An efficient genetic algorithm for large-scale planning of robust industrial wireless networks

An industrial indoor environment is harsh for wireless communications compared to an office environment, because the prevalent metal easily causes shadowing effects and affects the availability of an industrial wireless local area network (IWLAN). On the one hand, it is costly, time-consuming, and ineffective to perform trial-and-error manual deployment of wireless nodes. On the other hand, the existing wireless planning tools only focus on office environments such that it is hard to plan IWLANs due to the larger problem size and the deployed IWLANs are vulnerable to prevalent shadowing effects in harsh industrial indoor environments. To fill this gap, this paper proposes an overdimensioning model and a genetic algorithm based over-dimensioning (GAOD) algorithm for deploying large-scale robust IWLANs. As a progress beyond the state-of-the-art wireless planning, two full coverage layers are created. The second coverage layer serves as redundancy in case of shadowing. Meanwhile, the deployment cost is reduced by minimizing the number of access points (APs); the hard constraint of minimal inter-AP spatial paration avoids multiple APs covering the same area to be simultaneously shadowed by the same obstacle. The computation time and occupied memory are dedicatedly considered in the design of GAOD for large-scale optimization. A greedy heuristic based over-dimensioning (GHOD) algorithm and a random OD algorithm are taken as benchmarks. In two vehicle manufacturers with a small and large indoor environment, GAOD outperformed GHOD with up to 20% less APs, while GHOD outputted up to 25% less APs than a random OD algorithm. Furthermore, the effectiveness of this model and GAOD was experimentally validated with a real deployment system

First-principles molecular structure search with a genetic algorithm

The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment of the conformation space of molecules. The algorithm is designed to work with first-principles methods, facilitated by the incorporation of local optimization and blacklisting conformers to prevent repeated evaluations of very similar solutions. The aim of the search is not only to find the global minimum, but to predict all conformers within an energy window above the global minimum. The performance of the search strategy is: (i) evaluated for a reference data set extracted from a database with amino acid dipeptide conformers obtained by an extensive combined force field and first-principles search and (ii) compared to the performance of a systematic search and a random conformer generator for the example of a drug-like ligand with 43 atoms, 8 rotatable bonds and 1 cis/trans bond

Link communities reveal multiscale complexity in networks

Networks have become a key approach to understanding systems of interacting objects, unifying the study of diverse phenomena including biological organisms and human society. One crucial step when studying the structure and dynamics of networks is to identify communities: groups of related nodes that correspond to functional subunits such as protein complexes or social spheres. Communities in networks often overlap such that nodes simultaneously belong to several groups. Meanwhile, many networks are known to possess hierarchical organization, where communities are recursively grouped into a hierarchical structure. However, the fact that many real networks have communities with pervasive overlap, where each and every node belongs to more than one group, has the consequence that a global hierarchy of nodes cannot capture the relationships between overlapping groups. Here we reinvent communities as groups of links rather than nodes and show that this unorthodox approach successfully reconciles the antagonistic organizing principles of overlapping communities and hierarchy. In contrast to the existing literature, which has entirely focused on grouping nodes, link communities naturally incorporate overlap while revealing hierarchical organization. We find relevant link communities in many networks, including major biological networks such as protein-protein interaction and metabolic networks, and show that a large social network contains hierarchically organized community structures spanning inner-city to regional scales while maintaining pervasive overlap. Our results imply that link communities are fundamental building blocks that reveal overlap and hierarchical organization in networks to be two aspects of the same phenomenon.Comment: Main text and supplementary informatio

Detailed evaluation of data analysis tools for subtyping of bacterial isolates based on whole genome sequencing : Neisseria meningitidis as a proof of concept

Whole genome sequencing is increasingly recognized as the most informative approach for characterization of bacterial isolates. Success of the routine use of this technology in public health laboratories depends on the availability of well-characterized and verified data analysis methods. However, multiple subtyping workflows are now often being used for a single organism, and differences between them are not always well described. Moreover, methodologies for comparison of subtyping workflows, and assessment of their performance are only beginning to emerge. Current work focuses on the detailed comparison of WGS-based subtyping workflows and evaluation of their suitability for the organism and the research context in question. We evaluated the performance of pipelines used for subtyping of Neisseria meningitidis, including the currently widely applied cgMLST approach and different SNP-based methods. In addition, the impact of the use of different tools for detection and filtering of recombinant regions and of different reference genomes were tested. Our benchmarking analysis included both assessment of technical performance of the pipelines and functional comparison of the generated genetic distance matrices and phylogenetic trees. It was carried out using replicate sequencing datasets of high- and low-coverage, consisting mainly of isolates belonging to the clonal complex 269. We demonstrated that cgMLST and some of the SNP-based subtyping workflows showed very good performance characteristics and highly similar genetic distance matrices and phylogenetic trees with isolates belonging to the same clonal complex. However, only two of the tested workflows demonstrated reproducible results for a group of more closely related isolates. Additionally, results of the SNP-based subtyping workflows were to some level dependent on the reference genome used. Interestingly, the use of recombination-filtering software generally reduced the similarity between the gene-by-gene and SNP-based methodologies for subtyping of N. meningitidis. Our study, where N. meningitidis was taken as an example, clearly highlights the need for more benchmarking comparative studies to eventually contribute to a justified use of a specific WGS data analysis workflow within an international public health laboratory context

Asteroid lightcurves from the Palomar Transient Factory survey: Rotation periods and phase functions from sparse photometry

We fit 54,296 sparsely-sampled asteroid lightcurves in the Palomar Transient Factory to a combined rotation plus phase-function model. Each lightcurve consists of 20+ observations acquired in a single opposition. Using 805 asteroids in our sample that have reference periods in the literature, we find the reliability of our fitted periods is a complicated function of the period, amplitude, apparent magnitude and other attributes. Using the 805-asteroid ground-truth sample, we train an automated classifier to estimate (along with manual inspection) the validity of the remaining 53,000 fitted periods. By this method we find 9,033 of our lightcurves (of 8,300 unique asteroids) have reliable periods. Subsequent consideration of asteroids with multiple lightcurve fits indicate 4% contamination in these reliable periods. For 3,902 lightcurves with sufficient phase-angle coverage and either a reliably-fit period or low amplitude, we examine the distribution of several phase-function parameters, none of which are bimodal though all correlate with the bond albedo and with visible-band colors. Comparing the theoretical maximal spin rate of a fluid body with our amplitude versus spin-rate distribution suggests that, if held together only by self-gravity, most asteroids are in general less dense than 2 g/cm$^3$, while C types have a lower limit of between 1 and 2 g/cm$^3$, in agreement with previous density estimates. For 5-20km diameters, S types rotate faster and have lower amplitudes than C types. If both populations share the same angular momentum, this may indicate the two types' differing ability to deform under rotational stress. Lastly, we compare our absolute magnitudes and apparent-magnitude residuals to those of the Minor Planet Center's nominal $G=0.15$, rotation-neglecting model; our phase-function plus Fourier-series fitting reduces asteroid photometric RMS scatter by a factor of 3.Comment: 35 pages, 29 figures. Accepted 15-Apr-2015 to The Astronomical Journal (AJ). Supplementary material including ASCII data tables will be available through the publishing journal's websit