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Predicting Protein Secondary Structure with Neural N...

Created: 2012-05-11 02:34:20

Credits: Mohd Saberi

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Protein secondary structure prediction has benefited largely from the improvements in machine learning techniques. A novel neural network classifier based on the Dempster-Shafer theory has been introduced by Denoeux. It demonstrated favourable performance in some artificial and real world problems when compared against methods such as Support Vector Machines and Kernel Fisher Discriminants. However, it has not been used for protein secondary structure prediction. In this work, we examin...

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Pathway-Based Microarray Analysis for Defining Stati...

Created: 2012-05-11 02:33:00

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In this reiew, we have discussed about approaches in pathway based microarray analysis. Commonly, there are two approaches in pathway based analysis, Enrichment Score and Supervised Machine Learning. These pathway based approaches usually aim to statistically define significant pathways that related to phenotypes of interest. Firstly we discussed an overview of pathway based microarray analysis and its general flow processes in scoring the pathways, the methods applied in both a...

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Parameter Estimation for Simulation of Glycolysis Pa...

Created: 2012-05-11 02:28:43 | Last updated: 2012-05-11 02:28:44

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An improved differential evolution (DE) algorithm is proposed in this paper to optimize its performance in estimating the germane parameters for metabolic pathway data which is used to simulate glycolysis pathway for Satcharomyces cerevisiae. This study presents an improved algorithm of parameter sensitivity test into the process of DE algorithm. The result of the improved algorithm is testified to be better than the other estimation algorithms. The outcomes from this study promot...

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Optimized Local Protein Structure with Support Vecto...

Created: 2012-05-11 02:27:24

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Protein includes many substances, such as enzymes, hormones and antibodies that are necessary for the organisms. Living cells are controlled by proteins and genes that interact 1fo1sngh complex molecular pathways to achieve a specific function. These proteins have different shapes and structures which distinct them from each other. By having unique structures, only proteins able to carried out their function efficiently. Therefore, determination of protein structure is fundamental...

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One-Class Classifier to Predict Protein-Protein Inte...

Created: 2012-05-11 02:25:30

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Protein-protein interactions are important in a wide range of biological processes. The development of drugs that target such interactions is a very active research field. Hence predicting protein-protein interactions represent an important challenge in bioinformatics research. Machine learning techniques have been applied to predict protein-protein interactions. Most of these techniques address this problem as a binary classification problem. While it is easy to get a dataset of...

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Multi-Objective Optimization Using Genetic Algorithm...

Created: 2012-05-11 02:23:50

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Microarray technology has been increasingly used in cancer research because of its potential for measuring expression levels of thousands of genes simultaneously in tissue samples. It is used to collect the information from tissue samples regarding gene expression differences that could be useful for cancer classification. However, this classification task faces many challenges due to availability of a smaller number of samples compared to the huge number of genes, and many of ...

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Intelligent Hybrid Algorithm using Constraint-Based ...

Created: 2012-05-11 02:21:50

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Almost all hospital has its own nurses and still use the old fashion manual way of managing nurse scheduling in daily business. Nurse scheduling problem represents a difficult class of multi-objective optimisation problems consisting of a number of interfering objectives between the hospitals and individual nurses. Nurse scheduling consists of assignment of shifts and holidays to nurses for each day on the time horizon, taking into consideration a variety of conflicting interests or obj...

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Inferring Gene Regulatory Networks from Gene Express...

Created: 2012-05-11 02:20:28

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Enabled by recent advances in bioinformatics, the inference of gene regulatory networks (GRNs) from gene expression data has garnered much interest from researchers. This is due to the need of researchers to understand the dynamic behavior and uncover the vast information lay hidden within the networks. In this regard, dynamic Bayesian network (DBN) is extensively used to infer GRNs due to its ability to handle time-series microarray data and modeling feedback loops. However, the ...

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Identifying Metabolic Pathway within Microarray Gene...

