AN INTRODUCTION TO HIDDEN MARKOV MODELS AND BAYESIAN NETWORKS

Author(s):  
ZOUBIN GHAHRAMANI

We provide a tutorial on learning and inference in hidden Markov models in the context of the recent literature on Bayesian networks. This perspective makes it possible to consider novel generalizations of hidden Markov models with multiple hidden state variables, multiscale representations, and mixed discrete and continuous variables. Although exact inference in these generalizations is usually intractable, one can use approximate inference algorithms such as Markov chain sampling and variational methods. We describe how such methods are applied to these generalized hidden Markov models. We conclude this review with a discussion of Bayesian methods for model selection in generalized HMMs.

Multiclass classification problems such as document classification, medical diagnosis or scene classification are very challenging to address due to similarities between mutual classes. The use of reliable tools is necessary to get good classification results. This paper addresses the scene classification problem using objects as attributes. The process of classification is modeled by a famous mathematical tool: The Hidden Markov Models. We introduce suitable relations that scale the parameters of the Hidden Markov Model into variables of scene classification. The construction of Hidden Markov Chains is supported with weight measures and sorting functions. Lastly, inference algorithms extract most suitable scene categories from the Discrete Markov Chain. A parallelism approach constructs several Discrete Markov Chains in order to improve the accuracy of the classification process. We provide numerous tests on different datasets and compare classification accuracies with some state of the art methods. The proposed approach distinguishes itself by outperforming the other.


2014 ◽  
Vol 1 (24) ◽  
pp. 165
Author(s):  
Alexander Lvovich Tulupyev ◽  
Andrey Alexandrovich Filchenkov ◽  
Anton Mikhailovich Alexeyev

2018 ◽  
Author(s):  
Regev Schweiger ◽  
Yaniv Erlich ◽  
Shai Carmi

MotivationHidden Markov models (HMMs) are powerful tools for modeling processes along the genome. In a standard genomic HMM, observations are drawn, at each genomic position, from a distribution whose parameters depend on a hidden state; the hidden states evolve along the genome as a Markov chain. Often, the hidden state is the Cartesian product of multiple processes, each evolving independently along the genome. Inference in these so-called Factorial HMMs has a naïve running time that scales as the square of the number of possible states, which by itself increases exponentially with the number of subchains; such a running time scaling is impractical for many applications. While faster algorithms exist, there is no available implementation suitable for developing bioinformatics applications.ResultsWe developed FactorialHMM, a Python package for fast exact inference in Factorial HMMs. Our package allows simulating either directly from the model or from the posterior distribution of states given the observations. Additionally, we allow the inference of all key quantities related to HMMs: (1) the (Viterbi) sequence of states with the highest posterior probability; (2) the likelihood of the data; and (3) the posterior probability (given all observations) of the marginal and pairwise state probabilities. The running time and space requirement of all procedures is linearithmic in the number of possible states. Our package is highly modular, providing the user with maximal flexibility for developing downstream applications.Availabilityhttps://github.com/regevs/factorialhmm


2014 ◽  
Vol 1 (20) ◽  
pp. 186
Author(s):  
Leonid Markovich Revzin ◽  
Andrey Alexandrovich Filchenkov ◽  
Alexander Lvovich Tulupyev

2014 ◽  
Vol 1 (12) ◽  
pp. 134
Author(s):  
Maria Petrovna Momzikova ◽  
Olga Igorevna Velikodnaya ◽  
Mikhail Iakovlevich Pinsky ◽  
Alexander Vladimirovich Sirotkin ◽  
Alexander Lvovich Tulupyev ◽  
...  

2014 ◽  
Vol 2 (13) ◽  
pp. 122
Author(s):  
Maria Petrovna Momzikova ◽  
Olga Igorevna Velikodnaya ◽  
Mikhail Iakovlevich Pinsky ◽  
Alexander Vladimirovich Sirotkin ◽  
Alexander Lvovich Tulupyev ◽  
...  

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Guillaume Kon Kam King ◽  
Omiros Papaspiliopoulos ◽  
Matteo Ruggiero

2018 ◽  
Vol 35 (12) ◽  
pp. 2162-2164
Author(s):  
Regev Schweiger ◽  
Yaniv Erlich ◽  
Shai Carmi

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