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Robustification of Naive Bayes Classifier and Its Application for Microarray Gene Expression Data Analysis.

ABSTRACT: The naïve Bayes classifier (NBC) is one of the most popular classifiers for class prediction or pattern recognition from microarray gene expression data (MGED). However, it is very much sensitive to outliers with the classical estimates of the location and scale parameters. It is one of the most important drawbacks for gene expression data analysis by the classical NBC. The gene expression dataset is often contaminated by outliers due to several steps involved in the data generating process from hybridization of DNA samples to image analysis. Therefore, in this paper, an attempt is made to robustify the Gaussian NBC by the minimum ?-divergence method. The role of minimum ?-divergence method in this article is to produce the robust estimators for the location and scale parameters based on the training dataset and outlier detection and modification in test dataset. The performance of the proposed method depends on the tuning parameter ?. It reduces to the traditional naïve Bayes classifier when ? ? 0. We investigated the performance of the proposed beta naïve Bayes classifier (?-NBC) in a comparison with some popular existing classifiers (NBC, KNN, SVM, and AdaBoost) using both simulated and real gene expression datasets. We observed that the proposed method improved the performance over the others in presence of outliers. Otherwise, it keeps almost equal performance.

SUBMITTER: Ahmed MS

PROVIDER: S-EPMC5564130 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Robustification of Naïve Bayes Classifier and Its Application for Microarray Gene Expression Data Analysis.

Ahmed Md Shakil MS Ahmed Md Shakil MS Shahjaman Md M Rana Md Masud MM Mollah Md Nurul Haque MNH

BioMed research international 20170807

The naïve Bayes classifier (NBC) is one of the most popular classifiers for class prediction or pattern recognition from microarray gene expression data (MGED). However, it is very much sensitive to outliers with the classical estimates of the location and scale parameters. It is one of the most important drawbacks for gene expression data analysis by the classical NBC. The gene expression dataset is often contaminated by outliers due to several steps involved in the data generating process from ...[more]

PMID: 28848763

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Project description:Verbal autopsy (VA) deals with post-mortem surveys about deaths, mostly in low and middle income countries, where the majority of deaths occur at home rather than a hospital, for retrospective assignment of causes of death (COD) and subsequently evidence-based health system strengthening. Automated algorithms for VA COD assignment have been developed and their performance has been assessed against physician and clinical diagnoses. Since the performance of automated classification methods remains low, we aimed to enhance the Naïve Bayes Classifier (NBC) algorithm to produce better ranked COD classifications on 26,766 deaths from four globally diverse VA datasets compared to some of the leading VA classification methods, namely Tariff, InterVA-4, InSilicoVA and NBC. We used a different strategy, by training multiple NBC algorithms using the one-against-all approach (OAA-NBC). To compare performance, we computed the cumulative cause-specific mortality fraction (CSMF) accuracies for population-level agreement from rank one to five COD classifications. To assess individual-level COD assignments, cumulative partially-chance corrected concordance (PCCC) and sensitivity was measured for up to five ranked classifications. Overall results show that OAA-NBC consistently assigns CODs that are the most alike physician and clinical COD assignments compared to some of the leading algorithms based on the cumulative CSMF accuracy, PCCC and sensitivity scores. The results demonstrate that our approach improves the performance of classification (sensitivity) by between 6% and 8% compared with other VA algorithms. Population-level agreements for OAA-NBC and NBC were found to be similar or higher than the other algorithms used in the experiments. Although OAA-NBC still requires improvement for individual-level COD assignment, the one-against-all approach improved its ability to assign CODs that more closely resemble physician or clinical COD classifications compared to some of the other leading VA classifiers.

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Dataset Information

Robustification of Naive Bayes Classifier and Its Application for Microarray Gene Expression Data Analysis.

Publications

Robustification of Naïve Bayes Classifier and Its Application for Microarray Gene Expression Data Analysis.

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