Hidden Markov models for bioinformatics
Markov chains (discrete-time Markov processes on discrete state spaces) (60J10) Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Applications of statistics to biology and medical sciences; meta analysis (62P10) Computing methodologies and applications (68U99) Research exposition (monographs, survey articles) pertaining to biology (92-02) General biology and biomathematics (92B05) Biochemistry, molecular biology (92C40)
The purpose of this book is to give a thorough and systematic introduction to probabilistic modelling in bioinformatics, the special attention being paid to the kind of probabilistic models useful in genome analysis. The model families and the methods are presented in an order of increasing complexity and flexibility, in three steps, starting from the multinomial processes through Markov chains to hidden Markov models, including a number of sophisticated modifications (e.g., frame-dependent models, mixture transition models and hidden semi-Markov models) which are necessary in successful biological sequence analysis. Questions of parametric inference, selection between model families and various architectures are treated. This book is originally intended for advanced undergraduate and graduate students with a fairly limited background in probability theory, but otherwise well trained in mathematics and already familiar with some techniques of algorithmic sequence analysis.
- A minimum description length approach to hidden Markov models with Poisson and Gaussian emissions. Application to order identification
- Entropy of hidden Markov processes via cycle expansion
- Subspace estimation and prediction methods for hidden Markov models
- A hidden Markov model for latent temporal clustering with application to ideological alignment in the U.S. Supreme Court
- HMM with emission process resulting from a special combination of independent Markovian emissions
- Global Markov models for eukaryote nucleotide data
- An efficient technique for superfamily classification of amino acid sequences: feature extraction, fuzzy clustering and prototype selection
- Strong law of large numbers for hidden Markov chains indexed by Cayley trees
- Strong law of large numbers for hidden Markov chains indexed by an infinite tree with uniformly bounded degrees
- A coarse-grained Markov chain is a hidden Markov model
- A stochastic model of gene transcription: an application to L1 retrotransposition events
- Model for comparative analysis of antigen receptor repertoires
- Estimation of Viterbi path in Bayesian hidden Markov models
- Moments of the count of a regular expression in a heterogeneous random sequence
- Membrane automata for modeling biomolecular processes
- Markov models for pattern recognition. From theory to applications
- Distributions associated with general runs and patterns in hidden Markov models
- Latent Markov models: a review of a general framework for the analysis of longitudinal data with covariates
- Sparse Markov chains for sequence data
- Hidden Markov processes. Theory and applications to biology
- Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model
- Sensitivity of hidden Markov models
- On the accuracy of the MAP inference in HMMs
- Hidden Markov Models for Microarray Time Course Data in Multiple Biological Conditions
- Statistical analysis of biological sequences: Markov modelling, alignments and motifs
- State Estimation Schemes for Independent Component Coupled Hidden Markov Models
- Inference with constrained hidden Markov models in PRISM
- Robust estimation for order of hidden Markov models based on density power divergences
- scientific article; zbMATH DE number 1222687 (Why is no real title available?)
- Biological Sequence Analysis
- Asymptotic risks of Viterbi segmentation
- Self-organizing hidden Markov model map (SOHMMM)
- scientific article; zbMATH DE number 2087054 (Why is no real title available?)
- Multiple hidden Markov models for categorical time series
- MAP segmentation in Bayesian hidden Markov models: a case study
- Recursive learning for sparse Markov models
- Markov models for pattern recognition. From theory to applications.
- Learning gradients from nonidentical data
- Statistical mechanics of transcription-factor binding site discovery using hidden Markov models
- Hidden Markov models with applications in cell adhesion experiments
- Bayesian Variable Selection in Markov Mixture Models
- Algorithmic Learning Theory
- Viterbi algorithms for hidden semi-Markov models with application to DNA analysis
- Effective hidden Markov models for detecting splicing junction sites in DNA sequences
- Non-stationary data segmentation with hidden evidential semi-Markov chains
- Unsupervised segmentation of randomly switching data hidden with non-Gaussian correlated noise
- On approximation of smoothing probabilities for hidden Markov models
- Uniform accuracy of the maximum likelihood estimates for probabilistic models of biological sequences
- Hidden Markov models for longitudinal rating data with dynamic response styles
- Matrix-variate hidden Markov regression models: fixed and random covariates
- Recursive and Viterbi estimation for semi-Markov chains
- New representations for a semi-Markov chain and related filters
- Asymptotic properties of the maximum likelihood estimator for hidden Markov models indexed by binary trees
- On the definitions of hidden Markov models
- Probabilistic modelling in bioinformatics and medical informatics.
- Unsupervised segmentation of new semi-Markov chains hidden with long dependence noise
- Multisensor triplet Markov chains and theory of evidence
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