19 research outputs found

    Solving the DNA fragment assembly problem with a parallel discrete firefly algorithm implemented on GPU

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    The Deoxyribonucleic Acid Fragment Assembly Problem (DNA-FAP) consists in reconstructing a DNA chain from a set of fragments taken randomly. This problem represents an important step in the genome project. Several authors are proposed different approaches to solve the DNA-FAP. In particular, nature-inspired algorithms have been used for its resolution. Even they were obtaining good results; its computational time associated is high. The bio-inspired algorithms are iterative search processes that can explore and exploit efficiently the solution space. Firefly Algorithm is one of the recent evolutionary computing models which is inspired by the flashing light behaviour of fireflies. Recently, the Graphics Processing Units (GPUs) technology are emerge as a novel environment for a parallel implementation and execution of bio-inspired algorithms. Therefore, the use of GPU-based parallel computing it is possible as a complementary tool to speed-up the search. In this work, we design and implement a Discrete Firefly Algorithm (DFA) on a GPU architecture in order to speed-up the search process for solving the DNA Fragment Assembly Problem. Through several experiments, the efficiency of the algorithm and the quality of the results are demonstrated with the potential to applied for longer sequences or sequences of unknown length as well.Fil: Vidal, Pablo Javier. Universidad Nacional de la Patagonia Austral. Unidad Académica Caleta Olivia. Departamento de Ciencias Exactas y Naturales; Argentina. Universidad Nacional de la Patagonia Austral. Centro de Investigaciones y Transferencia Golfo San Jorge. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia Golfo San Jorge. Universidad Nacional de la Patagonia "San Juan Bosco". Centro de Investigaciones y Transferencia Golfo San Jorge; ArgentinaFil: Olivera, Ana Carolina. Universidad Nacional de la Patagonia Austral. Centro de Investigaciones y Transferencia Golfo San Jorge. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia Golfo San Jorge. Universidad Nacional de la Patagonia "San Juan Bosco". Centro de Investigaciones y Transferencia Golfo San Jorge; Argentina. Universidad Nacional de la Patagonia Austral. Unidad Académica Caleta Olivia. Departamento de Ciencias Exactas y Naturales; Argentin

    Maximising overlap score in DNA sequence assembly problem by Stochastic Diffusion Search

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    This paper introduces a novel study on the performance of Stochastic Diffusion Search (SDS)—a swarm intelligence algorithm—to address DNA sequence assembly problem. This is an NP-hard problem and one of the primary problems in computational molecular biology that requires optimisation methodologies to reconstruct the original DNA sequence. In this work, SDS algorithm is adapted for this purpose and several experiments are run in order to evaluate the performance of the presented technique over several frequently used benchmarks. Given the promising results of the newly proposed algorithm and its success in assembling the input fragments, its behaviour is further analysed, thus shedding light on the process through which the algorithm conducts the task. Additionally, the algorithm is applied to overlap score matrices which are generated from the raw input fragments; the algorithm optimises the overlap score matrices to find better results. In these experiments real-world data are used and the performance of SDS is compared with several other algorithms which are used by other researchers in the field, thus demonstrating its weaknesses and strengths in the experiments presented in the paper

    Contributions `a la r´esolution de probl`emes d’optimisation combinatoires NP-difficiles

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    Cette th�ese porte sur des algorithmes e�caces pour la r�esolution de probl�emes d'optimisation combinatoires NP-di�ciles, avec deux contributions. La premi�ere contribution consiste en la proposition d'un nouvel algorithme multiob- jectif hybride combinant un algorithme g�en�etique avec un op�erateur de recherche bas�e sur l'optimisation par essaims de particules. L'objectif de cette hybridation est de surmonter les situations de convergence lente des algorithmes g�en�etiques multiobjectifs lors de la r�e- solution de probl�emes di�ciles �a plus de deux objectifs. Dans le sch�ema hybride propos�e, un algorithme g�en�etique multiobjectif Pareto applique p�eriodiquement un algorithme d'op- timisation par essaim de particules pour optimiser une fonction d'adaptation scalaire sur une population archive. Deux variantes de cet algorithme hybride sont propos�ees et adap- t�ees pour la r�esolution du probl�eme du sac �a dos multiobjectif. Les r�esultats exp�erimentaux prouvent que les algorithmes hybrides sont plus performants que les algorithmes standards. La seconde contribution concerne l'am�elioration d'un algorithme heuristique de recherche locale dit PALS (pour l'anglais Problem Aware Local Search) sp�eci�que au probl�eme d'as- semblage de fragments d'ADN, un probl�eme d'optimisation combinatoire NP-di�cile en bio-informatique des s�equences. Deux modi�cations �a PALS sont propos�ees. La premi�ere modi�cation permet d'�eviter les ph�enom�enes de convergence pr�ematur�ee vers des optima lo- caux. La seconde modi�cation conduit �a une r�eduction signi�cative des temps de calcul tout en conservant la pr�ecision des r�esultats. Apr�es des exp�erimentations r�ealis�ees sur les jeux de donn�ees disponibles dans la litt�erature, nos nouvelles variantes de PALS se r�ev�elent tr�es comp�etitives par rapport aux variantes existantes et �a d'autres algorithmes d'assemblage

