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Identifying differentially expressed genes using the Polya urn scheme
Saraiva, Erlandson Ferreira,Suzuki, Adriano Kamimura,Milan, Luis Aparecido The Korean Statistical Society 2017 Communications for statistical applications and me Vol.24 No.6
A common interest in gene expression data analysis is to identify genes that present significant changes in expression levels among biological experimental conditions. In this paper, we develop a Bayesian approach to make a gene-by-gene comparison in the case with a control and more than one treatment experimental condition. The proposed approach is within a Bayesian framework with a Dirichlet process prior. The comparison procedure is based on a model selection procedure developed using the discreteness of the Dirichlet process and its representation via Polya urn scheme. The posterior probabilities for models considered are calculated using a Gibbs sampling algorithm. A numerical simulation study is conducted to understand and compare the performance of the proposed method in relation to usual methods based on analysis of variance (ANOVA) followed by a Tukey test. The comparison among methods is made in terms of a true positive rate and false discovery rate. We find that proposed method outperforms the other methods based on ANOVA followed by a Tukey test. We also apply the methodologies to a publicly available data set on Plasmodium falciparum protein.
Saraiva, Erlandson F.,Suzuki, Adriano K.,Filho, Ciro A.O.,Louzada, Francisco The Korean Statistical Society 2016 Communications for statistical applications and me Vol.23 No.4
Football match predictions are of great interest to fans and sports press. In the last few years it has been the focus of several studies. In this paper, we propose the Poisson regression model in order to football match outcomes. We applied the proposed methodology to two national competitions: the 2012-2013 English Premier League and the 2015 Brazilian Football League. The number of goals scored by each team in a match is assumed to follow Poisson distribution, whose average reflects the strength of the attack, defense and the home team advantage. Inferences about all unknown quantities involved are made using a Bayesian approach. We calculate the probabilities of win, draw and loss for each match using a simulation procedure. Besides, also using simulation, the probability of a team qualifying for continental tournaments, being crowned champion or relegated to the second division is obtained.
A new extended Birnbaum-Saunders model with cure fraction: classical and Bayesian approach
Ortega, Edwin M.M.,Cordeiro, Gauss M.,Suzuki, Adriano K.,Ramires, Thiago G. The Korean Statistical Society 2017 Communications for statistical applications and me Vol.24 No.4
A four-parameter extended fatigue lifetime model called the odd Birnbaum-Saunders geometric distribution is proposed. This model extends the odd Birnbaum-Saunders and Birnbaum-Saunders distributions. We derive some properties of the new distribution that include expressions for the ordinary moments and generating and quantile functions. The method of maximum likelihood and a Bayesian approach are adopted to estimate the model parameters; in addition, various simulations are performed for different parameter settings and sample sizes. We propose two new models with a cure rate called the odd Birnbaum-Saunders mixture and odd Birnbaum-Saunders geometric models by assuming that the number of competing causes for the event of interest has a geometric distribution. The applicability of the new models are illustrated by means of ethylene data and melanoma data with cure fraction.
Cure rate proportional odds models with spatial frailties for interval-censored data
Yiqi, Bao,Cancho, Vicente Garibay,Louzada, Francisco,Suzuki, Adriano Kamimura The Korean Statistical Society 2017 Communications for statistical applications and me Vol.24 No.6
This paper presents proportional odds cure models to allow spatial correlations by including spatial frailty in the interval censored data setting. Parametric cure rate models with independent and dependent spatial frailties are proposed and compared. Our approach enables different underlying activation mechanisms that lead to the event of interest; in addition, the number of competing causes which may be responsible for the occurrence of the event of interest follows a Geometric distribution. Markov chain Monte Carlo method is used in a Bayesian framework for inferential purposes. For model comparison some Bayesian criteria were used. An influence diagnostic analysis was conducted to detect possible influential or extreme observations that may cause distortions on the results of the analysis. Finally, the proposed models are applied for the analysis of a real data set on smoking cessation. The results of the application show that the parametric cure model with frailties under the first activation scheme has better findings.
Regression models generated by gamma random variables with long-term survivors
Ortega, Edwin M.M.,Cordeiro, Gauss M.,Hashimoto, Elizabeth M.,Suzuki, Adriano K. The Korean Statistical Society 2017 Communications for statistical applications and me Vol.24 No.1
We propose a flexible cure rate survival model by assuming that the number of competing causes of the event of interest has the Poisson distribution and the time for the event follows the gamma-G family of distributions. The extended family of gamma-G failure-time models with long-term survivors is flexible enough to include many commonly used failure-time distributions as special cases. We consider a frequentist analysis for parameter estimation and derive appropriate matrices to assess local influence on the parameters. Further, various simulations are performed for different parameter settings, sample sizes and censoring percentages. We illustrate the performance of the proposed regression model by means of a data set from the medical area (gastric cancer).
