Search results for: gene ontology; genetic algorithm

Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias, Zalmiyah Zakaria, Saberi M. Mohamad

Abstract:

Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology has caused problems in maintaining and processing them. One way to obtain their accessibility is by clustering them into fragmented groups. Clustering the Gene Ontology is a difficult combinatorial problem and can be modeled as a graph partitioning problem. Additionally, deciding the number k of clusters to use is not easily perceived and is a hard algorithmic problem. Therefore, an approach for solving the automatic clustering of the Gene Ontology is proposed by incorporating cohesion-and-coupling metric into a hybrid algorithm consisting of a genetic algorithm and a split-and-merge algorithm. Experimental results and an example of modularized Gene Ontology in RDF/XML format are given to illustrate the effectiveness of the algorithm.

Keywords: Automatic clustering, cohesion-and-coupling metric, gene ontology; genetic algorithm, split-and-merge algorithm.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias, Hany T. Alashwal, Rohayanti Hassan, FarhanMohamed

Abstract:

The most important property of the Gene Ontology is the terms. These control vocabularies are defined to provide consistent descriptions of gene products that are shareable and computationally accessible by humans, software agent, or other machine-readable meta-data. Each term is associated with information such as definition, synonyms, database references, amino acid sequences, and relationships to other terms. This information has made the Gene Ontology broadly applied in microarray and proteomic analysis. However, the process of searching the terms is still carried out using traditional approach which is based on keyword matching. The weaknesses of this approach are: ignoring semantic relationships between terms, and highly depending on a specialist to find similar terms. Therefore, this study combines semantic similarity measure and genetic algorithm to perform a better retrieval process for searching semantically similar terms. The semantic similarity measure is used to compute similitude strength between two terms. Then, the genetic algorithm is employed to perform batch retrievals and to handle the situation of the large search space of the Gene Ontology graph. The computational results are presented to show the effectiveness of the proposed algorithm.

Keywords: Gene Ontology, Semantic similarity measure, Genetic algorithm, Ontology search

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

Abstract:

Gene Ontology terms have been actively used to annotate various protein sets. SWISS-PROT, TrEMBL, and InterPro are protein databases that are annotated according to the Gene Ontology terms. However, direct implementation of the Gene Ontology terms for annotation of anonymous protein sequences is not easy, especially for species not commonly represented in biological databases. UTMGO is developed as a tool that allows the user to quickly and easily search for a group of semantically related Gene Ontology terms. The applicability of the UTMGO is demonstrated by applying it to annotation of anonymous protein sequence. The extended UTMGO uses the Gene Ontology terms together with protein sequences associated with the terms to perform the annotation task. GOPET, GOtcha, GoFigure, and JAFA are used to compare the performance of the extended UTMGO.

Keywords: Anonymous protein sequence, Gene Ontology, Protein sequence annotation, Protein sequence alignment

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Authors: Razagh Hafezi, Ahmad Keshavarz, Vida Moshfegh

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This paper presents a novel algorithm of stereo correspondence with rank transform. In this algorithm we used the genetic algorithm to achieve the accurate disparity map. Genetic algorithms are efficient search methods based on principles of population genetic, i.e. mating, chromosome crossover, gene mutation, and natural selection. Finally morphology is employed to remove the errors and discontinuities.

Keywords: genetic algorithm, morphology, rank transform, stereo correspondence

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Authors: Ines Hamdi, Mohamed Ben Ahmed

Abstract:

The understanding of the system level of biological behavior and phenomenon variously needs some elements such as gene sequence, protein structure, gene functions and metabolic pathways. Challenging problems are representing, learning and reasoning about these biochemical reactions, gene and protein structure, genotype and relation between the phenotype, and expression system on those interactions. The goal of our work is to understand the behaviors of the interactions networks and to model their evolution in time and in space. We propose in this study an ontological meta-model for the knowledge representation of the genetic regulatory networks. Ontology in artificial intelligence means the fundamental categories and relations that provide a framework for knowledge models. Domain ontology's are now commonly used to enable heterogeneous information resources, such as knowledge-based systems, to communicate with each other. The interest of our model is to represent the spatial, temporal and spatio-temporal knowledge. We validated our propositions in the genetic regulatory network of the Aarbidosis thaliana flower

Keywords: Ontological model, spatio-temporal modeling, Genetic Regulatory Networks (GRNs), knowledge representation.

