accuracy Power Quality Disturbance Classification Using the Adaptive ABC-PSO as Optimal Feature Selection Algorithm

Energies ◽  
2021 ◽  
Vol 14 (5) ◽  
pp. 1238
Author(s):  
Supanat Chamchuen ◽  
Apirat Siritaratiwat ◽  
Pradit Fuangfoo ◽  
Puripong Suthisopapan ◽  
Pirat Khunkitti
Keyword(s):  
Feature Selection ◽  
Power Quality ◽  
Distribution System ◽  
Classification Accuracy ◽  
Selection Algorithm ◽  
Feature Selection Algorithm ◽  
Electrical Distribution ◽  
Power Quality Disturbance ◽  
Optimal Feature Selection ◽  
Optimal Feature

Power quality disturbance (PQD) is an important issue in electrical distribution systems that needs to be detected promptly and identified to prevent the degradation of system reliability. This work proposes a PQD classification using a novel algorithm, comprised of the artificial bee colony (ABC) and the particle swarm optimization (PSO) algorithms, called “adaptive ABC-PSO” as the feature selection algorithm. The proposed adaptive technique is applied to a combination of ABC and PSO algorithms, and then used as the feature selection algorithm. A discrete wavelet transform is used as the feature extraction method, and a probabilistic neural network is used as the classifier. We found that the highest classification accuracy (99.31%) could be achieved through nine optimally selected features out of all 72 extracted features. Moreover, the proposed PQD classification system demonstrated high performance in a noisy environment, as well as the real distribution system. When comparing the presented PQD classification system’s performance to previous studies, PQD classification accuracy using adaptive ABC-PSO as the optimal feature selection algorithm is considered to be at a high-range scale; therefore, the adaptive ABC-PSO algorithm can be used to classify the PQD in a practical electrical distribution system.

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