Viterbi Algorithm

2011 ◽  
pp. 1025-1025
Author(s):  
Michail G. Lagoudakis ◽  
Thomas Zeugmann ◽  
Claude Sammut
Keyword(s):  
Viterbi Algorithm

Hidden Markov Processes

2014 ◽  
Author(s):  
M. Vidyasagar
Keyword(s):  
Hidden Markov Models ◽  
Markov Processes ◽  
Viterbi Algorithm ◽  
Markov Models ◽  
Hidden Markov ◽  
Local Alignment ◽  
Biological Applications ◽  
Standard Material ◽  
Hidden Markov Processes ◽  
Genomics And Proteomics

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.

scholarly journals A graph-based algorithm for detecting rigid domains in protein structures

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Truong Khanh Linh Dang ◽  
Thach Nguyen ◽  
Michael Habeck ◽  
Mehmet Gültas ◽  
Stephan Waack
Keyword(s):  
Structural Changes ◽  
Viterbi Algorithm ◽  
Structural Information ◽  
Line Graph ◽  
Clustering Algorithms ◽  
Protein Structures ◽  
Alternative Methods ◽  
Structural Transitions ◽  
Tuning Parameters ◽  
Conformational Ensembles

Abstract Background Conformational transitions are implicated in the biological function of many proteins. Structural changes in proteins can be described approximately as the relative movement of rigid domains against each other. Despite previous efforts, there is a need to develop new domain segmentation algorithms that are capable of analysing the entire structure database efficiently and do not require the choice of protein-dependent tuning parameters such as the number of rigid domains. Results We develop a graph-based method for detecting rigid domains in proteins. Structural information from multiple conformational states is represented by a graph whose nodes correspond to amino acids. Graph clustering algorithms allow us to reduce the graph and run the Viterbi algorithm on the associated line graph to obtain a segmentation of the input structures into rigid domains. In contrast to many alternative methods, our approach does not require knowledge about the number of rigid domains. Moreover, we identified default values for the algorithmic parameters that are suitable for a large number of conformational ensembles. We test our algorithm on examples from the DynDom database and illustrate our method on various challenging systems whose structural transitions have been studied extensively. Conclusions The results strongly suggest that our graph-based algorithm forms a novel framework to characterize structural transitions in proteins via detecting their rigid domains. The web server is available at http://azifi.tz.agrar.uni-goettingen.de/webservice/.

scholarly journals Audio-to-score singing transcription based on a CRNN-HSMM hybrid model

2021 ◽  
Vol 10 ◽  
Author(s):  
Ryo Nishikimi ◽  
Eita Nakamura ◽  
Masataka Goto ◽  
Kazuyoshi Yoshii
Keyword(s):  
Hybrid Model ◽  
Viterbi Algorithm ◽  
Language Model ◽  
Expressive Power ◽  
Acoustic Model ◽  
Musical Language ◽  
Musical Score ◽  
Singing Voice ◽  
Generative Process ◽  
Music Signal

This paper describes an automatic singing transcription (AST) method that estimates a human-readable musical score of a sung melody from an input music signal. Because of the considerable pitch and temporal variation of a singing voice, a naive cascading approach that estimates an F0 contour and quantizes it with estimated tatum times cannot avoid many pitch and rhythm errors. To solve this problem, we formulate a unified generative model of a music signal that consists of a semi-Markov language model representing the generative process of latent musical notes conditioned on musical keys and an acoustic model based on a convolutional recurrent neural network (CRNN) representing the generative process of an observed music signal from the notes. The resulting CRNN-HSMM hybrid model enables us to estimate the most-likely musical notes from a music signal with the Viterbi algorithm, while leveraging both the grammatical knowledge about musical notes and the expressive power of the CRNN. The experimental results showed that the proposed method outperformed the conventional state-of-the-art method and the integration of the musical language model with the acoustic model has a positive effect on the AST performance.

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