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Authors: Panpan Xu, Shulin Sui

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The crossover probability and mutation probability are the two important factors in genetic algorithm. The adaptive genetic algorithm can improve the convergence performance of genetic algorithm, in which the crossover probability and mutation probability are adaptively designed with the changes of fitness value. We apply adaptive genetic algorithm into a function optimization problem. The numerical experiment represents that adaptive genetic algorithm improves the convergence speed and avoids local convergence.

Keywords: Genetic algorithm, Adaptive genetic algorithm, Function optimization.

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Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati

Abstract:

Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.

Keywords: Metabolic network, gene knockout, flux balance analysis, microarray data, integration.

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Authors: S. M. Khalessizadeh, R. Zaefarian, S.H. Nasseri, E. Ardil

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Today, Genetic Algorithm has been used to solve wide range of optimization problems. Some researches conduct on applying Genetic Algorithm to text classification, summarization and information retrieval system in text mining process. This researches show a better performance due to the nature of Genetic Algorithm. In this paper a new algorithm for using Genetic Algorithm in concept weighting and topic identification, based on concept standard deviation will be explored.

Keywords: Genetic Algorithm, Text Mining, Term Weighting, Concept Extraction, Concept Distribution.

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Authors: Amod P. Vaze

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Genetic Algorithm has been used to solve wide range of optimization problems. Some researches conduct on applying Genetic Algorithm to analog circuit design automation. These researches show a better performance due to the nature of Genetic Algorithm. In this paper a modified Genetic Algorithm is applied for analog circuit design automation. The modifications are made to the topology of the circuit. These modifications will lead to a more computationally efficient algorithm.

Keywords: Genetic algorithm, analog circuits, design.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

Abstract:

Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.

Keywords: automatic clustering, bioinformatics tool, gene ontology, protein sequence annotation, semantic similarity search

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Authors: Panpan Xu, Shulin Sui, Zongjie Du

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Genetic algorithm is widely used in optimization problems for its excellent global search capabilities and highly parallel processing capabilities; but, it converges prematurely and has a poor local optimization capability in actual operation. Simulated annealing algorithm can avoid the search process falling into local optimum. A hybrid genetic algorithm based on simulated annealing is designed by combining the advantages of genetic algorithm and simulated annealing algorithm. The numerical experiment represents the hybrid genetic algorithm can be applied to solve the function optimization problems efficiently.

Keywords: Genetic algorithm, Simulated annealing, Hybrid genetic algorithm, Function optimization.

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Authors: Yongzhong Wu, Ping Ji

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This paper proposes a genetic algorithm based on a new replacement strategy to solve the quadratic assignment problems, which are NP-hard. The new replacement strategy aims to improve the performance of the genetic algorithm through well balancing the convergence of the searching process and the diversity of the population. In order to test the performance of the algorithm, the instances in QAPLIB, a quadratic assignment problem library, are tried and the results are compared with those reported in the literature. The performance of the genetic algorithm is promising. The significance is that this genetic algorithm is generic. It does not rely on problem-specific genetic operators, and may be easily applied to various types of combinatorial problems.

Keywords: Quadratic assignment problem, Genetic algorithm, Replacement strategy, QAPLIB.

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Authors: M. A. Sharbafi, M. Shakiba Herfeh, Caro Lucas, A. Mohammadi Nejad

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Several researchers have proposed methods about combination of Genetic Algorithm (GA) and Fuzzy Logic (the use of GA to obtain fuzzy rules and application of fuzzy logic in optimization of GA). In this paper, we suggest a new method in which fuzzy decision making is used to improve the performance of genetic algorithm. In the suggested method, we determine the alleles that enhance the fitness of chromosomes and try to insert them to the next generation. In this algorithm we try to present an innovative vaccination in the process of reproduction in genetic algorithm, with considering the trade off between exploration and exploitation.

Keywords: Genetic Algorithm, Fuzzy Decision Making.

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Authors: Cheng-Hong Yang, Tsung-Mu Shih, Li-Yeh Chuang

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Serial Analysis of Gene Expression is a powerful quantification technique for generating cell or tissue gene expression data. The profile of the gene expression of cell or tissue in several different states is difficult for biologists to analyze because of the large number of genes typically involved. However, feature selection in machine learning can successfully reduce this problem. The method allows reducing the features (genes) in specific SAGE data, and determines only relevant genes. In this study, we used a genetic algorithm to implement feature selection, and evaluate the classification accuracy of the selected features with the K-nearest neighbor method. In order to validate the proposed method, we used two SAGE data sets for testing. The results of this study conclusively prove that the number of features of the original SAGE data set can be significantly reduced and higher classification accuracy can be achieved.