    Using MapReduce Streaming for Distributed Life Simulation on the Cloud

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    Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

    A Study of Ordered Gene Problems Featuring DNA Error Correction and DNA Fragment Assembly with a Variety of Heuristics, Genetic Algorithm Variations, and Dynamic Representations

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    Ordered gene problems are a very common classification of optimization problems. Because of their popularity countless algorithms have been developed in an attempt to find high quality solutions to the problems. It is also common to see many different types of problems reduced to ordered gene style problems as there are many popular heuristics and metaheuristics for them due to their popularity. Multiple ordered gene problems are studied, namely, the travelling salesman problem, bin packing problem, and graph colouring problem. In addition, two bioinformatics problems not traditionally seen as ordered gene problems are studied: DNA error correction and DNA fragment assembly. These problems are studied with multiple variations and combinations of heuristics and metaheuristics with two distinct types or representations. The majority of the algorithms are built around the Recentering- Restarting Genetic Algorithm. The algorithm variations were successful on all problems studied, and particularly for the two bioinformatics problems. For DNA Error Correction multiple cases were found with 100% of the codes being corrected. The algorithm variations were also able to beat all other state-of-the-art DNA Fragment Assemblers on 13 out of 16 benchmark problem instances

    LIPIcs, Volume 261, ICALP 2023, Complete Volume

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    LIPIcs, Volume 261, ICALP 2023, Complete Volum

    Investigation of Heterogeneous Proteins and Protein Complexes with Native Ion Mobility-Mass Spectrometry and Theory

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    Native ion mobility-mass spectrometry (IM-MS) offers many advantages for the study of biomolecules and their complexes. High mass accuracy and sensitivity enable unambiguous determination of complex stoichiometries with respect to subunit composition as well as bound ligands. Ion mobility spectrometry adds an additional dimension of separation and can provide some structural information. Native IM-MS experiments are also fast with minimal sample requirements. Because of these reasons, native IM-MS has become an important tool in structural biology, able to investigate challenging samples that may not be amenable to study by other techniques. However, there are still some major challenges for using native IM-MS in the study of biomolecules. Heterogeneity—arising from the presence of multiple conformations, subunit compositions, ligands and small molecules, for example—results in complicated native mass spectra that can be difficult or even impossible to deconvolute and interpret. Characterizing the heterogeneity of these samples is desirable, as reports of lipids, small drugs, and metals being important for physiological structure and function continue to accumulate. Additionally, interpretation of structural information from IM data has remained largely qualitative, and more fundamental questions about this technique persist, including detailed understanding of the nature of gas-phase protein structure and behavior and how it might differ from solution-phase. Investigation into this aspect is required to make structural interpretation from native IM-MS data quantitative. In the first half of this dissertation, strategies to overcome the challenges of heterogeneity are explored, and computational methods are developed to solve the quantitation problem. With these methods, key features of gas-phase protein ion compaction are revealed, allowing more informed interpretation of structural details from this technique. The second half of this dissertation illustrates the wealth of information that can be accessed for challenging, heterogeneous biomolecules in native IM-MS experiments upon application of these computational methods. With results from both experiment and computation, oligomeric states of the membrane pore-forming protein toxin Cytolysin A are identified, and the composition and topology of multimeric β-crystallin protein complexes, which are implicated in cataract formation, are characterized. This dissertation includes previously published and unpublished co-authored material

    A complex systems approach to education in Switzerland

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    The insights gained from the study of complex systems in biological, social, and engineered systems enables us not only to observe and understand, but also to actively design systems which will be capable of successfully coping with complex and dynamically changing situations. The methods and mindset required for this approach have been applied to educational systems with their diverse levels of scale and complexity. Based on the general case made by Yaneer Bar-Yam, this paper applies the complex systems approach to the educational system in Switzerland. It confirms that the complex systems approach is valid. Indeed, many recommendations made for the general case have already been implemented in the Swiss education system. To address existing problems and difficulties, further steps are recommended. This paper contributes to the further establishment complex systems approach by shedding light on an area which concerns us all, which is a frequent topic of discussion and dispute among politicians and the public, where billions of dollars have been spent without achieving the desired results, and where it is difficult to directly derive consequences from actions taken. The analysis of the education system's different levels, their complexity and scale will clarify how such a dynamic system should be approached, and how it can be guided towards the desired performance
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