A Multiobjective Approach Applied to the Protein Structure Prediction Problem

Interest in discovering a methodology for solving the Protein Structure Prediction problem extends into many fields of study including biochemistry, medicine, biology, and numerous engineering and science disciplines. Experimental approaches, such as, x-ray crystallographic studies or solution Nuclear Magnetic Resonance Spectroscopy, to mathematical modeling, such as minimum energy models are used to solve this problem. Recently, Evolutionary Algorithm studies at the Air Force Institute of Technology include the following: Simple Genetic Algorithm (GA), messy GA, fast messy GA, and Linkage Learning GA, as approaches for potential protein energy minimization. Prepackaged software like GENOCOP, GENESIS, and mGA are in use to facilitate experimentation of these techniques. In addition to this software, a parallelized version of the fmGA, the so-called parallel fast messy GA, is found to be good at finding semi-optimal answers in reasonable wall clock time. The aim of this work is to apply a Multiobjective approach to solving this problem using a modified fast messy GA. By dividing the CHARMm energy model into separate objectives, it should be possible to find structural configurations of a protein that yield lower energy values and ultimately more correct conformations

The Role of Distributed Computing in Big Data Science: Case Studies in Forensics and Bioinformatics

2014 - 2015The era of Big Data is leading the generation of large amounts of data, which require storage and analysis capabilities that can be only ad- dressed by distributed computing systems. To facilitate large-scale distributed computing, many programming paradigms and frame- works have been proposed, such as MapReduce and Apache Hadoop, which transparently address some issues of distributed systems and hide most of their technical details. Hadoop is currently the most popular and mature framework sup- porting the MapReduce paradigm, and it is widely used to store and process Big Data using a cluster of computers. The solutions such as Hadoop are attractive, since they simplify the transformation of an application from non-parallel to the distributed one by means of general utilities and without many skills. However, without any algorithm engineering activity, some target applications are not alto- gether fast and e cient, and they can su er from several problems and drawbacks when are executed on a distributed system. In fact, a distributed implementation is a necessary but not su cient condition to obtain remarkable performance with respect to a non-parallel coun- terpart. Therefore, it is required to assess how distributed solutions are run on a Hadoop cluster, and/or how their performance can be improved to reduce resources consumption and completion times. In this dissertation, we will show how Hadoop-based implementations can be enhanced by using carefully algorithm engineering activity, tuning, pro ling and code improvements. It is also analyzed how to achieve these goals by working on some critical points, such as: data local computation, input split size, number and granularity of tasks, cluster con guration, input/output representation, etc. i In particular, to address these issues, we choose some case studies coming from two research areas where the amount of data is rapidly increasing, namely, Digital Image Forensics and Bioinformatics. We mainly describe full- edged implementations to show how to design, engineer, improve and evaluate Hadoop-based solutions for Source Camera Identi cation problem, i.e., recognizing the camera used for taking a given digital image, adopting the algorithm by Fridrich et al., and for two of the main problems in Bioinformatics, i.e., alignment- free sequence comparison and extraction of k-mer cumulative or local statistics. The results achieved by our improved implementations show that they are substantially faster than the non-parallel counterparts, and re- markably faster than the corresponding Hadoop-based naive imple- mentations. In some cases, for example, our solution for k-mer statis- tics is approximately 30× faster than our Hadoop-based naive im- plementation, and about 40× faster than an analogous tool build on Hadoop. In addition, our applications are also scalable, i.e., execution times are (approximately) halved by doubling the computing units. Indeed, algorithm engineering activities based on the implementation of smart improvements and supported by careful pro ling and tun- ing may lead to a much better experimental performance avoiding potential problems. We also highlight how the proposed solutions, tips, tricks and insights can be used in other research areas and problems. Although Hadoop simpli es some tasks of the distributed environ- ments, we must thoroughly know it to achieve remarkable perfor- mance. It is not enough to be an expert of the application domain to build Hadop-based implementations, indeed, in order to achieve good performance, an expert of distributed systems, algorithm engi- neering, tuning, pro ling, etc. is also required. Therefore, the best performance depend heavily on the cooperation degree between the domain expert and the distributed algorithm engineer. [edited by Author]XIV n.s

Advances in Evolutionary Algorithms

With the recent trends towards massive data sets and significant computational power, combined with evolutionary algorithmic advances evolutionary computation is becoming much more relevant to practice. Aim of the book is to present recent improvements, innovative ideas and concepts in a part of a huge EA field

First Annual Workshop on Space Operations Automation and Robotics (SOAR 87)

Several topics relative to automation and robotics technology are discussed. Automation of checkout, ground support, and logistics; automated software development; man-machine interfaces; neural networks; systems engineering and distributed/parallel processing architectures; and artificial intelligence/expert systems are among the topics covered