Keywords: Serial Analysis of Gene Expression, Feature selection, Genetic Algorithm, K-nearest neighbor method.

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Authors: R. K. Agrawal, Rajni Bala

Abstract:

Developing an accurate classifier for high dimensional microarray datasets is a challenging task due to availability of small sample size. Therefore, it is important to determine a set of relevant genes that classify the data well. Traditionally, gene selection method often selects the top ranked genes according to their discriminatory power. Often these genes are correlated with each other resulting in redundancy. In this paper, we have proposed a hybrid method using feature ranking and wrapper method (Genetic Algorithm with multiclass SVM) to identify a set of relevant genes that classify the data more accurately. A new fitness function for genetic algorithm is defined that focuses on selecting the smallest set of genes that provides maximum accuracy. Experiments have been carried on four well-known datasets1. The proposed method provides better results in comparison to the results found in the literature in terms of both classification accuracy and number of genes selected.

Keywords: Gene selection, genetic algorithm, microarray datasets, multi-class SVM.

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Authors: Grigorios N. Beligiannis, Georgios A. Tsirogiannis, Panayotis E. Pintelas

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In this contribution, a way to enhance the performance of the classic Genetic Algorithm is proposed. The idea of restarting a Genetic Algorithm is applied in order to obtain better knowledge of the solution space of the problem. A new operator of 'insertion' is introduced so as to exploit (utilize) the information that has already been collected before the restarting procedure. Finally, numerical experiments comparing the performance of the classic Genetic Algorithm and the Genetic Algorithm with restartings, for some well known test functions, are given.

Keywords: Genetic Algorithms, Restartings, Search space exploration, Search space exploitation.

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Authors: Mohsen Ebrahimi, Milad M. Rabieh

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In this paper, two very different optimization algorithms, Genetic and DIRECT algorithms, are used to history match a bottomhole pressure response for a reservoir with wellbore storage and skin with the best possible analytical model. No initial guesses are available for reservoir parameters. The results show that the matching process is much faster and more accurate for DIRECT method in comparison with Genetic algorithm. It is furthermore concluded that the DIRECT algorithm does not need any initial guesses, whereas Genetic algorithm needs to be tuned according to initial guesses.

Keywords: DIRECT algorithm, Genetic algorithm, Analytical modeling, History match

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Authors: Rossitza M. Setchi, Qiao Tang

Abstract:

Nowadays, ontologies are the only widely accepted paradigm for the management of sharable and reusable knowledge in a way that allows its automatic interpretation. They are collaboratively created across the Web and used to index, search and annotate documents. The vast majority of the ontology based approaches, however, focus on indexing texts at document level. Recently, with the advances in ontological engineering, it became clear that information indexing can largely benefit from the use of general purpose ontologies which aid the indexing of documents at word level. This paper presents a concept indexing algorithm, which adds ontology information to words and phrases and allows full text to be searched, browsed and analyzed at different levels of abstraction. This algorithm uses a general purpose ontology, OntoRo, and an ontologically tagged corpus, OntoCorp, both developed for the purpose of this research. OntoRo and OntoCorp are used in a two-stage supervised machine learning process aimed at generating ontology tagging rules. The first experimental tests show a tagging accuracy of 78.91% which is encouraging in terms of the further improvement of the algorithm.

Keywords: Concepts, indexing, machine learning, ontology, tagging.

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Authors: Bashar Al-Shboul, Sung-Hyon Myaeng

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K-Means (KM) is considered one of the major algorithms widely used in clustering. However, it still has some problems, and one of them is in its initialization step where it is normally done randomly. Another problem for KM is that it converges to local minima. Genetic algorithms are one of the evolutionary algorithms inspired from nature and utilized in the field of clustering. In this paper, we propose two algorithms to solve the initialization problem, Genetic Algorithm Initializes KM (GAIK) and KM Initializes Genetic Algorithm (KIGA). To show the effectiveness and efficiency of our algorithms, a comparative study was done among GAIK, KIGA, Genetic-based Clustering Algorithm (GCA), and FCM [19].

Keywords: Clustering, Genetic Algorithms, K-means.

