Adding functionalities to precomputed holograms with random mask multiplexing in holographic optical tweezers

In this study, we present a method designed to generate dynamic holograms in holographic optical tweezers. The approach combines our random mask encoding method with iterative high-efficiency algorithms. This hybrid method can be used to dynamically modify precalculated holograms, giving them new functionalities¿temporarily or permanently¿with a low computational cost. This allows the easy addition or removal of a single trap or the independent control of groups of traps for manipulating a variety of rigid structures in real time.

Comparative performance of supertree algorithms in large data sets using the soapberry family (Sapindaceae) as a case study.

For the last 2 decades, supertree reconstruction has been an active field of research and has seen the development of a large number of major algorithms. Because of the growing popularity of the supertree methods, it has become necessary to evaluate the performance of these algorithms to determine which are the best options (especially with regard to the supermatrix approach that is widely used). In this study, seven of the most commonly used supertree methods are investigated by using a large empirical data set (in terms of number of taxa and molecular markers) from the worldwide flowering plant family Sapindaceae. Supertree methods were evaluated using several criteria: similarity of the supertrees with the input trees, similarity between the supertrees and the total evidence tree, level of resolution of the supertree and computational time required by the algorithm. Additional analyses were also conducted on a reduced data set to test if the performance levels were affected by the heuristic searches rather than the algorithms themselves. Based on our results, two main groups of supertree methods were identified: on one hand, the matrix representation with parsimony (MRP), MinFlip, and MinCut methods performed well according to our criteria, whereas the average consensus, split fit, and most similar supertree methods showed a poorer performance or at least did not behave the same way as the total evidence tree. Results for the super distance matrix, that is, the most recent approach tested here, were promising with at least one derived method performing as well as MRP, MinFlip, and MinCut. The output of each method was only slightly improved when applied to the reduced data set, suggesting a correct behavior of the heuristic searches and a relatively low sensitivity of the algorithms to data set sizes and missing data. Results also showed that the MRP analyses could reach a high level of quality even when using a simple heuristic search strategy, with the exception of MRP with Purvis coding scheme and reversible parsimony. The future of supertrees lies in the implementation of a standardized heuristic search for all methods and the increase in computing power to handle large data sets. The latter would prove to be particularly useful for promising approaches such as the maximum quartet fit method that yet requires substantial computing power.

Line search multilevel optimization as computational methods for dense optical flow

We evaluate the performance of different optimization techniques developed in the context of optical flow computation with different variational models. In particular, based on truncated Newton methods (TN) that have been an effective approach for large-scale unconstrained optimization, we de- velop the use of efficient multilevel schemes for computing the optical flow. More precisely, we evaluate the performance of a standard unidirectional mul- tilevel algorithm - called multiresolution optimization (MR/OPT), to a bidrec- tional multilevel algorithm - called full multigrid optimization (FMG/OPT). The FMG/OPT algorithm treats the coarse grid correction as an optimiza- tion search direction and eventually scales it using a line search. Experimental results on different image sequences using four models of optical flow com- putation show that the FMG/OPT algorithm outperforms both the TN and MR/OPT algorithms in terms of the computational work and the quality of the optical flow estimation.

A comparison of one- and two-compartment neighbourhoods in heuristic search with spatial forest management goals

Abstract

Fast Approximation of Nonlinearities for improving inversion algorithms of PNL mixtures and Wiener systems

This paper proposes a very fast method for blindly approximating a nonlinear mapping which transforms a sum of random variables. The estimation is surprisingly good even when the basic assumption is not satisfied.We use the method for providing a good initialization for inverting post-nonlinear mixtures and Wiener systems. Experiments show that the algorithm speed is strongly improved and the asymptotic performance is preserved with a very low extra computational cost.

