Refined Genetic Algorithms for Polypeptide Structure Prediction

Accurate and reliable prediction of macromolecular structures has eluded researchers for nearly 40 years. Prediction via energy minimization assumes the native conformation has the globally minimal energy potential. An exhaustive search is impossible since for molecules of normal size, the size of the search space exceeds the size of the universe. Domain knowledge sources, such as the Brookhaven PDB can be mined for constraints to limit the search space. Genetic algorithms (GAs) are stochastic, population based, search algorithms of polynomial (P) time complexity that can produce semi-optimal solutions for problems of nondeterministic polynomial (NP) time complexity such as PSP. Three refined GAs are presented: A farming model parallel hybrid GA (PHGA) preserves the effectiveness of the serial algorithm with substantial speed up. Portability across distributed and MPP platforms is accomplished with the Message Passing Interface (MPI) communications standard. A Real-valved GA system, real-valued Genetic Algorithm, Limited by constraints (REGAL), exploiting domain knowledge. Experiments with the pentapeptide Met-enkephalin have identified conformers with lower energies (CHARMM) than the accepted optimal conformer (Scheraga, et al), -31.98 vs -28.96 kcals/mol. Analysis of exogenous parameters yields additional insight into performance. A parallel version (Para-REGAL), an island model modified to allow different active constraints in the distributed subpopulations and novel concepts of Probability of Migration and Probability of Complete Migration

Optimization of Heterogeneous UAV Communications Using the Multiobjective Quadratic Assignment Problem

The Air Force has placed a high priority on developing new and innovative ways to use Unmanned Aerial Vehicles (UAVs). The Defense Advanced Research Projects Agency (DARPA) currently funds many projects that deal with the advancement of UAV research. The ultimate goal of the Air Force is to use UAVs in operations that are highly dangerous to pilots, mainly the suppression of enemy air defenses (SEAD). With this goal in mind, formation structuring of autonomous or semi-autonomous UAVs is of future importance. This particular research investigates the optimization of heterogeneous UAV multi-channel communications in formation. The problem maps to the multiobjective Quadratic Assignment Problem (mQAP). Optimization of this problem is done through the use of a Multiobjective Evolutionary Algorithm (MOEA) called the Multiobjective Messy Genetic Algorithm - II (MOMGA-II). Experimentation validates the attainment of an acceptable Pareto Front for a variety of mQAP benchmarks. It was observed that building block size can affect the location vectors along the current Pareto Front. The competitive templates used during testing perform best when they are randomized before each building block size evaluation. This tuning of the MOMGA-II parameters creates a more effective algorithm for the variety of mQAP benchmarks, when compared to the initial experiments. Thus this algorithmic approach would be useful for Air Force decision makers in determining the placement of UAVs in formations

The Application of Hybridized Genetic Algorithms to the Protein Folding Problem

The protein folding problem consists of attempting to determine the native conformation of a protein given its primary structure. This study examines various methods of hybridizing a genetic algorithm implementation in order to minimize an energy function and predict the conformation (structure) of Met-enkephalin. Genetic Algorithms are semi-optimal algorithms designed to explore and exploit a search space. The genetic algorithm uses selection, recombination, and mutation operators on populations of strings which represent possible solutions to the given problem. One step in solving the protein folding problem is the design of efficient energy minimization techniques. A conjugate gradient minimization technique is described and tested with different replacement frequencies. Baidwinian, Lamarckian, and probabilistic Lamarckian evolution are all tested. Another extension of simple genetic algorithms can be accomplished with niching. Niching works by de-emphasizing solutions based on their proximity to other solutions in the space. Several variations of niching are tested. Experiments are conducted to determine the benefits of each hybridization technique versus each other and versus the genetic algorithm by itself. The experiments are geared toward trying to find the lowest possible energy and hence the minimum conformation of Met-enkephalin. In the experiments, probabilistic Lamarckian strategies were successful in achieving energies below that of the published minimum in QUANTA

Discrete and fuzzy dynamical genetic programming in the XCSF learning classifier system

A number of representation schemes have been presented for use within learning classifier systems, ranging from binary encodings to neural networks. This paper presents results from an investigation into using discrete and fuzzy dynamical system representations within the XCSF learning classifier system. In particular, asynchronous random Boolean networks are used to represent the traditional condition-action production system rules in the discrete case and asynchronous fuzzy logic networks in the continuous-valued case. It is shown possible to use self-adaptive, open-ended evolution to design an ensemble of such dynamical systems within XCSF to solve a number of well-known test problems

The Application of Artificial Intelligence in Project Management Research: A Review

The field of artificial intelligence is currently experiencing relentless growth, with innumerable models emerging in the research and development phases across various fields, including science, finance, and engineering. In this work, the authors review a large number of learning techniques aimed at project management. The analysis is largely focused on hybrid systems, which present computational models of blended learning techniques. At present, these models are at a very early stage and major efforts in terms of development is required within the scientific community. In addition, we provide a classification of all the areas within project management and the learning techniques that are used in each, presenting a brief study of the different artificial intelligence techniques used today and the areas of project management in which agents are being applied. This work should serve as a starting point for researchers who wish to work in the exciting world of artificial intelligence in relation to project leadership and management

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

Recursive pattern based hybrid training

Ph.DDOCTOR OF PHILOSOPH