Created: 2012-05-11 02:18:43 | Last updated: 2012-05-11 02:18:44

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Extracting metabolic pathway that dictates a specific biological response is cunently one of the important disciplines in metabolic system biology research. Previous methods have successfirlly identified those pathways but without concerning the genetic effect and relationship of the genes, the underlying structw€ is not precisely represented and cannot be justified to be significant biologically. In this article, probabilistic models capable of identi&ing the significant...

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Identifying Gene Knockout Strategies Using a Hybrid ...

Created: 2012-05-11 02:16:43

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Genome-scale metabolic networks reconstructions from different organisms have become popular in recent years. Genetic engineering is proven to be able to obtain the desirable phenotypes. Optimization algorithms are implemented in previous works to identify the effects of gene knockout on the results. However, the previous works face the problem of falling into local minima. Thus, a hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA) is proposed in this paper to solve the lo...

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Identifying Gene Knockout Strategies Using a Hybrid ...

Created: 2012-05-11 02:15:08 | Last updated: 2012-05-11 02:15:09

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

Genome-scale metabolic networks reconstructions from different organisms have become popular in recent years. Genetic engineering is proven to be able to obtain the desirable phenotypes. Optimization algorithms are implemented in previous works to identify the effects of gene knockout on the results. However, the previous works face the problem of falling into local minima. Thus, a hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA) is proposed in this paper to solve the lo...

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Genetic Algorithms Wrapper Approach to Select Inform...

Created: 2012-05-11 02:13:44

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Constantly improving gene expression technology offer the ability to measure the expression levels of thousand of genes in parallel. Gene expression data is expected to significantly aid in the development of efficient cancer diagnosis and classification platforms. Key issues that need to be addressed under such circumstances are the efficient selection of minimum number of genes that contribute to a disease from the thousands of genes measured on microarrays that are inherently noisy. ...

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Feature Selection Method Using Genetic Algorithm for...

Created: 2012-05-11 02:10:56

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Practical pattern classification problems require selection of a subset of attributes or features to represent the patterns to be classified. The feature selection process is very important which selects the informative features for used classification process. This is due to the fact that performance of the classifier is sensitive to the choice of the features used to construct the good classifier from small or high dimension data that are inherently noisy. In this paper, we propose an...

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Distributed Data Partitioning Interface for Homogene...

Created: 2012-05-11 02:09:31

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The effort required to write efficient parallel programmes or to parallelize existing sequential algorithms remains daunting. This is true even for regularly structured problems. Much of the work takes place when partitioning and distributing workloads over processors in a distributed computing environment. To alleviate this task, we present a data parallel interface called Distributed Data Partitioning Interface (DDPI). Its simple interface permits parallel implementation even by users...

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Bioinformatics: A Tool for Bio-Knowledge Generation ...

Created: 2012-05-11 02:08:16

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With the knowledge-based economy (KBE) emerging as a new paradigm, it becomes important that economic actors acquire new knowledge and technology. This will stimulate innovation and contribute further growth and development. In the knowledge-based economy, it is not tangible capital but intangible and innovations that determine international competitiveness, productivity growth and worker’s status in the labour market. This intangible capital and innovation are supplied by knowled...

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Automation of DNA Computing Readout Method Based on ...

Created: 2012-05-11 02:05:16

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Preaiausly, an eutornatian of a DNA mmputing rcodad methd far the HamiJtoni,an Path Prcblen (EPP) hos been implementd bosed on, LightCgcler Sgstem. In this stud,y, a simiJar reoilmrt approach is implemented baseil on DNA Engine Opticon 2 System. The rcadott appmaeh consists of tuo steps: rcnl-time arnplification in vitro us'i,ng TaqMowbaseil rcal-time PCR, followed by on in sili,co phase. The in silico phase consists of a d,ata clwtering algorithm and an information processing to e...

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Applying Filter Approach and Genetic Algorithm Wrapp...

Created: 2012-05-11 02:02:28

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Gene expression microarray data is expected to significantly aid in the development of efficient cancer diagnosis and classification platforms. One problem arising from this data is how to select a small subset of genes from thousands of genes and much fewer samples that are inherently noisy. This research deals with finding a small subset of informative genes from the gene expression data which maximize the classification accuracy and minimize the running time. This paper proposed a mo...

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An Iterative GASVM-Based Method: Gene Selection and ...