Local optima networks of hard combinatorial landscapes

Combinatorial optimization involves finding an optimal solution in a finite set of options; many everyday life problems are of this kind. However, the number of options grows exponentially with the size of the problem, such that an exhaustive search for the best solution is practically infeasible beyond a certain problem size. When efficient algorithms are not available, a practical approach to obtain an approximate solution to the problem at hand, is to start with an educated guess and gradually refine it until we have a good-enough solution. Roughly speaking, this is how local search heuristics work. These stochastic algorithms navigate the problem search space by iteratively turning the current solution into new candidate solutions, guiding the search towards better solutions. The search performance, therefore, depends on structural aspects of the search space, which in turn depend on the move operator being used to modify solutions. A common way to characterize the search space of a problem is through the study of its fitness landscape, a mathematical object comprising the space of all possible solutions, their value with respect to the optimization objective, and a relationship of neighborhood defined by the move operator. The landscape metaphor is used to explain the search dynamics as a sort of potential function. The concept is indeed similar to that of potential energy surfaces in physical chemistry. Borrowing ideas from that field, we propose to extend to combinatorial landscapes the notion of the inherent network formed by energy minima in energy landscapes. In our case, energy minima are the local optima of the combinatorial problem, and we explore several definitions for the network edges. At first, we perform an exhaustive sampling of local optima basins of attraction, and define weighted transitions between basins by accounting for all the possible ways of crossing the basins frontier via one random move. Then, we reduce the computational burden by only counting the chances of escaping a given basin via random kick moves that start at the local optimum. Finally, we approximate network edges from the search trajectory of simple search heuristics, mining the frequency and inter-arrival time with which the heuristic visits local optima. Through these methodologies, we build a weighted directed graph that provides a synthetic view of the whole landscape, and that we can characterize using the tools of complex networks science. We argue that the network characterization can advance our understanding of the structural and dynamical properties of hard combinatorial landscapes. We apply our approach to prototypical problems such as the Quadratic Assignment Problem, the NK model of rugged landscapes, and the Permutation Flow-shop Scheduling Problem. We show that some network metrics can differentiate problem classes, correlate with problem non-linearity, and predict problem hardness as measured from the performances of trajectory-based local search heuristics.

Reporting of methodologic information on trial registries for quality assessment: a study of trial records retrieved from the WHO search portal

Background: Although randomized clinical trials (RCTs) are considered the gold standard of evidence, their reporting is often suboptimal. Trial registries have the potential to contribute important methodologic information for critical appraisal of study results. Methods and Findings: The objective of the study was to evaluate the reporting of key methodologic study characteristics in trial registries. We identified a random sample (n = 265) of actively recruiting RCTs using the World Health Organization International Clinical Trials Registry Platform (ICTRP) search portal in 2008. We assessed the reporting of relevant domains from the Cochrane Collaboration’s ‘Risk of bias’ tool and other key methodological aspects. Our primary outcomes were the proportion of registry records with adequate reporting of random sequence generation, allocation concealment, blinding, and trial outcomes. Two reviewers independently assessed each record. Weighted overall proportions in the ICTRP search portal for adequate reporting of sequence generation, allocation concealment, blinding (including and excluding open label RCT) and primary outcomes were 5.7% (95% CI 3.0–8.4%), 1.4% (0–2.8%), 41% (35–47%), 8.4% (4.1–13%), and 66% (60–72%), respectively. The proportion of adequately reported RCTs was higher for registries that used specific methodological fields for describing methods of randomization and allocation concealment compared to registries that did not. Concerning other key methodological aspects, weighted overall proportions of RCTs with adequately reported items were as follows: eligibility criteria (81%), secondary outcomes (46%), harm (5%) follow-up duration (62%), description of the interventions (53%) and sample size calculation (1%). Conclusions: Trial registries currently contain limited methodologic information about registered RCTs. In order to permit adequate critical appraisal of trial results reported in journals and registries, trial registries should consider requesting details on key RCT methods to complement journal publications. Full protocols remain the most comprehensive source of methodologic information and should be made publicly available.

Generating highly balanced sudoku problems as hard problems

Sudoku problems are some of the most known and enjoyed pastimes, with a never diminishing popularity, but, for the last few years those problems have gone from an entertainment to an interesting research area, a twofold interesting area, in fact. On the one side Sudoku problems, being a variant of Gerechte Designs and Latin Squares, are being actively used for experimental design, as in [8, 44, 39, 9]. On the other hand, Sudoku problems, as simple as they seem, are really hard structured combinatorial search problems, and thanks to their characteristics and behavior, they can be used as benchmark problems for refining and testing solving algorithms and approaches. Also, thanks to their high inner structure, their study can contribute more than studies of random problems to our goal of solving real-world problems and applications and understanding problem characteristics that make them hard to solve. In this work we use two techniques for solving and modeling Sudoku problems, namely, Constraint Satisfaction Problem (CSP) and Satisfiability Problem (SAT) approaches. To this effect we define the Generalized Sudoku Problem (GSP), where regions can be of rectangular shape, problems can be of any order, and solution existence is not guaranteed. With respect to the worst-case complexity, we prove that GSP with block regions of m rows and n columns with m = n is NP-complete. For studying the empirical hardness of GSP, we define a series of instance generators, that differ in the balancing level they guarantee between the constraints of the problem, by finely controlling how the holes are distributed in the cells of the GSP. Experimentally, we show that the more balanced are the constraints, the higher the complexity of solving the GSP instances, and that GSP is harder than the Quasigroup Completion Problem (QCP), a problem generalized by GSP. Finally, we provide a study of the correlation between backbone variables – variables with the same value in all the solutions of an instance– and hardness of GSP.