The Bivariate Kumaraswamy Weibull regression model: a complete classical and Bayesian analysis
Fachini-Gomes, Juliana B.,Ortega, Edwin M.M.,Cordeiro, Gauss M.,Suzuki, Adriano K. The Korean Statistical Society 2018 Communications for statistical applications and me Vol.25 No.5
Bivariate distributions play a fundamental role in survival and reliability studies. We consider a regression model for bivariate survival times under right-censored based on the bivariate Kumaraswamy Weibull (Cordeiro et al., Journal of the Franklin Institute, 347, 1399-1429, 2010) distribution to model the dependence of bivariate survival data. We describe some structural properties of the marginal distributions. The method of maximum likelihood and a Bayesian procedure are adopted to estimate the model parameters. We use diagnostic measures based on the local influence and Bayesian case influence diagnostics to detect influential observations in the new model. We also show that the estimates in the bivariate Kumaraswamy Weibull regression model are robust to deal with the presence of outliers in the data. In addition, we use some measures of goodness-of-fit to evaluate the bivariate Kumaraswamy Weibull regression model. The methodology is illustrated by means of a real lifetime data set for kidney patients.
Bivariate odd-log-logistic-Weibull regression model for oral health-related quality of life
Cruz, Jose N. da,Ortega, Edwin M.M.,Cordeiro, Gauss M.,Suzuki, Adriano K.,Mialhe, Fabio L. The Korean Statistical Society 2017 Communications for statistical applications and me Vol.24 No.3
We study a bivariate response regression model with arbitrary marginal distributions and joint distributions using Frank and Clayton's families of copulas. The proposed model is used for fitting dependent bivariate data with explanatory variables using the log-odd log-logistic Weibull distribution. We consider likelihood inferential procedures based on constrained parameters. For different parameter settings and sample sizes, various simulation studies are performed and compared to the performance of the bivariate odd-log-logistic-Weibull regression model. Sensitivity analysis methods (such as local and total influence) are investigated under three perturbation schemes. The methodology is illustrated in a study to assess changes on schoolchildren's oral health-related quality of life (OHRQoL) in a follow-up exam after three years and to evaluate the impact of caries incidence on the OHRQoL of adolescents.
A Bayesian cure rate model with dispersion induced by discrete frailty
Cancho, Vicente G.,Zavaleta, Katherine E.C.,Macera, Marcia A.C.,Suzuki, Adriano K.,Louzada, Francisco The Korean Statistical Society 2018 Communications for statistical applications and me Vol.25 No.5
In this paper, we propose extending proportional hazards frailty models to allow a discrete distribution for the frailty variable. Having zero frailty can be interpreted as being immune or cured. Thus, we develop a new survival model induced by discrete frailty with zero-inflated power series distribution, which can account for overdispersion. This proposal also allows for a realistic description of non-risk individuals, since individuals cured due to intrinsic factors (immunes) are modeled by a deterministic fraction of zero-risk while those cured due to an intervention are modeled by a random fraction. We put the proposed model in a Bayesian framework and use a Markov chain Monte Carlo algorithm for the computation of posterior distribution. A simulation study is conducted to assess the proposed model and the computation algorithm. We also discuss model selection based on pseudo-Bayes factors as well as developing case influence diagnostics for the joint posterior distribution through ${\psi}-divergence$ measures. The motivating cutaneous melanoma data is analyzed for illustration purposes.
The Marshall-Olkin generalized gamma distribution
Barriga, Gladys D.C.,Cordeiro, Gauss M.,Dey, Dipak K.,Cancho, Vicente G.,Louzada, Francisco,Suzuki, Adriano K. The Korean Statistical Society 2018 Communications for statistical applications and me Vol.25 No.3
Attempts have been made to define new classes of distributions that provide more flexibility for modelling skewed data in practice. In this work we define a new extension of the generalized gamma distribution (Stacy, The Annals of Mathematical Statistics, 33, 1187-1192, 1962) for Marshall-Olkin generalized gamma (MOGG) distribution, based on the generator pioneered by Marshall and Olkin (Biometrika, 84, 641-652, 1997). This new lifetime model is very flexible including twenty one special models. The main advantage of the new family relies on the fact that practitioners will have a quite flexible distribution to fit real data from several fields, such as engineering, hydrology and survival analysis. Further, we also define a MOGG mixture model, a modification of the MOGG distribution for analyzing lifetime data in presence of cure fraction. This proposed model can be seen as a model of competing causes, where the parameter associated with the Marshall-Olkin distribution controls the activation mechanism of the latent risks (Cooner et al., Statistical Methods in Medical Research, 15, 307-324, 2006). The asymptotic properties of the maximum likelihood estimation approach of the parameters of the model are evaluated by means of simulation studies. The proposed distribution is fitted to two real data sets, one arising from measuring the strength of fibers and the other on melanoma data.