Present-day indoor navigation systems are often not well adapted to the specific needs and requirements of its users. This research aims at improving those indoor navigation systems by providing navigation support that cognitively closer to user preferences and behaviour. More specifically, the focus is on the implementation of an accurate turn calculation method in a turn minimization algorithm, aiming to lower the complexity of routes and route instructions. This new-introduced perception-based turn calculation procedure is based on a direct door-to-door walking pattern, and, in contrast to previous algorithms, independent of the underlying indoor network type. It takes into account the effects of geometry of indoor space on human movement. To evaluate its functioning, both the traditional algorithm and the proposed perception-based algorithm are applied in the fewest turns path algorithm. It is demonstrated that the proposed algorithm accurately calculates turns in alignment with people’s perception. The implementation of the calculation algorithm in the fewest turns path algorithm also allows future applications in indoor simplest path algorithms, and overall contributes to cognitively richer indoor navigation systems.

BACKGROUND: Core collections provide genebank curators and plant breeders a way to reduce size of their collections and populations, while minimizing impact on genetic diversity and allele frequency. Many methods have been proposed to generate core collections, often using distance metrics to quantify the similarity of two accessions, based on genetic marker data or phenotypic traits. Core Hunter is a multi-purpose core subset selection tool that uses local search algorithms to generate subsets relying on one or more metrics, including several distance metrics and allelic richness. RESULTS: In version 3 of Core Hunter (CH3) we have incorporated two new, improved methods for summarizing distances to quantify diversity or representativeness of the core collection. A comparison of CH3 and Core Hunter 2 (CH2) showed that these new metrics can be effectively optimized with less complex algorithms, as compared to those used in CH2. CH3 is more effective at maximizing the improved diversity metric than CH2, still ensures a high average and minimum distance, and is faster for large datasets. Using CH3, a simple stochastic hill-climber is able to find highly diverse core collections, and the more advanced parallel tempering algorithm further increases the quality of the core and further reduces variability across independent samples. We also evaluate the ability of CH3 to simultaneously maximize diversity, and either representativeness or allelic richness, and compare the results with those of the GDOpt and SimEli methods. CH3 can sample equally representative cores as GDOpt, which was specifically designed for this purpose, and is able to construct cores that are simultaneously more diverse, and either are more representative or have higher allelic richness, than those obtained by SimEli. CONCLUSIONS: In version 3, Core Hunter has been updated to include two new core subset selection metrics that construct cores for representativeness or diversity, with improved performance. It combines and outperforms the strengths of other methods, as it (simultaneously) optimizes a variety of metrics. In addition, CH3 is an improvement over CH2, with the option to use genetic marker data or phenotypic traits, or both, and improved speed. Core Hunter 3 is freely available on http://www.corehunter.org .

Summary This paper describes the Java Metaheuristics Search framework (JAMES, v1.1): an object‐oriented Java framework for discrete optimization using local search algorithms that exploits the generality of such metaheuristics by clearly separating search implementation and application from problem specification. A wide range of generic local searches are provided, including (stochastic) hill climbing, tabu search, variable neighbourhood search and parallel tempering. These can be applied to any user‐defined problem by plugging in a custom neighbourhood for the corresponding solution type. Using an automated analysis workflow, the performance of different search algorithms can be compared in order to select an appropriate optimization strategy. Implementations of specific components are included for subset selection, such as a predefined solution type, generic problem definition and several subset neighbourhoods used to modify the set of selected items. Additional components for other types of problems (e.g. permutation problems) are provided through an extensions module which also includes the analysis workflow. In comparison with existing Java metaheuristics frameworks that mainly focus on population‐based algorithms, JAMES has a much lower memory footprint and promotes efficient application of local searches by taking full advantage of move‐based evaluation. Releases of JAMES are deployed to the Maven Central Repository so that the framework can easily be included as a dependency in other Java applications. The project is fully open source and hosted on GitHub. More information can be found at http://www.jamesframework.org . Copyright © 2016 John Wiley & Sons, Ltd.

BACKGROUND: Rapid evolutions in sequencing technology force read mappers into flexible adaptation to longer reads, changing error models, memory barriers and novel applications. RESULTS: ALFALFA achieves a high performance in accurately mapping long single-end and paired-end reads to gigabase-scale reference genomes, while remaining competitive for mapping shorter reads. Its seed-and-extend workflow is underpinned by fast retrieval of super-maximal exact matches from an enhanced sparse suffix array, with flexible parameter tuning to balance performance, memory footprint and accuracy. CONCLUSIONS: ALFALFA is open source and available at http://alfalfa.ugent.be .

