Engineering Commons^™

Natural Selection Of Asphalt Mix Stiffness Predictive Models With Genetic Programming, Kasthurirangan Gopalakrishnan, Sunghwan Kim, Halil Ceylan, Siddhartha K. Khaitan

Siddhartha Khaitan

Genetic Programming (GP) is a systematic, domain-independent evolutionary computation technique that stochastically evolves populations of computer programs to perform a user-defined task. Similar to Genetic Algorithms (GA) which evolves a population of individuals to better ones, GP iteratively transforms a population of computer programs into a new generation of programs by applying biologically inspired operations such as crossover, mutation, etc. In this paper, a population of Hot-Mix Asphalt (HMA) dynamic modulus stiffness prediction models is genetically evolved to better ones by applying the principles of genetic programming. The HMA dynamic modulus (|E*|), one of the stiffness measures, is the primary …

Feedback Control For Multi-Modal Optimization Using Genetic Algorithms, Jun Shi, Ole J. Mengshoel, Dipan K. Pal

Ole J Mengshoel

Biogeography-Based Optimization And The Solution Of The Power Flow Problem, Rick Rarick, Daniel Simon, F. Villaseca, B. Vyakaranam

F. Eugenio Villaseca

Biogeography-based optimization (BBO) is a novel evolutionary algorithm that is based on the mathematics of biogeography. Biogeography is the study of the geographical distribution of biological organisms. In the BBO model, problem solutions are represented as islands, and the sharing of features between solutions is represented as immigration and emigration between the islands. This paper presents an application of the BBO algorithm to the power flow problem for an IEEE 30-bus Test Case system. The BBO solution is compared with the solution of the same problem using a genetic algorithm (GA). The results of Monte Carlo simulations indicate that the …

Biogeography-Based Optimization And The Solution Of The Power Flow Problem, Rick Rarick, Daniel J. Simon, F. Eugenio Villaseca, B. Vyakaranam

F. Eugenio Villaseca

Biogeography-based optimization (BBO) is a novel evolutionary algorithm that is based on the mathematics of biogeography. Biogeography is the study of the geographical distribution of biological organisms. In the BBO model, problem solutions are represented as islands, and the sharing of features between solutions is represented as immigration and emigration between the islands. This paper presents an application of the BBO algorithm to the power flow problem for an IEEE 30-bus test case system. The BBO solution is compared with the solution of the same problem using a genetic algorithm (GA). The results of Monte Carlo simulations indicate that the …

Efficient Non-Coding Rna Gene Searches Through Classical And Evolutionary Methods, Jennifer Smith

Jennifer A. Smith

Successful non-coding RNA gene searching requires examination of long-range intramolecular base pairing possibilities. This results in search algorithms with extremely long run times such that large-scale use of the algorithms often becomes computationally infeasible. Methods for the efficient search of the solution space are examined. A review of the standard dynamic-programming covariance model search algorithm is given. An analysis of the statistically probable regions of the search space is undertaken and a method of limiting the traditional dynamic-programming algorithm to this region is shown. An alternative search method using a Genetic Algorithm (GA) which favours the probable region of the …

Computation Intelligence Method To Find Generic Non-Coding Rna Search Models, Jennifer A. Smith

Jennifer A. Smith

Fairly effective methods exist for finding new noncoding RNA genes using search models based on known families of ncRNA genes (for example covariance models). However, these models only find new members of the existing families and are not useful in finding potential members of novel ncRNA families. Other problems with family-specific search include large processing requirements, ambiguity in defining which sequences form a family and lack of sufficient numbers of known sequences to properly estimate model parameters. An ncRNA search model is proposed which includes a collection of non-overlapping RNA hairpin structure covariance models. The hairpin models are chosen from …

Generalized Crowding For Genetic Algorithms, Ole J. Mengshoel, Severino F. Galan

Ole J Mengshoel

Rna Gene Finding With Biased Mutation Operators, Jennifer A. Smith

Jennifer A. Smith

The use of genetic algorithms for non-coding RNA gene finding has previously been investigated and found to be a potentially viable method for accelerating covariance-model-based database search relative to full dynamic-programming methods. The mutation operators in previous work chose new alignment insertion and deletion locations uniformly over the length of the model consensus sequence. Since the covariance models are estimated from multiple known members of a non-coding RNA family, information is available as to the likelihood of insertions or deletions at the individual model positions. This information is implicit in the state-transition parameters of the estimated covariance models. In the …

Searching For Protein Classification Features, Jennifer A. Smith

Jennifer A. Smith

A genetic algorithm is used to search for a set of classification features for a protein superfamily which is as unique as possible to the superfamily. These features may then be used for very fast classification of a query sequence into a protein superfamily. The features are based on windows onto modified consensus sequences of multiple aligned members of a training set for the protein superfamily. The efficacy of the method is demonstrated using receiver operating characteristic (ROC) values and the performance of resulting algorithm is compared with other database search algorithms.

A Genetic Algorithms Approach To Non-Coding Rna Gene Searches, Jennifer A. Smith

Jennifer A. Smith

A genetic algorithm is proposed as an alternative to the traditional linear programming method for scoring covariance models in non-coding RNA (ncRNA) gene searches. The standard method is guaranteed to find the best score, but it is too slow for general use. The observation that most of the search space investigated by the linear programming method does not even remotely resemble any observed sequence in real sequence data can be used to motivate the use of genetic algorithms (GAs) to quickly reject regions of the search space. A search space with many local minima makes gradient decent an unattractive alternative. …

Constraint Handling Using Tournament Selection: Abductive Inference In Partly Deterministic Bayesian Network, Severino F. Galan, Ole J. Mengshoel

Ole J Mengshoel

Constraints occur in many application areas of interest to evolutionary computation. The area considered here is Bayesian networks (BNs), which is a probability-based method for representing and reasoning with uncertain knowledge. This work deals with constraints in BNs and investigates how tournament selection can be adapted to better process such constraints in the context of abductive inference. Abductive inference in BNs consists of finding the most probable explanation given some evidence. Since exact abductive inference is NP-hard, several approximate approaches to this inference task have been developed. One of them applies evolutionary techniques in order to find optimal or close-to-optimal …

Efficient Non-Coding Rna Gene Searches Through Classical And Evolutionary Methods, Jennifer Smith

Jennifer A. Smith

Successful non-coding RNA gene searching requires examination of long-range intramolecular base pairing possibilities. This results in search algorithms with extremely long run times such that large-scale use of the algorithms often becomes computationally infeasible. Methods for the efficient search of the solution space are examined. A review of the standard dynamic-programming covariance model search algorithm is given. An analysis of the statistically probable regions of the search space is undertaken and a method of limiting the traditional dynamic-programming algorithm to this region is shown. An alternative search method using a Genetic Algorithm (GA) which favours the probable region of the …

The Crowding Approach To Niching In Genetic Algorithms, Ole J. Mengshoel, David E. Goldberg

Ole J Mengshoel

A wide range of niching techniques have been investigated in evolutionary and genetic algorithms. In this article, we focus on niching using crowding techniques in the context of what we call local tournament algorithms. In addition to deterministic and probabilistic crowding, the family of local tournament algorithms includes the Metropolis algorithm, simulated annealing, restricted tournament selection, and parallel recombinative simulated annealing. We describe an algorithmic and analytical framework which is applicable to a wide range of crowding algorithms. As an example of utilizing this framework, we present and analyze the probabilistic crowding niching algorithm. Like the closely related deterministic crowding …