Fast and scalable non-parametric Bayesian inference for Poisson point processes

We study the problem of non-parametric Bayesian estimation of the intensity function of a Poisson point process. The observations are $n$ independent realisations of a Poisson point process on the interval $[0,T]$. We propose two related approaches. In both approaches we model the intensity function as piecewise constant on $N$ bins forming a partition of the interval $[0,T]$. In the first approach the coefficients of the intensity function are assigned independent gamma priors, leading to a closed form posterior distribution. On the theoretical side, we prove that as $n\rightarrow\infty,$ the posterior asymptotically concentrates around the "true", data-generating intensity function at an optimal rate for $h$-H\"older regular intensity functions ($0 < h\leq 1$). In the second approach we employ a gamma Markov chain prior on the coefficients of the intensity function. The posterior distribution is no longer available in closed form, but inference can be performed using a straightforward version of the Gibbs sampler. Both approaches scale well with sample size, but the second is much less sensitive to the choice of $N$. Practical performance of our methods is first demonstrated via synthetic data examples. We compare our second method with other existing approaches on the UK coal mining disasters data. Furthermore, we apply it to the US mass shootings data and Donald Trump's Twitter data.Comment: 45 pages, 22 figure

A Nonparametric Bayesian Approach to Uncovering Rat Hippocampal Population Codes During Spatial Navigation

Rodent hippocampal population codes represent important spatial information about the environment during navigation. Several computational methods have been developed to uncover the neural representation of spatial topology embedded in rodent hippocampal ensemble spike activity. Here we extend our previous work and propose a nonparametric Bayesian approach to infer rat hippocampal population codes during spatial navigation. To tackle the model selection problem, we leverage a nonparametric Bayesian model. Specifically, to analyze rat hippocampal ensemble spiking activity, we apply a hierarchical Dirichlet process-hidden Markov model (HDP-HMM) using two Bayesian inference methods, one based on Markov chain Monte Carlo (MCMC) and the other based on variational Bayes (VB). We demonstrate the effectiveness of our Bayesian approaches on recordings from a freely-behaving rat navigating in an open field environment. We find that MCMC-based inference with Hamiltonian Monte Carlo (HMC) hyperparameter sampling is flexible and efficient, and outperforms VB and MCMC approaches with hyperparameters set by empirical Bayes

Source detection using a 3D sparse representation: application to the Fermi gamma-ray space telescope

The multiscale variance stabilization Transform (MSVST) has recently been proposed for Poisson data denoising. This procedure, which is nonparametric, is based on thresholding wavelet coefficients. We present in this paper an extension of the MSVST to 3D data (in fact 2D-1D data) when the third dimension is not a spatial dimension, but the wavelength, the energy, or the time. We show that the MSVST can be used for detecting and characterizing astrophysical sources of high-energy gamma rays, using realistic simulated observations with the Large Area Telescope (LAT). The LAT was launched in June 2008 on the Fermi Gamma-ray Space Telescope mission. The MSVST algorithm is very fast relative to traditional likelihood model fitting, and permits efficient detection across the time dimension and immediate estimation of spectral properties. Astrophysical sources of gamma rays, especially active galaxies, are typically quite variable, and our current work may lead to a reliable method to quickly characterize the flaring properties of newly-detected sources.Comment: Accepted. Full paper will figures available at http://jstarck.free.fr/aa08_msvst.pd

On the "Poisson Trick" and its Extensions for Fitting Multinomial Regression Models

This article is concerned with the fitting of multinomial regression models using the so-called "Poisson Trick". The work is motivated by Chen & Kuo (2001) and Malchow-M{\o}ller & Svarer (2003) which have been criticized for being computationally inefficient and sometimes producing nonsense results. We first discuss the case of independent data and offer a parsimonious fitting strategy when all covariates are categorical. We then propose a new approach for modelling correlated responses based on an extension of the Gamma-Poisson model, where the likelihood can be expressed in closed-form. The parameters are estimated via an Expectation/Conditional Maximization (ECM) algorithm, which can be implemented using functions for fitting generalized linear models readily available in standard statistical software packages. Compared to existing methods, our approach avoids the need to approximate the intractable integrals and thus the inference is exact with respect to the approximating Gamma-Poisson model. The proposed method is illustrated via a reanalysis of the yogurt data discussed by Chen & Kuo (2001)

Rethinking LDA: moment matching for discrete ICA

We consider moment matching techniques for estimation in Latent Dirichlet Allocation (LDA). By drawing explicit links between LDA and discrete versions of independent component analysis (ICA), we first derive a new set of cumulant-based tensors, with an improved sample complexity. Moreover, we reuse standard ICA techniques such as joint diagonalization of tensors to improve over existing methods based on the tensor power method. In an extensive set of experiments on both synthetic and real datasets, we show that our new combination of tensors and orthogonal joint diagonalization techniques outperforms existing moment matching methods.Comment: 30 pages; added plate diagrams and clarifications, changed style, corrected typos, updated figures. in Proceedings of the 29-th Conference on Neural Information Processing Systems (NIPS), 201

Joint segmentation of multivariate astronomical time series : bayesian sampling with a hierarchical model

Astronomy and other sciences often face the problem of detecting and characterizing structure in two or more related time series. This paper approaches such problems using Bayesian priors to represent relationships between signals with various degrees of certainty, and not just rigid constraints. The segmentation is conducted by using a hierarchical Bayesian approach to a piecewise constant Poisson rate model. A Gibbs sampling strategy allows joint estimation of the unknown parameters and hyperparameters. Results obtained with synthetic and real photon counting data illustrate the performance of the proposed algorithm