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Showing 2 results for Pezeshk
Nasim Ejlali, Hamid Pezeshk,
Volume 2, Issue 2 (2-2009)
Abstract
Hidden Markov models are widely used in Bioinformatics. They are applied to protein sequence alignment, protein family annotation and gene-finding.The Baum-Welch training is an expectation-maximization algorithm for training the emission and transition probabilities of hidden Markov models. For very long training sequence, even the most efficient algorithms are memory-consuming. In this paper we discuss different approaches to decrease the memory use and compare the performance of different algorithms. In addition, we propose a bidirection algorithm with linear memory. We apply this algorithm to simulated data of protein profile to analyze the strength and weakness of the algorithm.
Abdollah Safari, Ali Sharifi, Hamid Pezeshk, Peyman Nickchi, Sayed-Amir Marashi, Changiz Eslahchi,
Volume 6, Issue 2 (2-2013)
Abstract
There are several methods for inference about gene networks, but there are few cases in which the historical information have been considered. In this research we deal with Bayesian inference on gene network. We apply a Bayesian framework to use the available information. Assuming a proper prior distribution and taking the dependency of parameters into account, we seek a model to obtain promising results. We also deal with the hyper parameter estimation. Two methods are considered. The results will be compared by the use of a simulation based on Gibbs sampler. The strengths and weaknesses of each method are briefly mentioned.
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