1,892 research outputs found
Exploiting informative priors for Bayesian classification and regression trees
A general method for defining informative priors
on statistical models is presented and applied
specifically to the space of classification and regression
trees. A Bayesian approach to learning such
models from data is taken, with the Metropolis-
Hastings algorithm being used to approximately
sample from the posterior. By only using proposal
distributions closely tied to the prior, acceptance
probabilities are easily computable via marginal
likelihood ratios, whatever the prior used. Our approach
is empirically tested by varying (i) the data,
(ii) the prior and (iii) the proposal distribution. A
comparison with related work is given
Conjugate Bayes for probit regression via unified skew-normal distributions
Regression models for dichotomous data are ubiquitous in statistics. Besides
being useful for inference on binary responses, these methods serve also as
building blocks in more complex formulations, such as density regression,
nonparametric classification and graphical models. Within the Bayesian
framework, inference proceeds by updating the priors for the coefficients,
typically set to be Gaussians, with the likelihood induced by probit or logit
regressions for the responses. In this updating, the apparent absence of a
tractable posterior has motivated a variety of computational methods, including
Markov Chain Monte Carlo routines and algorithms which approximate the
posterior. Despite being routinely implemented, Markov Chain Monte Carlo
strategies face mixing or time-inefficiency issues in large p and small n
studies, whereas approximate routines fail to capture the skewness typically
observed in the posterior. This article proves that the posterior distribution
for the probit coefficients has a unified skew-normal kernel, under Gaussian
priors. Such a novel result allows efficient Bayesian inference for a wide
class of applications, especially in large p and small-to-moderate n studies
where state-of-the-art computational methods face notable issues. These
advances are outlined in a genetic study, and further motivate the development
of a wider class of conjugate priors for probit models along with methods to
obtain independent and identically distributed samples from the unified
skew-normal posterior
Collaborative sparse regression using spatially correlated supports - Application to hyperspectral unmixing
This paper presents a new Bayesian collaborative sparse regression method for
linear unmixing of hyperspectral images. Our contribution is twofold; first, we
propose a new Bayesian model for structured sparse regression in which the
supports of the sparse abundance vectors are a priori spatially correlated
across pixels (i.e., materials are spatially organised rather than randomly
distributed at a pixel level). This prior information is encoded in the model
through a truncated multivariate Ising Markov random field, which also takes
into consideration the facts that pixels cannot be empty (i.e, there is at
least one material present in each pixel), and that different materials may
exhibit different degrees of spatial regularity. Secondly, we propose an
advanced Markov chain Monte Carlo algorithm to estimate the posterior
probabilities that materials are present or absent in each pixel, and,
conditionally to the maximum marginal a posteriori configuration of the
support, compute the MMSE estimates of the abundance vectors. A remarkable
property of this algorithm is that it self-adjusts the values of the parameters
of the Markov random field, thus relieving practitioners from setting
regularisation parameters by cross-validation. The performance of the proposed
methodology is finally demonstrated through a series of experiments with
synthetic and real data and comparisons with other algorithms from the
literature
Classification of protein interaction sentences via gaussian processes
The increase in the availability of protein interaction studies in textual format coupled with the demand for easier access to the key results has lead to a need for text mining solutions. In the text processing pipeline, classification is a key step for extraction of small sections of relevant text. Consequently, for the task of locating protein-protein interaction sentences, we examine the use of a classifier which has rarely been applied to text, the Gaussian processes (GPs). GPs are a non-parametric probabilistic analogue to the more popular support vector machines (SVMs). We find that GPs outperform the SVM and na\"ive Bayes classifiers on binary sentence data, whilst showing equivalent performance on abstract and multiclass sentence corpora. In addition, the lack of the margin parameter, which requires costly tuning, along with the principled multiclass extensions enabled by the probabilistic framework make GPs an appealing alternative worth of further adoption
Adaptive Markov random fields for joint unmixing and segmentation of hyperspectral image
Linear spectral unmixing is a challenging problem in hyperspectral imaging that consists of decomposing an observed pixel into a linear combination of pure spectra (or endmembers) with their corresponding proportions (or abundances). Endmember extraction algorithms can be employed for recovering the spectral signatures while abundances are estimated using an inversion step. Recent works have shown that exploiting spatial dependencies between image pixels can improve spectral unmixing. Markov random fields (MRF) are classically used to model these spatial correlations and partition the image into multiple classes with homogeneous abundances. This paper proposes to define the MRF sites using similarity regions. These regions are built using a self-complementary area filter that stems from the morphological theory. This kind of filter divides the original image into flat zones where the underlying pixels have the same spectral values. Once the MRF has been clearly established, a hierarchical Bayesian algorithm is proposed to estimate the abundances, the class labels, the noise variance, and the corresponding hyperparameters. A hybrid Gibbs sampler is constructed to generate samples according to the corresponding posterior distribution of the unknown parameters and hyperparameters. Simulations conducted on synthetic and real AVIRIS data demonstrate the good performance of the algorithm
Distributional logic programming for Bayesian knowledge representation
We present a formalism for combining logic programming and its flavour of nondeterminism with probabilistic reasoning. In particular, we focus on representing prior knowledge for Bayesian inference. Distributional logic programming (Dlp), is considered in the context of a class of generative probabilistic languages. A characterisation based on probabilistic paths which can play a central role in clausal probabilistic reasoning is presented. We illustrate how the characterisation can be utilised to clarify derived distributions with regards to mixing the logical and probabilistic constituents of generative languages. We use this operational characterisation to define a class of programs that exhibit probabilistic determinism. We show how Dlp can be used to define generative priors over statistical model spaces. For example, a single program can generate all possible Bayesian networks having N nodes while at the same time it defines a prior that penalises networks with large families. Two classes of statistical models are considered: Bayesian networks and classification and regression trees. Finally we discuss: (1) a Metropolis–Hastings algorithm that can take advantage of the defined priors and the probabilistic choice points in the prior programs and (2) its application to real-world machine learning tasks
Classification of newborn EEG maturity with Bayesian averaging over decision trees
EEG experts can assess a newborn’s brain maturity by visual analysis of age-related patterns in sleep EEG. It is highly desirable to make the results of assessment most accurate and reliable. However, the expert analysis is limited in capability to provide the estimate of uncertainty in assessments. Bayesian inference has been shown providing the most accurate estimates of uncertainty by using Markov Chain Monte Carlo (MCMC) integration over the posterior distribution. The use of MCMC enables to approximate the desired distribution by sampling the areas of interests in which the density of distribution is high. In practice, the posterior distribution can be multimodal, and so that the existing MCMC techniques cannot provide the proportional sampling from the areas of interest. The lack of prior information makes MCMC integration more difficult when a model parameter space is large and cannot be explored in detail within a reasonable time. In particular, the lack of information about EEG feature importance can affect the results of Bayesian assessment of EEG maturity. In this paper we explore how the posterior information about EEG feature importance can be used to reduce a negative influence of disproportional sampling on the results of Bayesian assessment. We found that the MCMC integration tends to oversample the areas in which a model parameter space includes one or more features, the importance of which counted in terms of their posterior use is low. Using this finding, we proposed to cure the results of MCMC integration and then described the results of testing the proposed method on a set of sleep EEG recordings
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