7,743 research outputs found
Detection of recombination in DNA multiple alignments with hidden markov models
CConventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets from certain bacteria and viruses due to recombination, a process that leads to the creation of mosaic sequences from different strains and, if undetected, causes systematic errors in phylogenetic tree estimation. In the current work, a hidden Markov model (HMM) is employed to detect recombination events in multiple alignments of DNA sequences. The emission probabilities in a given state are determined by the branching order (topology) and the branch lengths of the respective phylogenetic tree, while the transition probabilities depend on the global recombination probability. The present study improves on an earlier heuristic parameter optimization scheme and shows how the branch lengths and the recombination probability can be optimized in a maximum likelihood sense by applying the expectation maximization (EM) algorithm. The novel algorithm is tested on a synthetic benchmark problem and is found to clearly outperform the earlier heuristic approach. The paper concludes with an application of this scheme to a DNA sequence alignment of the argF gene from four Neisseria strains, where a likely recombination event is clearly detected
A generalized risk approach to path inference based on hidden Markov models
Motivated by the unceasing interest in hidden Markov models (HMMs), this
paper re-examines hidden path inference in these models, using primarily a
risk-based framework. While the most common maximum a posteriori (MAP), or
Viterbi, path estimator and the minimum error, or Posterior Decoder (PD), have
long been around, other path estimators, or decoders, have been either only
hinted at or applied more recently and in dedicated applications generally
unfamiliar to the statistical learning community. Over a decade ago, however, a
family of algorithmically defined decoders aiming to hybridize the two standard
ones was proposed (Brushe et al., 1998). The present paper gives a careful
analysis of this hybridization approach, identifies several problems and issues
with it and other previously proposed approaches, and proposes practical
resolutions of those. Furthermore, simple modifications of the classical
criteria for hidden path recognition are shown to lead to a new class of
decoders. Dynamic programming algorithms to compute these decoders in the usual
forward-backward manner are presented. A particularly interesting subclass of
such estimators can be also viewed as hybrids of the MAP and PD estimators.
Similar to previously proposed MAP-PD hybrids, the new class is parameterized
by a small number of tunable parameters. Unlike their algorithmic predecessors,
the new risk-based decoders are more clearly interpretable, and, most
importantly, work "out of the box" in practice, which is demonstrated on some
real bioinformatics tasks and data. Some further generalizations and
applications are discussed in conclusion.Comment: Section 5: corrected denominators of the scaled beta variables (pp.
27-30), => corrections in claims 1, 3, Prop. 12, bottom of Table 1. Decoder
(49), Corol. 14 are generalized to handle 0 probabilities. Notation is more
closely aligned with (Bishop, 2006). Details are inserted in eqn-s (43); the
positivity assumption in Prop. 11 is explicit. Fixed typing errors in
equation (41), Example
Accuracy of MAP segmentation with hidden Potts and Markov mesh prior models via Path Constrained Viterbi Training, Iterated Conditional Modes and Graph Cut based algorithms
In this paper, we study statistical classification accuracy of two different
Markov field environments for pixelwise image segmentation, considering the
labels of the image as hidden states and solving the estimation of such labels
as a solution of the MAP equation. The emission distribution is assumed the
same in all models, and the difference lays in the Markovian prior hypothesis
made over the labeling random field. The a priori labeling knowledge will be
modeled with a) a second order anisotropic Markov Mesh and b) a classical
isotropic Potts model. Under such models, we will consider three different
segmentation procedures, 2D Path Constrained Viterbi training for the Hidden
Markov Mesh, a Graph Cut based segmentation for the first order isotropic Potts
model, and ICM (Iterated Conditional Modes) for the second order isotropic
Potts model.
We provide a unified view of all three methods, and investigate goodness of
fit for classification, studying the influence of parameter estimation,
computational gain, and extent of automation in the statistical measures
Overall Accuracy, Relative Improvement and Kappa coefficient, allowing robust
and accurate statistical analysis on synthetic and real-life experimental data
coming from the field of Dental Diagnostic Radiography. All algorithms, using
the learned parameters, generate good segmentations with little interaction
when the images have a clear multimodal histogram. Suboptimal learning proves
to be frail in the case of non-distinctive modes, which limits the complexity
of usable models, and hence the achievable error rate as well.
All Matlab code written is provided in a toolbox available for download from
our website, following the Reproducible Research Paradigm
Bayesian Detection of Changepoints in Finite-State Markov Chains for Multiple Sequences
We consider the analysis of sets of categorical sequences consisting of
piecewise homogeneous Markov segments. The sequences are assumed to be governed
by a common underlying process with segments occurring in the same order for
each sequence. Segments are defined by a set of unobserved changepoints where
the positions and number of changepoints can vary from sequence to sequence. We
propose a Bayesian framework for analyzing such data, placing priors on the
locations of the changepoints and on the transition matrices and using Markov
chain Monte Carlo (MCMC) techniques to obtain posterior samples given the data.
Experimental results using simulated data illustrates how the methodology can
be used for inference of posterior distributions for parameters and
changepoints, as well as the ability to handle considerable variability in the
locations of the changepoints across different sequences. We also investigate
the application of the approach to sequential data from two applications
involving monsoonal rainfall patterns and branching patterns in trees
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