21,928 research outputs found
Improved estimation of hidden Markov model parameters from multiple observation sequences
The huge popularity of Hidden Markov models in pattern recognition is due to the ability to 'learn' model parameters from an observation sequence through Baum-Welch and other re-estimation procedures. In the case of HMM parameter estimation from an ensemble of observation sequences, rather than a single sequence, we require techniques for finding the parameters which maximize the likelihood of the estimated model given the entire set of observation sequences. The importance of this study is that HMMs with parameters estimated from multiple observations are shown to be many orders of magnitude more probable than HMM models learned from any single observation sequence - thus the effectiveness of HMM 'learning' is greatly enhanced. In this paper, we present techniques that usually find models significantly more likely than Rabiner's well-known method on both seen and unseen sequences
Hidden Markov Models for Gene Sequence Classification: Classifying the VSG genes in the Trypanosoma brucei Genome
The article presents an application of Hidden Markov Models (HMMs) for
pattern recognition on genome sequences. We apply HMM for identifying genes
encoding the Variant Surface Glycoprotein (VSG) in the genomes of Trypanosoma
brucei (T. brucei) and other African trypanosomes. These are parasitic protozoa
causative agents of sleeping sickness and several diseases in domestic and wild
animals. These parasites have a peculiar strategy to evade the host's immune
system that consists in periodically changing their predominant cellular
surface protein (VSG). The motivation for using patterns recognition methods to
identify these genes, instead of traditional homology based ones, is that the
levels of sequence identity (amino acid and DNA sequence) amongst these genes
is often below of what is considered reliable in these methods. Among pattern
recognition approaches, HMM are particularly suitable to tackle this problem
because they can handle more naturally the determination of gene edges. We
evaluate the performance of the model using different number of states in the
Markov model, as well as several performance metrics. The model is applied
using public genomic data. Our empirical results show that the VSG genes on T.
brucei can be safely identified (high sensitivity and low rate of false
positives) using HMM.Comment: Accepted article in July, 2015 in Pattern Analysis and Applications,
Springer. The article contains 23 pages, 4 figures, 8 tables and 51
reference
Parameter estimation in pair hidden Markov models
This paper deals with parameter estimation in pair hidden Markov models
(pair-HMMs). We first provide a rigorous formalism for these models and discuss
possible definitions of likelihoods. The model being biologically motivated,
some restrictions with respect to the full parameter space naturally occur.
Existence of two different Information divergence rates is established and
divergence property (namely positivity at values different from the true one)
is shown under additional assumptions. This yields consistency for the
parameter in parametrization schemes for which the divergence property holds.
Simulations illustrate different cases which are not covered by our results.Comment: corrected typo
Generalized Species Sampling Priors with Latent Beta reinforcements
Many popular Bayesian nonparametric priors can be characterized in terms of
exchangeable species sampling sequences. However, in some applications,
exchangeability may not be appropriate. We introduce a {novel and
probabilistically coherent family of non-exchangeable species sampling
sequences characterized by a tractable predictive probability function with
weights driven by a sequence of independent Beta random variables. We compare
their theoretical clustering properties with those of the Dirichlet Process and
the two parameters Poisson-Dirichlet process. The proposed construction
provides a complete characterization of the joint process, differently from
existing work. We then propose the use of such process as prior distribution in
a hierarchical Bayes modeling framework, and we describe a Markov Chain Monte
Carlo sampler for posterior inference. We evaluate the performance of the prior
and the robustness of the resulting inference in a simulation study, providing
a comparison with popular Dirichlet Processes mixtures and Hidden Markov
Models. Finally, we develop an application to the detection of chromosomal
aberrations in breast cancer by leveraging array CGH data.Comment: For correspondence purposes, Edoardo M. Airoldi's email is
[email protected]; Federico Bassetti's email is
[email protected]; Michele Guindani's email is
[email protected] ; Fabrizo Leisen's email is
[email protected]. To appear in the Journal of the American
Statistical Associatio
Substructure and Boundary Modeling for Continuous Action Recognition
This paper introduces a probabilistic graphical model for continuous action
recognition with two novel components: substructure transition model and
discriminative boundary model. The first component encodes the sparse and
global temporal transition prior between action primitives in state-space model
to handle the large spatial-temporal variations within an action class. The
second component enforces the action duration constraint in a discriminative
way to locate the transition boundaries between actions more accurately. The
two components are integrated into a unified graphical structure to enable
effective training and inference. Our comprehensive experimental results on
both public and in-house datasets show that, with the capability to incorporate
additional information that had not been explicitly or efficiently modeled by
previous methods, our proposed algorithm achieved significantly improved
performance for continuous action recognition.Comment: Detailed version of the CVPR 2012 paper. 15 pages, 6 figure
Learning to automatically detect features for mobile robots using second-order Hidden Markov Models
In this paper, we propose a new method based on Hidden Markov Models to
interpret temporal sequences of sensor data from mobile robots to automatically
detect features. Hidden Markov Models have been used for a long time in pattern
recognition, especially in speech recognition. Their main advantages over other
methods (such as neural networks) are their ability to model noisy temporal
signals of variable length. We show in this paper that this approach is well
suited for interpretation of temporal sequences of mobile-robot sensor data. We
present two distinct experiments and results: the first one in an indoor
environment where a mobile robot learns to detect features like open doors or
T-intersections, the second one in an outdoor environment where a different
mobile robot has to identify situations like climbing a hill or crossing a
rock.Comment: 200
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