The Learning Algorithms of Coupled Discrete Hidden Markov Models

2013 ◽  
Vol 411-414 ◽  
pp. 2106-2110
Author(s):  
Shi Ping Du ◽  
Jian Wang ◽  
Yu Ming Wei

A hidden Markov model (HMM) encompasses a large class of stochastic process models and has been successfully applied to a number of scientific and engineering problems, including speech and other pattern recognition problems, and biological sequence analysis. A major restriction is found, however, in conventional HMM, i.e., it is ill-suited to capture the interactions among different models. A variety of coupled hidden Markov models (CHMMs) have recently been proposed as extensions of HMM to better characterize multiple interdependent sequences. The resulting models have multiple state variables that are temporally coupled via matrices of conditional probabilities. This paper study is focused on the coupled discrete HMM, there are two state variables in the network. By generalizing forward-backward algorithm, Viterbi algorithm and Baum-Welch algorithm commonly used in conventional HMM to accommodate two state variables, several new formulae solving the 2-chain coupled discrete HMM probability evaluation, decoding and training problem are theoretically derived.

2019 ◽  
Vol 35 (19) ◽  
pp. 3829-3830 ◽  
Author(s):  
Shaun P Wilkinson

Abstract Summary Hidden Markov models (HMMs) and profile HMMs form an integral part of biological sequence analysis, supporting an ever-growing list of applications. The aphid R package can be used to derive, train, plot, import and export HMMs and profile HMMs in the R environment. Computationally-intensive dynamic programing recursions, such as the Viterbi, forward and backward algorithms are implemented in C++ and parallelized for increased speed and efficiency. Availability and implementation The aphid package is released under the GPL-3 license, and is freely available for download from CRAN and GitHub (https://github.com/shaunpwilkinson/aphid). Supplementary information Supplementary data are available at Bioinformatics online.


2014 ◽  
Vol 568-570 ◽  
pp. 254-259
Author(s):  
Shi Ping Du ◽  
Jian Wang ◽  
Yu Ming Wei

A variety of coupled hidden Markov models (CHMMs) have recently been proposed as extensions of HMM to better characterize multiple interdependent sequences. The resulting models have multiple state variables that are temporally coupled via matrices of conditional probabilities. A generalised fuzzy approach to statistical modelling techniques is proposed in this paper. Fuzzy C-means (FCM) and fuzzy entropy (FE) techniques are combined into a generalised fuzzy technique and applied to coupled hidden Markov models. The CHMM based on the fuzzy c-means (FCM) and fuzzy entropy (FE) is referred to as FCM-FE-CHMM in this paper. By building up a generalised fuzzy objective function, several new formulae solving Training algorithms are theoretically derived for FCM-FE-CHMM. The fuzzy modelling techniques are very flexible since the degree of fuzziness, the degree of fuzzy entropy.


2019 ◽  
Vol 35 (24) ◽  
pp. 5309-5312
Author(s):  
Ioannis A Tamposis ◽  
Konstantinos D Tsirigos ◽  
Margarita C Theodoropoulou ◽  
Panagiota I Kontou ◽  
Georgios N Tsaousis ◽  
...  

Abstract Summary JUCHMME is an open-source software package designed to fit arbitrary custom Hidden Markov Models (HMMs) with a discrete alphabet of symbols. We incorporate a large collection of standard algorithms for HMMs as well as a number of extensions and evaluate the software on various biological problems. Importantly, the JUCHMME toolkit includes several additional features that allow for easy building and evaluation of custom HMMs, which could be a useful resource for the research community. Availability and implementation http://www.compgen.org/tools/juchmme, https://github.com/pbagos/juchmme. Supplementary information Supplementary data are available at Bioinformatics online.


Author(s):  
M. Vidyasagar

This book explores important aspects of Markov and hidden Markov processes and the applications of these ideas to various problems in computational biology. It starts from first principles, so that no previous knowledge of probability is necessary. However, the work is rigorous and mathematical, making it useful to engineers and mathematicians, even those not interested in biological applications. A range of exercises is provided, including drills to familiarize the reader with concepts and more advanced problems that require deep thinking about the theory. Biological applications are taken from post-genomic biology, especially genomics and proteomics. The topics examined include standard material such as the Perron–Frobenius theorem, transient and recurrent states, hitting probabilities and hitting times, maximum likelihood estimation, the Viterbi algorithm, and the Baum–Welch algorithm. The book contains discussions of extremely useful topics not usually seen at the basic level, such as ergodicity of Markov processes, Markov Chain Monte Carlo (MCMC), information theory, and large deviation theory for both i.i.d and Markov processes. It also presents state-of-the-art realization theory for hidden Markov models. Among biological applications, it offers an in-depth look at the BLAST (Basic Local Alignment Search Technique) algorithm, including a comprehensive explanation of the underlying theory. Other applications such as profile hidden Markov models are also explored.


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