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Authors: Soottipoom Yaowiwat, Manoj Lohatepanont, Proadpran Punyabukkana

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Several approaches such as linear programming, network modeling, greedy heuristic and decision support system are well-known approaches in solving irregular airline operation problem. This paper presents an alternative approach based on Multi Objective Micro Genetic Algorithm. The aim of this research is to introduce the concept of Multi Objective Micro Genetic Algorithm as a tool to solve irregular airline operation, combine and reroute problem. The experiment result indicated that the model could obtain optimal solutions within a few second.

Keywords: Irregular Airline Operation, Combine and RerouteRoutine, Genetic Algorithm, Micro Genetic Algorithm, Multi ObjectiveOptimization, Evolutionary Algorithm.

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Authors: Warattapop Chainate, Peeraya Thapatsuwan, Pupong Pongcharoen

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The hybridisation of genetic algorithm with heuristics has been shown to be one of an effective way to improve its performance. In this work, genetic algorithm hybridised with four heuristics including a new heuristic called neighbourhood improvement were investigated through the classical travelling salesman problem. The experimental results showed that the proposed heuristic outperformed other heuristics both in terms of quality of the results obtained and the computational time.

Keywords: Genetic Algorithm, Hybridisation, Metaheuristics, Travelling Salesman Problem.

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Authors: Hiba Hasan, Khalid Raza

Abstract:

Reverse engineering of genetic regulatory network involves the modeling of the given gene expression data into a form of the network. Computationally it is possible to have the relationships between genes, so called gene regulatory networks (GRNs), that can help to find the genomics and proteomics based diagnostic approach for any disease. In this paper, clustering based method has been used to reconstruct genetic regulatory network from time series gene expression data. Supercoiled data set from Escherichia coli has been taken to demonstrate the proposed method.

Keywords: Gene expression, gene regulatory networks (GRNs), clustering, data preprocessing, network visualization.

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Authors: Mohammad Ali Tabarzad, Caro Lucas, Ali Hamzeh

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Adaptive Genetic Algorithms extend the Standard Gas to use dynamic procedures to apply evolutionary operators such as crossover, mutation and selection. In this paper, we try to propose a new adaptive genetic algorithm, which is based on the statistical information of the population as a guideline to tune its crossover, selection and mutation operators. This algorithms is called Statistical Genetic Algorithm and is compared with traditional GA in some benchmark problems.

Keywords: Genetic Algorithms, Statistical Information ofthe Population, PAUX, SSO.

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Authors: Z. G. Wang, M. Rahman, Y. S. Wong, K. S. Neo

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In this paper, a new hybrid of genetic algorithm (GA) and simulated annealing (SA), referred to as GSA, is presented. In this algorithm, SA is incorporated into GA to escape from local optima. The concept of hierarchical parallel GA is employed to parallelize GSA for the optimization of multimodal functions. In addition, multi-niche crowding is used to maintain the diversity in the population of the parallel GSA (PGSA). The performance of the proposed algorithms is evaluated against a standard set of multimodal benchmark functions. The multi-niche crowding PGSA and normal PGSA show some remarkable improvement in comparison with the conventional parallel genetic algorithm and the breeder genetic algorithm (BGA).

Keywords: Crowding, genetic algorithm, parallel geneticalgorithm, simulated annealing.

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Authors: Kolar Jan, Dvorak Vaclav

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In this study, an optimization of supersonic air-to-air ejector is carried out by a recently developed single-objective genetic algorithm based on adaption of sequence of individuals. Adaptation of sequence is based on Shape-based distance of individuals and embedded micro-genetic algorithm. The optimal sequence found defines the succession of CFD-aimed objective calculation within each generation of regular micro-genetic algorithm. A spring-based deformation mutates the computational grid starting the initial individualvia adapted population in the optimized sequence. Selection of a generation initial individual is knowledge-based. A direct comparison of the newly defined and standard micro-genetic algorithm is carried out for supersonic air-to-air ejector. The only objective is to minimize the loose of total stagnation pressure in the ejector. The result is that sequence-adopted micro-genetic algorithm can provide comparative results to standard algorithm but in significantly lower number of overall CFD iteration steps.

Keywords: Grid deformation, Micro-genetic algorithm, shapebased sequence, supersonic ejector.

