Biological Sequence Analysis
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(only showing first 100 items - show all)- The adjusted Viterbi training for hidden Markov models
- Protein secondary structure prediction using three neural networks and a segmental semi-Markov model
- A grammatical approach to RNA-RNA interaction prediction
- A hidden Markov model applied to the protein 3D structure analysis
- Polarity formation by a higher order interaction Markov-like chain
- A segmental semi Markov model for protein secondary structure prediction
- Maximum likelihood analysis of algorithms and data structures
- Parsimonious hidden Markov models for matrix-variate longitudinal data
- Exact MLE and asymptotic properties for nonparametric semi-Markov models
- Inverting random functions
- Orphan gene finding -- an exon assembly approach.
- Exact distribution for the local score of a Markov chain
- An optimization approach to multiple sequence alignment
- On the state of the art in machine learning: A personal review
- Fast estimation of posterior probabilities in change-point analysis through a constrained hidden Markov model
- Witnessing the quasiperiodic-ordering transition of one-dimensional \(k\)-component Fibonacci sequences
- 2-adic clustering of the PAM matrix
- Selecting effective siRNA target sequences by using Bayes' theorem
- Computation of mutual information from hidden Markov models
- Lower bounds on the generalized central moments of the optimal alignments score of random sequences
- A statistical method for analysing cospeciation in tritrophic ecology using electrical circuit theory
- Non-normal limiting distribution for optimal alignment scores of strings in binary alphabets
- Latent tree models for hierarchical topic detection
- HMM with emission process resulting from a special combination of independent Markovian emissions
- Accelerating Viterbi algorithm on graphics processing units
- Generalization bounds for learning weighted automata
- Hardness of RNA folding problem with four symbols
- Large-scale frequent stem pattern mining in RNA families
- A novel statistical measure for sequence comparison on the basis of \(k\)-word counts
- Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA
- Applying length-dependent stochastic context-free grammars to RNA secondary structure prediction
- Modeling dynamic programming problems over sequences and trees with inverse coupled rewrite systems
- Integrating Pareto optimization into dynamic programming
- siEDM: an efficient string index and search algorithm for edit distance with moves
- Lower bounds for moments of global scores of pairwise Markov chains
- Inference in population genetics using forward and backward, discrete and continuous time processes
- Reconstructing trees from subtree weights.
- Averaging fuzzy biopolymers
- Characterization of protein primary sequences based on partial ordering
- Using Bayesian multinomial classifier to predict whether a given protein sequence is intrinsically disordered
- A fast algorithm for all-pairs Hamming distances
- Approximate p-values for local sequence alignments.
- Identification of genetic networks by strategic gene disruptions and gene overexpressions under a Boolean model.
- Trees and ultrametric spaces: A categorical equivalence
- Predicting partial customer churn using Markov for discrimination for modeling first purchase sequences
- Efficient identification of transcription factor binding sites with a graph theoretic approach
- Strong law of large numbers for hidden Markov chains indexed by Cayley trees
- Automatic identification of audio recordings based on statistical modeling
- gBoost: a mathematical programming approach to graph classification and regression
- Inference attacks on genomic privacy with an improved HMM and an RCNN model for unrelated individuals
- Strong law of large numbers for hidden Markov chains indexed by an infinite tree with uniformly bounded degrees
- Hidden Markov model with Markovian emission
- Improved DNA-versus-protein homology search for protein fossils
- A comprehensive survey and analysis of generative models in machine learning
- Hidden Markov models with binary dependence
- Compositional properties of alignments
- Information geometry approach to parameter estimation in hidden Markov model
- Order selection for regression-based hidden Markov model
- An impossibility result for phylogeny reconstruction from \(k\)-mer counts
- Estimation of steady-state quantities of an HMM with some rarely generated emissions
- A coarse-grained Markov chain is a hidden Markov model
- Statistical physics and representations in real and artificial neural networks
- Duality between the local score of one sequence and constrained hidden Markov model
- The Modular Subset-Sum Problem and the size of deletion correcting codes
- An ambiguity hierarchy of weighted context-free grammars
- Structured hierarchical models for probabilistic inference from perturbation screening data
- Comparison methods for branching and axillary flowering sequences
- Improving RNA secondary structure prediction via state inference with deep recurrent neural networks
- A causal discovery algorithm based on the prior selection of leaf nodes
- Implementation of a Markov model for phylogenetic trees
- Chernoff information between Gaussian trees
- Hidden Markov models for multivariate functional data
- Bayesian protein structure alignment
- Spectral graph features for the classification of graphs and graph sequences
- Greedy learning of latent tree models for multidimensional clustering
- Phylogenetic analysis of DNA sequences based on the generalized pseudo-amino acid composition
- Sequence comparison via polar coordinates representation and curve tree
- Analyzing ambiguity of context-free grammars
- Component-based discriminative classification for hidden Markov models
- On suboptimal LCS-alignments for independent Bernoulli sequences with asymmetric distributions
- POMDPs under probabilistic semantics
- Sequence annotation with HMMs: new problems and their complexity
- A disambiguation algorithm for weighted automata
- A survey of temporal data mining
- A time warping approach to multiple sequence alignment
- Extraction of high quality \(k\)-words for alignment-free sequence comparison
- Recursive stochastic games with positive rewards
- Penalized estimation in high-dimensional hidden Markov models with state-specific graphical models
- A note on probabilistic models over strings: the linear algebra approach
- A Markovian approach for the prediction of mouse isochores
- Case-factor diagrams for structured probabilistic modeling
- A fuzzy model of predicting RNA secondary structure
- Distributions associated with general runs and patterns in hidden Markov models
- Exact distribution of the local score for Markovian sequences
- Links between probabilistic automata and hidden Markov models: probability distributions, learning models and induction algorithms
- Estimation of a matrix of intensities for model of Markov process
- A signal-to-noise analysis of phylogeny estimation by neighbor-joining: Insufficiency of polynomial length sequences
- On some stochastic models for replication of character strings
- Identification of related gene/protein names based on an HMM of name variations
- A C\(++\) computational environment for biomolecular sequence management
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