Abstract Summary: We have developed essaMEM, a tool for finding maximal exact matches that can be used in genome comparison and read mapping. essaMEM enhances an existing sparse suffix array implementation with a sparse child array. Tests indicate that the enhanced algorithm for finding maximal exact matches is much faster, while maintaining the same memory footprint. In this way, sparse suffix arrays remain competitive with the more complex compressed suffix arrays. Availability: Source code is freely available at https://github.ugent.be/ComputationalBiology/essaMEM. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

BACKGROUND: Sampling core subsets from genetic resources while maintaining as much as possible the genetic diversity of the original collection is an important but computationally complex task for gene bank managers. The Core Hunter computer program was developed as a tool to generate such subsets based on multiple genetic measures, including both distance measures and allelic diversity indices. At first we investigate the effect of minimum (instead of the default mean) distance measures on the performance of Core Hunter. Secondly, we try to gain more insight into the performance of the original Core Hunter search algorithm through comparison with several other heuristics working with several realistic datasets of varying size and allelic composition. Finally, we propose a new algorithm (Mixed Replica search) for Core Hunter II with the aim of improving the diversity of the constructed core sets and their corresponding generation times. RESULTS: Our results show that the introduction of minimum distance measures leads to core sets in which all accessions are sufficiently distant from each other, which was not always obtained when optimizing mean distance alone. Comparison of the original Core Hunter algorithm, Replica Exchange Monte Carlo (REMC), with simpler heuristics shows that the simpler algorithms often give very good results but with lower runtimes than REMC. However, the performance of the simpler algorithms is slightly worse than REMC under lower sampling intensities and some heuristics clearly struggle with minimum distance measures. In comparison the new advanced Mixed Replica search algorithm (MixRep), which uses heterogeneous replicas, was able to sample core sets with equal or higher diversity scores than REMC and the simpler heuristics, often using less computation time than REMC. CONCLUSION: The REMC search algorithm used in the original Core Hunter computer program performs well, sometimes leading to slightly better results than some of the simpler methods, although it doesn't always give the best results. By switching to the new Mixed Replica algorithm overall results and runtimes can be significantly improved. Finally we recommend including minimum distance measures in the objective function when looking for core sets in which all accessions are sufficiently distant from each other. Core Hunter II is freely available as an open source project at http://www.corehunter.org.

The experiments described in this article combine response time measurements and eye movement data to gain insight into the users' cognitive processes while working with dynamic and interactive maps. Experts and novices participated in a user study with a ‘between user’ design. Twenty screen maps were presented in a random order to each participant, on which he had to execute a visual search. The combined information of the button actions and eye tracker reveals that both user groups showed a similar pattern in the time intervals needed to locate the subsequent names. From this pattern, information about the users' cognitive load could be derived: use of working memory, learning effect and so on. Moreover, the response times also showed that experts were significantly faster in finding the names in the map image. This is further explained by the eye movement metrics: experts had significantly shorter fixations and more fixations per second meaning that they could interpret a larger part of the map in the same amount of time. As a consequence, they could locate objects in the map image more efficiently and thus faster.

We propose a simple and effective heuristic that allows fast generation of a large set of shortest path alternatives in weighted directed graphs. The heuristic is based on existing deviation path algorithms for exact k shortest paths. It precalculates a backward shortest path tree and thus avoids doing many shortest path computations, but as a result it does not necessarily find the exact set of k shortest paths. Computational results on real-world road networks are reported. Our tests show that the quality of the paths produced by the heuristic is most satisfactory: typically, the kth path found by the heuristic is less than 1% longer than the exact kth shortest path, for values of k up to 10,000. Moreover, the heuristic runs very fast. We also show how the heuristic can be enhanced to an exact k shortest paths algorithm, which performs well in comparison with the existing exact k shortest path algorithms.

The aim of this work is a systematic investigation of the possible parameters of quasi-perfect (QP) binary and ternary linear codes of small dimensions and preparing a complete classification of all such codes. First, we give a list of infinite families of QP codes which includes all binary, ternary, and quaternary codes known to us. We continue further with a list of sporadic examples of binary and ternary QP codes. Later we present the results of our investigation where binary QP codes of dimensions up to 14 and ternary QP codes of dimensions up to 13 are classified.