Technical Note—On Nested Partitions Method for Global Optimization

Finite-Time Behavior of Nested Partitions Method for Global Optimization

perfectphyloR: An R package for reconstructing perfect phylogenies

Background A perfect phylogeny is a rooted binary tree that recursively partitions sequences. The nested partitions of a perfect phylogeny provide insight into the pattern of ancestry of genetic sequence data. For example, sequences may cluster together in a partition indicating that they arise from a common ancestral haplotype. Results We present an R package to reconstruct the local perfect phylogenies underlying a sample of binary sequences. The package enables users to associate the reconstructed partitions with a user-defined partition. We describe and demonstrate the major functionality of the package. Conclusion The package should be of use to researchers seeking insight into the ancestral structure of their sequence data. The reconstructed partitions have many applications, including the mapping of trait-influencing variants.

perfectphyloR: An R package for reconstructing perfect phylogenies

BackgroundA perfect phylogeny is a rooted binary tree that recursively partitions sequences. The nested partitions of a perfect phylogeny provide insight into the pattern of ancestry of genetic sequence data. For example, sequences may cluster together in a partition indicating that they arise from a common ancestral haplotype.ResultsWe present an R packageperfectphyloRto reconstruct the local perfect phylogenies underlying a sample of binary sequences. The package enables users to associate the reconstructed partitions with a user-defined partition. We describe and demonstrate the major functionality of the package.ConclusionTheperfectphyloRpackage should be of use to researchers seeking insight into the ancestral structure of their sequence data. The reconstructed partitions have many applications, including the mapping of trait-influencing variants.

Scalable Clustering of Individual Electrical Curves for Profiling and Bottom-Up Forecasting

Smart grids require flexible data driven forecasting methods. We propose clustering tools for bottom-up short-term load forecasting. We focus on individual consumption data analysis which plays a major role for energy management and electricity load forecasting. The first section is dedicated to the industrial context and a review of individual electrical data analysis. Then, we focus on hierarchical time-series for bottom-up forecasting. The idea is to decompose the global signal and obtain disaggregated forecasts in such a way that their sum enhances the prediction. This is done in three steps: identify a rather large number of super-consumers by clustering their energy profiles, generate a hierarchy of nested partitions and choose the one that minimize a prediction criterion. Using a nonparametric model to handle forecasting, and wavelets to define various notions of similarity between load curves, this disaggregation strategy gives a 16% improvement in forecasting accuracy when applied to French individual consumers. Then, this strategy is implemented using R—the free software environment for statistical computing—so that it can scale when dealing with massive datasets. The proposed solution is to make the algorithm scalable combine data storage, parallel computing and double clustering step to define the super-consumers. The resulting software is openly available.

Simulation Optimization for MRO Systems Operations

In this paper, we address the scheduling issues in a class of maintenance, repair and overhaul systems. By considering all key characteristics such as disassembly, material recovery uncertainty, material matching requirements, stochastic routings and variable processing times, the scheduling problem is formulated into a simulation optimization problem. To solve this difficult problem, we developed two hybrid algorithms based on nested partitions method and optimal computing budged allocation technology. Asymptotic convergence of these two algorithms is proved and numerical results show that the proposed algorithms can generate high quality solutions which outperform the performance of many heuristics.