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Authors: C. Gunavathi, K. Premalatha

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Tumor classification is a key area of research in the field of bioinformatics. Microarray technology is commonly used in the study of disease diagnosis using gene expression levels. The main drawback of gene expression data is that it contains thousands of genes and a very few samples. Feature selection methods are used to select the informative genes from the microarray. These methods considerably improve the classification accuracy. In the proposed method, Genetic Algorithm (GA) is used for effective feature selection. Informative genes are identified based on the T-Statistics, Signal-to-Noise Ratio (SNR) and F-Test values. The initial candidate solutions of GA are obtained from top-m informative genes. The classification accuracy of k-Nearest Neighbor (kNN) method is used as the fitness function for GA. In this work, kNN and Support Vector Machine (SVM) are used as the classifiers. The experimental results show that the proposed work is suitable for effective feature selection. With the help of the selected genes, GA-kNN method achieves 100% accuracy in 4 datasets and GA-SVM method achieves in 5 out of 10 datasets. The GA with kNN and SVM methods are demonstrated to be an accurate method for microarray based tumor classification.

Keywords: F-Test, Gene Expression, Genetic Algorithm, k- Nearest-Neighbor, Microarray, Signal-to-Noise Ratio, Support Vector Machine, T-statistics, Tumor Classification.

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Authors: V. K. Banga, Y. Singh, R. Kumar

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In this paper, we have proposed a low cost optimized solution for the movement of a three-arm manipulator using Genetic Algorithm (GA) and Analytical Hierarchy Process (AHP). A scheme is given for optimizing the movement of robotic arm with the help of Genetic Algorithm so that the minimum energy consumption criteria can be achieved. As compared to Direct Kinematics, Inverse Kinematics evolved two solutions out of which the best-fit solution is selected with the help of Genetic Algorithm and is kept in search space for future use. The Inverse Kinematics, Fitness Value evaluation and Binary Encoding like tasks are simulated and tested. Although, three factors viz. Movement, Friction and Least Settling Time (or Min. Vibration) are used for finding the Fitness Function / Fitness Values, however some more factors can also be considered.

Keywords: Inverse Kinematics, Genetic Algorithm (GA), Analytical Hierarchy Process (AHP), Fitness Value, Fitness Function.

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Authors: Tarek M. Mahmoud

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Selecting the routes and the assignment of link flow in a computer communication networks are extremely complex combinatorial optimization problems. Metaheuristics, such as genetic or simulated annealing algorithms, are widely applicable heuristic optimization strategies that have shown encouraging results for a large number of difficult combinatorial optimization problems. This paper considers the route selection and hence the flow assignment problem. A genetic algorithm and simulated annealing algorithm are used to solve this problem. A new hybrid algorithm combining the genetic with the simulated annealing algorithm is introduced. A modification of the genetic algorithm is also introduced. Computational experiments with sample networks are reported. The results show that the proposed modified genetic algorithm is efficient in finding good solutions of the flow assignment problem compared with other techniques.

Keywords: Genetic Algorithms, Flow Assignment, Routing, Computer network, Simulated Annealing.

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Authors: Qin Ding, Jim Gasvoda

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Clustering is the process of subdividing an input data set into a desired number of subgroups so that members of the same subgroup are similar and members of different subgroups have diverse properties. Many heuristic algorithms have been applied to the clustering problem, which is known to be NP Hard. Genetic algorithms have been used in a wide variety of fields to perform clustering, however, the technique normally has a long running time in terms of input set size. This paper proposes an efficient genetic algorithm for clustering on very large data sets, especially on image data sets. The genetic algorithm uses the most time efficient techniques along with preprocessing of the input data set. We test our algorithm on both artificial and real image data sets, both of which are of large size. The experimental results show that our algorithm outperforms the k-means algorithm in terms of running time as well as the quality of the clustering.

Keywords: Clustering, data mining, genetic algorithm, image data.

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Authors: Junjie Gao, Guishi Deng

Abstract:

In order to integrate knowledge in heterogeneous case-based reasoning (CBR) systems, ontology-based CBR system has become a hot topic. To solve the facing problems of ontology-based CBR system, for example, its architecture is nonstandard, reusing knowledge in legacy CBR is deficient, ontology construction is difficult, etc, we propose a novel approach for semi-automatically construct ontology-based CBR system whose architecture is based on two-layer ontology. Domain knowledge implied in legacy case bases can be mapped from relational database schema and knowledge items to relevant OWL local ontology automatically by a mapping algorithm with low time-complexity. By concept clustering based on formal concept analysis, computing concept equation measure and concept inclusion measure, some suggestions about enriching or amending concept hierarchy of OWL local ontologies are made automatically that can aid designers to achieve semi-automatic construction of OWL domain ontology. Validation of the approach is done by an application example.

Keywords: OWL ontology, Case-based Reasoning, FormalConcept Analysis, Knowledge Integration

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