arXiv subjects

Meili Baragatti

Publications and source records attributed to Meili Baragatti.

6 recordsLinked to original sources

arXiv2025

Approximate Bayesian Computation with Deep Learning and Conformal prediction

Approximate Bayesian Computation (ABC) methods are commonly used to approximate posterior distributions in models with unknown or computationally intractable likelihoods. Classical ABC methods are based on nearest neighbor type algorithms and rely on the choice of so-called summary statistics, distances between datasets and a tolerance threshold. Recently, methods combining ABC with more complex machine learning algorithms have been proposed to mitigate the impact of these ``user-choices''. In this paper, we propose the first, to our knowledge, ABC method completely free of summary statistics, distance, and tolerance threshold. Moreover, in contrast with usual generalizations of the ABC method, it associates a confidence interval (having a proper frequentist marginal coverage) with the posterior mean estimation (or other moment-type estimates). Our method, named ABCD-Conformal, uses a neural network with Monte Carlo Dropout to provide an estimation of the posterior mean (or other moment type functionals), and conformal theory to obtain associated confidence sets. Efficient for estimating multidimensional parameters and amortized, we test this new method on four different applications and compare it with other ABC methods in the literature.

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arXiv2017

A Bayesian approach for the segmentation of series corrupted by a functional part

We propose a Bayesian approach to detect multiple change-points in a piecewise-constant signal corrupted by a functional part corresponding to environmental or experimental disturbances. The piecewise constant part (also called segmentation part) is expressed as the product of a lower triangular matrix by a sparse vector. The functional part is a linear combination of functions from a large dictionary. A Stochastic Search Variable Selection approach is used to obtain sparse estimations of the segmentation parameters (the change-points and the means over the segments) and of the functional part. The performance of our proposed method is assessed using simulation experiments. Applications to two real datasets from geodesy and economy fields are also presented.

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arXiv2012

Likelihood-Free Parallel Tempering

Approximate Bayesian Computational (ABC) methods (or likelihood-free methods) have appeared in the past fifteen years as useful methods to perform Bayesian analyses when the likelihood is analytically or computationally intractable. Several ABC methods have been proposed: Monte Carlo Markov Chains (MCMC) methods have been developped by Marjoramet al. (2003) and by Bortotet al. (2007) for instance, and sequential methods have been proposed among others by Sissonet al. (2007), Beaumont et al. (2009) and Del Moral et al. (2009). Until now, while ABC-MCMC methods remain the reference, sequential ABC methods have appeared to outperforms them (see for example McKinley et al. (2009) or Sisson et al. (2007)). In this paper a new algorithm combining population-based MCMC methods with ABC requirements is proposed, using an analogy with the Parallel Tempering algorithm (Geyer, 1991). Performances are compared with existing ABC algorithms on simulations and on a real example.

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arXiv2012

Parallel Tempering with Equi-Energy Moves

The Equi-Energy Sampler (EES) introduced by Kou et al [2006] is based on a population of chains which are updated by local moves and global moves, also called equi-energy jumps. The state space is partitioned into energy rings, and the current state of a chain can jump to a past state of an adjacent chain that has energy level close to its level. This algorithm has been developed to facilitate global moves between different chains, resulting in a good exploration of the state space by the target chain. This method seems to be more efficient than the classical Parallel Tempering (PT) algorithm. However it is difficult to use in combination with a Gibbs sampler and it necessitates increased storage. In this paper we propose an adaptation of this EES that combines PT with the principle of swapping between chains with same levels of energy. This adaptation, that we shall call Parallel Tempering with Equi-Energy Moves (PTEEM), keeps the original idea of the EES method while ensuring good theoretical properties, and practical implementation even if combined with a Gibbs sampler. Performances of the PTEEM algorithm are compared with those of the EES and of the standard PT algorithms in the context of mixture models, and in a problem of identification of gene regulatory binding motifs.

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arXiv2011

A study of variable selection using g-prior distribution with ridge parameter

In the Bayesian stochastic search variable selection framework, a common prior distribution for the regression coefficients is the g-prior of Zellner (1986). However, there are two standard cases in which the associated covariance matrix does not exist, and the conventional prior of Zellner can not be used: if the number of observations is lower than the number of variables (large p and small n paradigm), or if some variables are linear combinations of others. In such situations a prior distribution derived from the prior of Zellner can be used, by introducing a ridge parameter. This prior introduced by Gupta and Ibrahim (2007) is a flexible and simple adaptation of the g-prior. In this paper we study the influence of the ridge parameter on the selection of variables. A simple way to choose the associated hyper-parameters is proposed. The method is valid for any generalized linear mixed model and we focus on the case of probit mixed models when some variables are linear combinations of others. The method is applied to both simulated and real datasets obtained from Affymetrix microarray experiments. Results are compared to those obtained with the Bayesian Lasso.

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arXiv2011

Bayesian Variable Selection for Probit Mixed Models Applied to Gene Selection

In computational biology, gene expression datasets are characterized by very few individual samples compared to a large number of measurements per sample. Thus, it is appealing to merge these datasets in order to increase the number of observations and diversify the data, allowing a more reliable selection of genes relevant to the biological problem. Besides, the increased size of a merged dataset facilitates its re-splitting into training and validation sets. This necessitates the introduction of the dataset as a random effect. In this context, extending a work of Lee et al. (2003), a method is proposed to select relevant variables among tens of thousands in a probit mixed regression model, considered as part of a larger hierarchical Bayesian model. Latent variables are used to identify subsets of selected variables and the grouping (or blocking) technique of Liu (1994) is combined with a Metropolis-within-Gibbs algorithm (Robert and Casella 2004). The method is applied to a merged dataset made of three individual gene expression datasets, in which tens of thousands of measurements are available for each of several hundred human breast cancer samples. Even for this large dataset comprised of around 20000 predictors, the method is shown to be efficient and feasible. As an illustration, it is used to select the most important genes that characterize the estrogen receptor status of patients with breast cancer.

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