Anther culture properties of oat x wild red oat progenies and a search for RAPD markers associated with anther culture ability

Selostus: Ponsiviljeltävyys ja siihen liittyvät geenimerkit peltokauran ja susikauran risteytysjälkeläisissä

Matkapuhelimen puhelinmuistiopalvelimen tietorakenteiden ja lajittelualgoritmien analysointi ja suunnittelu

Puhelinmuistio on yksi matkapuhelimen käytetyimmistä ominaisuuksista. Puhelinmuistion tulee siksi olla kaikissa tilanteissa mahdollisimman nopeasti käytettävissä. Tämä edellyttää puhelinmuistiopalvelimelta tehokkaita tietorakenteita ja lajittelualgoritmeja. Nokian matkapuhelimissa puhelinmuistiopalvelin käyttää hakurakenteena järjestettyjä taulukoita. Työn tavoitteena oli kehittää puhelinmuistiopalvelimen hakutaulukoiden lajittelu mahdollisimman nopeaksi. Useita eri lajittelualgoritmeja vertailtiin ja niiden suoritusaikoja analysoitiin eri tilanteissa. Insertionsort-lajittelualgoritmin todettiin olevan nopein algoritmi lähes järjestyksessä olevien taulukoiden lajitteluun. Analyysin perusteella Quicksort-algoritmi lajittelee nopeimmin satunnaisessa järjestyksessä olevat taulukot. Quicksort-insertionsort –hybridialgoritmin havaittiin olevan paras lajittelualgoritmi puhelinmuistion lajitteluun. Sopivalla parametroinnilla tämä algoritmi on nopea satunnaisessa järjestyksessä olevalle aineistolle. Se kykenee hyödyntämään lajiteltavassa aineistossa valmiina olevaa järjestystä. Algoritmi ei kasvata merkittävästi muistinkulutusta. Uuden algoritmin ansiosta hakutaulukoiden lajittelu nopeutuu parhaimmillaan useita kymmeniä prosentteja.

Evolutionary computing in search-based software engineering

This master’s thesis aims to study and represent from literature how evolutionary algorithms are used to solve different search and optimisation problems in the area of software engineering. Evolutionary algorithms are methods, which imitate the natural evolution process. An artificial evolution process evaluates fitness of each individual, which are solution candidates. The next population of candidate solutions is formed by using the good properties of the current population by applying different mutation and crossover operations. Different kinds of evolutionary algorithm applications related to software engineering were searched in the literature. Applications were classified and represented. Also the necessary basics about evolutionary algorithms were presented. It was concluded, that majority of evolutionary algorithm applications related to software engineering were about software design or testing. For example, there were applications about classifying software production data, project scheduling, static task scheduling related to parallel computing, allocating modules to subsystems, N-version programming, test data generation and generating an integration test order. Many applications were experimental testing rather than ready for real production use. There were also some Computer Aided Software Engineering tools based on evolutionary algorithms.

Question Waves: A multicast query routing algorithm for social search

This paper describes Question Waves, an algorithm that can be applied to social search protocols, such as Asknext or Sixearch. In this model, the queries are propagated through the social network, with faster propagation through more trustable acquaintances. Question Waves uses local information to make decisions and obtain an answer ranking. With Question Waves, the answers that arrive first are the most likely to be relevant, and we computed the correlation of answer relevance with the order of arrival to demonstrate this result. We obtained correlations equivalent to the heuristics that use global knowledge, such as profile similarity among users or the expertise value of an agent. Because Question Waves is compatible with the social search protocol Asknext, it is possible to stop a search when enough relevant answers have been found; additionally, stopping the search early only introduces a minimal risk of not obtaining the best possible answer. Furthermore, Question Waves does not require a re-ranking algorithm because the results arrive sorted

Evolutionary synthesis of stochastic gene network models using feature-based search spaces

A feature-based fitness function is applied in a genetic programming system to synthesize stochastic gene regulatory network models whose behaviour is defined by a time course of protein expression levels. Typically, when targeting time series data, the fitness function is based on a sum-of-errors involving the values of the fluctuating signal. While this approach is successful in many instances, its performance can deteriorate in the presence of noise. This thesis explores a fitness measure determined from a set of statistical features characterizing the time series' sequence of values, rather than the actual values themselves. Through a series of experiments involving symbolic regression with added noise and gene regulatory network models based on the stochastic 'if-calculus, it is shown to successfully target oscillating and non-oscillating signals. This practical and versatile fitness function offers an alternate approach, worthy of consideration for use in algorithms that evaluate noisy or stochastic behaviour.

