MATSuMoTo: The MATLAB Surrogate Model Toolbox For Computationally Expensive Black-Box Global Optimization Problems

MATSuMoTo is the MATLAB Surrogate Model Toolbox for computationally expensive, black-box, global optimization problems that may have continuous, mixed-integer, or pure integer variables. Due to the black-box nature of the objective function, derivatives are not available. Hence, surrogate models are used as computationally cheap approximations of the expensive objective function in order to guide the search for improved solutions. Due to the computational expense of doing a single function evaluation, the goal is to find optimal solutions within very few expensive evaluations. The multimodality of the expensive black-box function requires an algorithm that is able to search locally as well as globally. MATSuMoTo is able to address these challenges. MATSuMoTo offers various choices for surrogate models and surrogate model mixtures, initial experimental design strategies, and sampling strategies. MATSuMoTo is able to do several function evaluations in parallel by exploiting MATLAB's Parallel Computing Toolbox.Comment: 13 pages, 7 figure

A Parallel Algorithm for Exact Bayesian Structure Discovery in Bayesian Networks

Exact Bayesian structure discovery in Bayesian networks requires exponential time and space. Using dynamic programming (DP), the fastest known sequential algorithm computes the exact posterior probabilities of structural features in $O(2(d+1)n2^n)$ time and space, if the number of nodes (variables) in the Bayesian network is $n$ and the in-degree (the number of parents) per node is bounded by a constant $d$. Here we present a parallel algorithm capable of computing the exact posterior probabilities for all $n(n-1)$ edges with optimal parallel space efficiency and nearly optimal parallel time efficiency. That is, if $p=2^k$ processors are used, the run-time reduces to $O(5(d+1)n2^{n-k}+k(n-k)^d)$ and the space usage becomes $O(n2^{n-k})$ per processor. Our algorithm is based the observation that the subproblems in the sequential DP algorithm constitute a $n$-$D$ hypercube. We take a delicate way to coordinate the computation of correlated DP procedures such that large amount of data exchange is suppressed. Further, we develop parallel techniques for two variants of the well-known \emph{zeta transform}, which have applications outside the context of Bayesian networks. We demonstrate the capability of our algorithm on datasets with up to 33 variables and its scalability on up to 2048 processors. We apply our algorithm to a biological data set for discovering the yeast pheromone response pathways.Comment: 32 pages, 12 figure

FFPopSim: An efficient forward simulation package for the evolution of large populations

The analysis of the evolutionary dynamics of a population with many polymorphic loci is challenging since a large number of possible genotypes needs to be tracked. In the absence of analytical solutions, forward computer simulations are an important tool in multi-locus population genetics. The run time of standard algorithms to simulate sexual populations increases as 8^L with the number L of loci, or with the square of the population size N. We have developed algorithms that allow to simulate large populations with a run-time that scales as 3^L. The algorithm is based on an analog of the Fast-Fourier Transform (FFT) and allows for arbitrary fitness functions (i.e. any epistasis) and genetic maps. The algorithm is implemented as a collection of C++ classes and a Python interface.Comment: available from: http://code.google.com/p/ffpopsi