Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such ‘‘gene clusters’’ is an essential component of comparative genomic analyses. However, currently ther...

Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such "gene clusters" is an essential component of comparative genomic analyses. However, currently there ...

We show that it is possible to construct an accurate approximation to the variational coupled cluster method, limited to double substitutions, from the minimization of a functional that is rigorously extensive, exact for isolated two-electron subsystems and invariant to transformations of the underlying orbital basis. This approximate variational coupled cluster theory is a modification and enh...

Quick and incremental growth in the processor power of desktop personal computers and network bandwidth due to recent extraordinary technological advances, have shifted the trend of parallel processing from conventional costly massively parallel supercomputers to the comparatively inexpensive cluster of networked desktop PCs for solving data and computation intensive sequential as well as paral...

2 The cluster approach 4 2.1 Tiling the lattice into small clusters . . . . . . . . . . . . . . . . . . . . . . . . 4 2.2 Cluster perturbation theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2.3 Green’s function and exact diagonalization . . . . . . . . . . . . . . . . . . . . 5 2.4 Freedom in the CPT construction . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.5 The Ritz...

We consider an interacting particle system in continuous configuration space. The pair interaction has an attractive part. We show that, at low density, the system behaves approximately like an ideal mixture of clusters (droplets): we prove rigorous bounds (a) for the constrained free energy associated with a given cluster size distribution, considered as an order parameter, (b) for the free en...

This paper analyzes the hierarchical Bayesian optimization algorithm (hBOA) on the problem of finding ground states of Ising spin glasses with ±J couplings in two and three dimensions. The performance of hBOA is compared to that of the simple genetic algorithm (GA) and the univariate marginal distribution algorithm (UMDA). The performance of all tested algorithms is improved by incorporating a ...

We examine a model in which a nonequilibrium phase transition from an active to an extinct state is observed. The order of this phase transition has been shown to be either continuous or first-order, depending on the parameter values and the dimension of the system. Using increasingly large clusters, we use the cluster approximation method to obtain estimates for the critical points in 1+1 dime...

Kriging or Gaussian Process Regression is applied in many fields as a non-linear regression model as well as a surrogate model in the field of evolutionary computation. However, the computational and space complexity of Kriging, that is cubic and quadratic in the number of data points respectively, becomes a major bottleneck with more and more data available nowadays. In this paper, we propose ...

A two-species reaction-diffusion model, in which particles diffuse on a one-dimensional lattice and annihilate when meeting each other, has been investigated. Mean-field equations for general choice of reaction rates have been solved exactly. The cluster mean-field approximation of the model is also studied. It is shown that the general form of large time behavior of one- and two-point function...