Characterizing Dynamic Optimization Benchmarks for the Comparison of Multi-Modal Tracking Algorithms

Population-based metaheuristics, such as particle swarm optimization (PSO), have been employed to solve many real-world optimization problems. Although it is of- ten sufficient to find a single solution to these problems, there does exist those cases where identifying multiple, diverse solutions can be beneficial or even required. Some of these problems are further complicated by a change in their objective function over time. This type of optimization is referred to as dynamic, multi-modal optimization. Algorithms which exploit multiple optima in a search space are identified as niching algorithms. Although numerous dynamic, niching algorithms have been developed, their performance is often measured solely on their ability to find a single, global optimum. Furthermore, the comparisons often use synthetic benchmarks whose landscape characteristics are generally limited and unknown. This thesis provides a landscape analysis of the dynamic benchmark functions commonly developed for multi-modal optimization. The benchmark analysis results reveal that the mechanisms responsible for dynamism in the current dynamic bench- marks do not significantly affect landscape features, thus suggesting a lack of representation for problems whose landscape features vary over time. This analysis is used in a comparison of current niching algorithms to identify the effects that specific landscape features have on niching performance. Two performance metrics are proposed to measure both the scalability and accuracy of the niching algorithms. The algorithm comparison results demonstrate the algorithms best suited for a variety of dynamic environments. This comparison also examines each of the algorithms in terms of their niching behaviours and analyzing the range and trade-off between scalability and accuracy when tuning the algorithms respective parameters. These results contribute to the understanding of current niching techniques as well as the problem features that ultimately dictate their success.

Models and algorithms for the capacitated location-routing problem

Le problème de localisation-routage avec capacités (PLRC) apparaît comme un problème clé dans la conception de réseaux de distribution de marchandises. Il généralisele problème de localisation avec capacités (PLC) ainsi que le problème de tournées de véhicules à multiples dépôts (PTVMD), le premier en ajoutant des décisions liées au routage et le deuxième en ajoutant des décisions liées à la localisation des dépôts. Dans cette thèse on dévelope des outils pour résoudre le PLRC à l’aide de la programmation mathématique. Dans le chapitre 3, on introduit trois nouveaux modèles pour le PLRC basés sur des flots de véhicules et des flots de commodités, et on montre comment ceux-ci dominent, en termes de la qualité de la borne inférieure, la formulation originale à deux indices [19]. Des nouvelles inégalités valides ont été dévelopées et ajoutées aux modèles, de même que des inégalités connues. De nouveaux algorithmes de séparation ont aussi été dévelopés qui dans la plupart de cas généralisent ceux trouvés dans la litterature. Les résultats numériques montrent que ces modèles de flot sont en fait utiles pour résoudre des instances de petite à moyenne taille. Dans le chapitre 4, on présente une nouvelle méthode de génération de colonnes basée sur une formulation de partition d’ensemble. Le sous-problème consiste en un problème de plus court chemin avec capacités (PCCC). En particulier, on utilise une relaxation de ce problème dans laquelle il est possible de produire des routes avec des cycles de longueur trois ou plus. Ceci est complété par des nouvelles coupes qui permettent de réduire encore davantage le saut d’intégralité en même temps que de défavoriser l’apparition de cycles dans les routes. Ces résultats suggèrent que cette méthode fournit la meilleure méthode exacte pour le PLRC. Dans le chapitre 5, on introduit une nouvelle méthode heuristique pour le PLRC. Premièrement, on démarre une méthode randomisée de type GRASP pour trouver un premier ensemble de solutions de bonne qualité. Les solutions de cet ensemble sont alors combinées de façon à les améliorer. Finalement, on démarre une méthode de type détruir et réparer basée sur la résolution d’un nouveau modèle de localisation et réaffectation qui généralise le problème de réaffectaction [48].