Computational statistics using the Bayesian Inference Engine

This paper introduces the Bayesian Inference Engine (BIE), a general parallel, optimised software package for parameter inference and model selection. This package is motivated by the analysis needs of modern astronomical surveys and the need to organise and reuse expensive derived data. The BIE is the first platform for computational statistics designed explicitly to enable Bayesian update and model comparison for astronomical problems. Bayesian update is based on the representation of high-dimensional posterior distributions using metric-ball-tree based kernel density estimation. Among its algorithmic offerings, the BIE emphasises hybrid tempered MCMC schemes that robustly sample multimodal posterior distributions in high-dimensional parameter spaces. Moreover, the BIE is implements a full persistence or serialisation system that stores the full byte-level image of the running inference and previously characterised posterior distributions for later use. Two new algorithms to compute the marginal likelihood from the posterior distribution, developed for and implemented in the BIE, enable model comparison for complex models and data sets. Finally, the BIE was designed to be a collaborative platform for applying Bayesian methodology to astronomy. It includes an extensible object-oriented and easily extended framework that implements every aspect of the Bayesian inference. By providing a variety of statistical algorithms for all phases of the inference problem, a scientist may explore a variety of approaches with a single model and data implementation. Additional technical details and download details are available from http://www.astro.umass.edu/bie. The BIE is distributed under the GNU GPL.Comment: Resubmitted version. Additional technical details and download details are available from http://www.astro.umass.edu/bie. The BIE is distributed under the GNU GP

Sparse Automatic Differentiation for Large-Scale Computations Using Abstract Elementary Algebra

Most numerical solvers and libraries nowadays are implemented to use mathematical models created with language-specific built-in data types (e.g. real in Fortran or double in C) and their respective elementary algebra implementations. However, built-in elementary algebra typically has limited functionality and often restricts flexibility of mathematical models and analysis types that can be applied to those models. To overcome this limitation, a number of domain-specific languages with more feature-rich built-in data types have been proposed. In this paper, we argue that if numerical libraries and solvers are designed to use abstract elementary algebra rather than language-specific built-in algebra, modern mainstream languages can be as effective as any domain-specific language. We illustrate our ideas using the example of sparse Jacobian matrix computation. We implement an automatic differentiation method that takes advantage of sparse system structures and is straightforward to parallelize in MPI setting. Furthermore, we show that the computational cost scales linearly with the size of the system.Comment: Submitted to ACM Transactions on Mathematical Softwar