693 research outputs found
Exact Dimensionality Selection for Bayesian PCA
We present a Bayesian model selection approach to estimate the intrinsic
dimensionality of a high-dimensional dataset. To this end, we introduce a novel
formulation of the probabilisitic principal component analysis model based on a
normal-gamma prior distribution. In this context, we exhibit a closed-form
expression of the marginal likelihood which allows to infer an optimal number
of components. We also propose a heuristic based on the expected shape of the
marginal likelihood curve in order to choose the hyperparameters. In
non-asymptotic frameworks, we show on simulated data that this exact
dimensionality selection approach is competitive with both Bayesian and
frequentist state-of-the-art methods
Data Cube Approximation and Mining using Probabilistic Modeling
On-line Analytical Processing (OLAP) techniques commonly used in data warehouses allow the exploration of data cubes according to different analysis axes (dimensions) and under different abstraction levels in a dimension hierarchy. However, such techniques are not aimed at mining multidimensional data.
Since data cubes are nothing but multi-way tables, we propose to analyze the potential of two probabilistic modeling techniques, namely non-negative multi-way array factorization and log-linear modeling, with the ultimate objective of compressing and mining aggregate and multidimensional values. With the first technique, we compute the set of components that best fit the initial data set and whose superposition coincides with the original data; with the second technique we identify a parsimonious model (i.e., one with a reduced set of parameters), highlight strong associations among dimensions and discover possible outliers in data cells. A real life example will be
used to (i) discuss the potential benefits of the modeling output on cube exploration and mining, (ii) show how OLAP queries can be answered in an approximate way, and (iii) illustrate the strengths and limitations of these modeling approaches
Probabilistic principal component analysis for metabolomic data
Background:
Data from metabolomic studies are typically complex and high-dimensional. Principal component analysis (PCA) is currently the most widely used statistical technique for analyzing metabolomic data. However, PCA is limited by the fact that it is not based on a statistical model.
Results:
Here, probabilistic principal component analysis (PPCA) which addresses some of the limitations of PCA, is reviewed and extended. A novel extension of PPCA, called probabilistic principal component and covariates analysis (PPCCA), is introduced which provides a flexible approach to jointly model metabolomic data and additional covariate information. The use of a mixture of PPCA models for discovering the number of inherent groups in metabolomic data is demonstrated. The jackknife technique is employed to construct confidence intervals for estimated model parameters throughout. The optimal number of principal components is determined through the use of the Bayesian Information Criterion model selection tool, which is modified to address the high dimensionality of the data.
Conclusions:
The methods presented are illustrated through an application to metabolomic data sets. Jointly modeling metabolomic data and covariates was successfully achieved and has the potential to provide deeper insight to the underlying data structure. Examination of confidence intervals for the model parameters, such as loadings, allows for principled and clear interpretation of the underlying data structure. A software package called MetabolAnalyze, freely available through the R statistical software, has been developed to facilitate implementation of the presented methods in the metabolomics field.Irish Research Council for Science, Engineering and TechnologyHealth Research Boar
High-Dimensional Regression with Gaussian Mixtures and Partially-Latent Response Variables
In this work we address the problem of approximating high-dimensional data
with a low-dimensional representation. We make the following contributions. We
propose an inverse regression method which exchanges the roles of input and
response, such that the low-dimensional variable becomes the regressor, and
which is tractable. We introduce a mixture of locally-linear probabilistic
mapping model that starts with estimating the parameters of inverse regression,
and follows with inferring closed-form solutions for the forward parameters of
the high-dimensional regression problem of interest. Moreover, we introduce a
partially-latent paradigm, such that the vector-valued response variable is
composed of both observed and latent entries, thus being able to deal with data
contaminated by experimental artifacts that cannot be explained with noise
models. The proposed probabilistic formulation could be viewed as a
latent-variable augmentation of regression. We devise expectation-maximization
(EM) procedures based on a data augmentation strategy which facilitates the
maximum-likelihood search over the model parameters. We propose two
augmentation schemes and we describe in detail the associated EM inference
procedures that may well be viewed as generalizations of a number of EM
regression, dimension reduction, and factor analysis algorithms. The proposed
framework is validated with both synthetic and real data. We provide
experimental evidence that our method outperforms several existing regression
techniques
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