Created: 2012-05-11 02:00:37

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

Microarray technology has provided biologists with the ability to measure the expression levels of thousands of genes in a single experiment. One of the urgent issues in the use of microarray data is the selection of a smaller subset of genes from the thousands of genes in the data that contributes to a disease. This selection process is difficult due to many irrelevant genes, noisy genes, and the availability of the small number of samples compared to the huge number of genes (hi...

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An Improved Binary Particle Swarm Optimisation for G...

Created: 2012-05-11 01:58:19

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The application of microarray data for cancer classification has recently gained in popularity. The main problem that needs to be addressed is the selection of a smaller subset of genes from the thousands of genes in the data that contributes to a disease. This selection process is difficult because of the availability of the small number of samples compared to the huge number of genes, many irrelevant genes, and noisy genes. Therefore, this paper proposes an improved binary parti...

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An Image Registration Technique To Enhance PCB Inspe...

Created: 2012-05-11 01:56:19

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is well k*atm that renl PCB inuge inipieetio* bwal 0n rclerential ap: proaches foces misalignment problems in detecting delects betwecn a template imoge arul a ilefectiae image. Hence, o reliable image registrtion techniqre is needed to aligt, these two irnages per{utly. Henre, a rqistrution trch*irye uhich inaryorvtes affme trcnsformotion anil bi-cubic interynlation has been prcposed. Etperimental rcsults haae shown that this regishation techniqte is suitoble to be employei to obt...

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A Two-Step Binary Particle Swarm Optimization Approa...

Created: 2012-05-11 01:52:33 | Last updated: 2012-05-11 01:52:34

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Manipitetibn of wdre itzing, buffer sizing, and futffer inseriiai atu a few techniques that con be used to i,mproae tfune d,eloy 'in aery lorge su,le intqrction (VLSI) circuit routing- Thi* paper enhances an eri,sting approach, which is based on Particl,e Swarrn Optimization (PSO) fur sofuing rcuting poblem in VLil circaits. A hoo-step Binary Particle Swarm Optimizatdon (BPSO) apprcach, which is based on BPSO, is chosen in thi^s stuily to improue time ilelay through finding the bes...

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A Study of Network-based Approach for Cancer Classif...

Created: 2012-05-11 01:49:20 | Last updated: 2012-05-11 01:49:21

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

The advent of high-throughput techniques such as microarray data enabled researchers to elucidate process in a cell that fruitfully useful for pathological and medical. For such opportunities, microarray gene expression data have been explored and applied for various types of studies e.g. gene association, gene classification and construction of gene network. Unfortunately, since gene expression data naturally have a few of samples and thousands of genes, this leads to a biologi...

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A Parallelizing Interface for K-Means Type Clusterin...

Created: 2012-05-11 01:46:24

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

The k-means clustering algorithm and neural network batch training becomes computationally intensive when the manipulated data is large. One way to reduce the computational demand of such techniques is to execute them in a concurrent manner. Unfortunately, the effort required to implement these techniques in a distributed computing environment remains daunting. Much of the work takes place when partitioning and distributing workloads over processors in the distributed computing environm...

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A New Hybrid Firefly Algorithm for Complex and Nonli...

Created: 2012-05-11 01:44:17 | Last updated: 2012-05-11 01:44:18

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Global optimization methods play an important role to solve many real-world problems. However, the implementation of single methods is excessively preventive for high dimensionality and nonlinear problems, especially in term of the accuracy of finding best solutions and convergence speed performance. In recent years, hybrid optimization methods have shown potential achievements to overcome such challenges. In this paper, a new hybrid optimization method called Hybrid Evolutionary ...

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A Hybrid of SVM and SCAD with Group-specific Tuning ...

Created: 2012-05-11 01:39:36

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The incorporation of pathway data into the microarray analysis had lead to a new era in advance understanding of biological processes. However, this advancement is limited by the two issues in quality of pathway data. First, the pathway data are usually made from the biological context free, when it comes to a specific cellular process (e.g. lung cancer development), it can be that only several genes within pathways are responsible for the corresponding cellular process. Second, p...

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