Browsing by Author "Rosner, Gary L."

Now showing 1 - 6 of 6
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    A Product Partition Model With Regression on Covariates
    (AMER STATISTICAL ASSOC, 2011) Mueller, Peter; Quintana, Fernando; Rosner, Gary L.
    We propose a probability model for random partitions in the presence of covariates. In other words, we develop a model-based clustering algorithm that exploits available covariates. The motivating application is predicting time to progression for patients in a breast cancer trial. We proceed by reporting a weighted average of the responses of clusters of earlier patients. The weights should be determined by the similarity of the new patient's covariate with the covariates of patients in each cluster. We achieve the desired inference by defining a random partition model that includes a regression on covariates. Patients with similar covariates are a priori more likely to be clustered together. Posterior predictive inference in this model formalizes the desired prediction.
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    A semiparametric Bayesian model for repeatedly repeated binary outcomes
    (WILEY-BLACKWELL, 2008) Quintana, Fernando A.; Mueller, Peter; Rosner, Gary L.; Relling, Mary V.
    We discuss the analysis of data from single-nucleotide polymorphism arrays comparing tumour and normal tissues. The data consist of sequences of indicators for loss of heterozygosity (LOH) and involve three nested levels of repetition: chromosomes for a given patient, regions within chromosomes and single-nucleotide polymorphisms nested within regions. We propose to analyse these data by using a semiparametric model for multilevel repeated binary data. At the top level of the hierarchy we assume a sampling model for the observed binary LOH sequences that arises from a partial exchangeability argument. This implies a mixture of Markov chains model. The mixture is defined with respect to the Markov transition probabilities. We assume a non-parametric prior for the random-mixing measure. The resulting model takes the form of a semiparametric random-effects model with the matrix of transition probabilities being the random effects. The model includes appropriate dependence assumptions for the two remaining levels of the hierarchy, i.e. for regions within chromosomes and for chromosomes within patient. We use the model to identify regions of increased LOH in a data set coming from a study of treatment-related leukaemia in children with an initial cancer diagnostic. The model successfully identifies the desired regions and performs well compared with other available alternatives.
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    DISCOVERING INTERACTIONS USING COVARIATE INFORMED RANDOM PARTITION MODELS
    (2021) Page, Garritt L.; Quintana, Fernando A.; Rosner, Gary L.
    Combination chemotherapy treatment regimens created for patients diagnosed with childhood acute lymphoblastic leukemia have had great success in improving cure rates. Unfortunately, patients prescribed these types of treatment regimens have displayed susceptibility to the onset of osteonecrosis. Some have suggested that this is due to pharmacokinetic interaction between two agents in the treatment regimen (asparaginase and dexamethasone) and other physiological variables. Determining which physiological variables to consider when searching for interactions in scenarios like these, minus a priori guidance, has proved to be a challenging problem, particularly if interactions influence the response distribution in ways beyond shifts in expectation or dispersion only. In this paper we propose an exploratory technique that is able to discover associations between covariates and responses in a general way. The procedure connects covariates to responses flexibly through dependent random partition distributions and then employs machine learning techniques to highlight potential associations found in each cluster. We provide a simulation study to show utility and apply the method to data produced from a study dedicated to learning which physiological predictors influence severity of osteonecrosis multiplicatively.
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    DPpackage: Bayesian Semi- and Nonparametric Modeling in R
    (JOURNAL STATISTICAL SOFTWARE, 2011) Jara, Alejandro; Hanson, Timothy E.; Quintana, Fernando A.; Mueller, Peter; Rosner, Gary L.
    Data analysis sometimes requires the relaxation of parametric assumptions in order to gain modeling flexibility and robustness against mis-specification of the probability model. In the Bayesian context, this is accomplished by placing a prior distribution on a function space, such as the space of all probability distributions or the space of all regression functions. Unfortunately, posterior distributions ranging over function spaces are highly complex and hence sampling methods play a key role. This paper provides an introduction to a simple, yet comprehensive, set of programs for the implementation of some Bayesian nonparametric and semiparametric models in R, DPpackage. Currently, DPpackage includes models for marginal and conditional density estimation, receiver operating characteristic curve analysis, interval-censored data, binary regression data, item response data, longitudinal and clustered data using generalized linear mixed models, and regression data using generalized additive models. The package also contains functions to compute pseudo-Bayes factors for model comparison and for eliciting the precision parameter of the Dirichlet process prior, and a general purpose Metropolis sampling algorithm. To maximize computational efficiency, the actual sampling for each model is carried out using compiled C, C++ or Fortran code.
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    Semi-parametric Bayesian Inference for Multi-Season Baseball Data
    (INT SOC BAYESIAN ANALYSIS, 2008) Quintana, Fernando A.; Mueller, Peter; Rosner, Gary L.; Munsell, Mark
    We analyze complete sequences of successes (hits, walks, and sacrifices) for a group of players from the American and National Leagues, collected over 4 seasons. The goal is to describe how players' performance vary from season to season. In particular, we wish to assess and compare the effect of available occasion-specific covariates over seasons. The data are binary sequences for each player and each season. We model dependence in the binary sequence by an autoregressive logistic model. The model includes lagged terms up to a fixed order. For each player and season we introduce a different set of autologistic regression coefficients, i.e., the regression coefficients are random effects that are specific of each season and player. We use a nonparametric approach to define a random effects distribution. The nonparametric model is defined as a mixture with a Dirichlet process prior for the mixing measure. The described model is justified by a representation theorem for order-k exchangeable sequences. Besides the repeated measurements for each season and player, multiple seasons within a given player define an additional level of repeated measurements. We introduce dependence at this level of repeated measurements by relating the season-specific random effects vectors in an autoregressive fashion. We ultimately conclude that while some covariates like the ERA of the opposing pitcher are always relevant, others like an indicator for the game being into the seventh inning may be significant only for certain season, and some others, like the score of the game, can safely be ignored.
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    Semiparametric Bayesian inference for multilevel repeated measurement data
    (WILEY, 2007) Muller, Peter; Quintana, Fernando A.; Rosner, Gary L.
    We discuss inference for data with repeated measurements at multiple levels. The motivating example is data with blood counts from cancer patients undergoing multiple cycles of chemotherapy, with days nested within cycles. Some inference questions relate to repeated measurements over days within cycle, while other questions are concerned with the dependence across cycles. When the desired inference relates to both levels of repetition, it becomes important to reflect the data structure in the model. We develop a semiparametric Bayesian modeling approach, restricting attention to two levels of repeated measurements. For the top-level longitudinal sampling model we use random effects to introduce the desired dependence across repeated measurements. We use a nonparametric prior for the random effects distribution. Inference about dependence across second-level repetition is implemented by the clustering implied in the nonparametric random effects model. Practical use of the model requires that the posterior distribution on the latent random effects be reasonably precise.