The quality-aware service selection problem: an adaptive evolutionary approach

Die Qualität der Serviceerbringung (kurz QoS) ist ein wichtiger Aspekt in verteilten, Service-orientierten Systemen. Wenn mehrere Implementierungen einer Funktionalität koexistieren, kann die Wahl eines konkreten Services aufgrund von QoS-Aspekten getroffen werden. Leistung, Verfügbarkeit und Kosten sind Beispiele für QoS-Attribute eines Services. In der vorliegenden Dissertation werden Aspekte dieses Selektionsproblems anhand eines konkreten, Service-orientieren Systems vertieft. Es handelt sich dabei um das TAG-System in ATLAS, einem Hochenergiephysikexperiment am CERN, der Europäischen Organisation für Kernforschung. Die Daten und Services des TAG-Systems sind weltweit verteilt und müssen auf Anfrage selektiert und zu einem Workflow zusammengesetzt werden. Die Optimierung wird aus zwei unterschiedlichen Blickwinkeln. Die Selektion wird als ein dynamisches Pfadoptimierungsproblem unter Nebenbedingungen modelliert, wodurch QoS-Attribute sowohl der Knoten (Services) als auch der Kanten (Netzwerk) berücksichtigt werden können. Dynamische Aspekte des verteilten sind in der Problemformulierung integriert, da sie eine spezifische Herausforderung und Anforderung an Lösungsalgorithmen stellen. Für die dynamische Pareto-Optimierung von Serviceselektionsproblemen wird im Rahmen dieser Arbeit ein Optimierungsansatz mit einem genetischen Algorithmus präsentiert, der über einen persistenten Speicher von früheren Lösungen sowie eine automatische Adaptierung der Mutationsrate eine effiziente Anpassung an das sich ständig verändernde System gewährleistet. Eine Ontologie der Systemkomponenten sowie deren QoS-Attribute bildet die Basis für die Optimierung. Der Ansatz wird im Rahmen der Dissertation hinsichtlich der Qualität der erzielten Lösungen, der Adaptierung an änderungen sowie der Laufzeit evaluiert. Teile des Ansatzes wurden schließ lich in das TAG-System integriert und darin evaluiert.Quality of Service (QoS) is an important aspect in distributed, service-oriented systems. When several concrete services exist that implement the same functionality, the choice of a service instance among many can be made based on QoS considerations, objectives and constraints. Typically considered properties are performance, availability, and costs. In this thesis, aspects of the QoS-aware service selection problem are studied in the context of a distributed, service-oriented system from ATLAS, a high-energy physics experiment at CERN, the European Organization for Nuclear Research. In this so-called TAG system, data and modular services are distributed world-wide and need to be selected and composed on the fly, as a user starts a request. There are two conflicting optimization viewpoints. The service selection is modeled as a dynamic multi-constrained optimal path problem, which allows considering QoS attributes of service instances and of the network. The dynamic aspects of the system are included in the problem definition, as they represent a specific challenge. To address these issues regarding dynamics and conflicting viewpoints, this work proposes a service selection optimization framework based on a multi-objective genetic algorithm capable of efficiently dealing with changing conditions by using a persistent memory of good solutions, and a stepwise adaptation of the mutation rate. A system and QoS attribute ontology as well as a description of dynamics of distributed systems build the basis of the framework. The presented approach is evaluated in terms of optimization quality, adaptability to changes, runtime performance and scalability

Algorithms for string matching with applications in molecular biology

As the volume of genetic sequence data increases due to improved sequencing techniques and increased interest, the computational tools available to analyze the data are becoming inadequate. This thesis seeks to improve a few of the computational methods available to access and analyze data in the genetic sequence databases. The first two results are parallel algorithms based on previously known sequential algorithms. The third result is a new approach, based on assumptions that we believe make sense in the biological context of the problem, to approximating an NP complete problem. The final result is a fundamentally new approach to approximate string matching using the divide and conquer paradigm instead of the dynamic programming approach that has been used almost exclusively in the past. Dynamic programming algorithms to measure the distance between sequences have been known since at least 1972. Recently there has been interest in developing parallel algorithms to measure the distance between two sequences. We have developed an optimal parallel algorithm to find the edit distance, a metric frequently used to measure distance, between two sequences. It is often interesting to find the substrings of length k that appear most frequently in a given string. We give a simple sequential algorithm to solve this problem and an efficient parallel version of the algorithm. The parallel algorithm uses an efficient novel parallel bucket sort. When sequencing a large segment of DNA, the original DNA sequence is reconstructed using the results of sequencing fragments, that may or may not contain errors, of many copies of the original DNA. New algorithms are given to solve the problem of reconstructing the original DNA sequence with and without errors introduced into the fragments. A program based on this algorithm is used to reconstruct the human beta globin region (HUMHBB) when given a set of 300 to 500 mers drawn randomly from the HUMHBB region. Approximate string matching is used in a biological context to model the steps of evolution. While such evolution may proceed base by base using the change, insert, or delete operators, there is also evidence that whole genes may be moved or inverted. We introduce a new problem, the string to string rearrangement problem, that allows movement and inversion of substrings. We give a divide and conquer algorithm for finding a rearrangement of one string within another

Efficient Passive Clustering and Gateways selection MANETs

Passive clustering does not employ control packets to collect topological information in ad hoc networks. In our proposal, we avoid making frequent changes in cluster architecture due to repeated election and re-election of cluster heads and gateways. Our primary objective has been to make Passive Clustering more practical by employing optimal number of gateways and reduce the number of rebroadcast packets

Microgravity science and applications program tasks, 1991 revision

Presented here is a compilation of the active research tasks for FY 1991 sponsored by the Microgravity Science and Applications Division of the NASA Office of Space Science and Applications. The purpose is to provide an overview of the program scope for managers and scientists in industry, university, and government communities. Included is an introductory description of the program, the strategy and overall goal, identification of the organizational structures and the people involved, and a description of each. The tasks are grouped into several categories: electronic materials; solidification of metals, alloys, and composites; fluids, interfaces, and transport; biotechnology; combustion science; glasses and ceramics; experimental technology, instrumentation, and facilities; and Physical and Chemistry Experiments (PACE). The tasks cover both the ground based and flight programs