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Conditional random fields: Probabilistic models for segmenting and labeling sequence data

by John Lafferty , 2001
"... We present conditional random fields, a framework for building probabilistic models to segment and label sequence data. Conditional random fields offer several advantages over hidden Markov models and stochastic grammars for such tasks, including the ability to relax strong independence assumptions ..."
Abstract - Cited by 3485 (85 self) - Add to MetaCart
We present conditional random fields, a framework for building probabilistic models to segment and label sequence data. Conditional random fields offer several advantages over hidden Markov models and stochastic grammars for such tasks, including the ability to relax strong independence assumptions

Shallow Parsing with Conditional Random Fields

by Fei Sha, Fernando Pereira , 2003
"... Conditional random fields for sequence labeling offer advantages over both generative models like HMMs and classifiers applied at each sequence position. Among sequence labeling tasks in language processing, shallow parsing has received much attention, with the development of standard evaluati ..."
Abstract - Cited by 581 (8 self) - Add to MetaCart
Conditional random fields for sequence labeling offer advantages over both generative models like HMMs and classifiers applied at each sequence position. Among sequence labeling tasks in language processing, shallow parsing has received much attention, with the development of standard

MAFFT version 5: improvement in accuracy of multiple sequence alignment

by Kazutaka Katoh, Kei-ichi Kuma, Hiroyuki Toh, Takashi Miyata - NUCLEIC ACIDS RES , 2005
"... The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed high ..."
Abstract - Cited by 801 (5 self) - Add to MetaCart
The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed

Learning Stochastic Logic Programs

by Stephen Muggleton , 2000
"... Stochastic Logic Programs (SLPs) have been shown to be a generalisation of Hidden Markov Models (HMMs), stochastic context-free grammars, and directed Bayes' nets. A stochastic logic program consists of a set of labelled clauses p:C where p is in the interval [0,1] and C is a first-order r ..."
Abstract - Cited by 1194 (81 self) - Add to MetaCart
Stochastic Logic Programs (SLPs) have been shown to be a generalisation of Hidden Markov Models (HMMs), stochastic context-free grammars, and directed Bayes' nets. A stochastic logic program consists of a set of labelled clauses p:C where p is in the interval [0,1] and C is a first

What is a hidden Markov model?

by Sean R. Eddy , 2004
"... Often, problems in biological sequence analysis are just a matter of putting the right label on each residue. In gene identification, we want to label nucleotides as exons, introns, or intergenic sequence. In sequence alignment, we want to associate residues in a query sequence with ho-mologous resi ..."
Abstract - Cited by 1344 (8 self) - Add to MetaCart
Often, problems in biological sequence analysis are just a matter of putting the right label on each residue. In gene identification, we want to label nucleotides as exons, introns, or intergenic sequence. In sequence alignment, we want to associate residues in a query sequence with ho

Incorporating non-local information into information extraction systems by Gibbs sampling

by Jenny Rose Finkel, Trond Grenager, Christopher Manning - IN ACL , 2005
"... Most current statistical natural language processing models use only local features so as to permit dynamic programming in inference, but this makes them unable to fully account for the long distance structure that is prevalent in language use. We show how to solve this dilemma with Gibbs sampling, ..."
Abstract - Cited by 730 (25 self) - Add to MetaCart
, a simple Monte Carlo method used to perform approximate inference in factored probabilistic models. By using simulated annealing in place of Viterbi decoding in sequence models such as HMMs, CMMs, and CRFs, it is possible to incorporate non-local structure while preserving tractable inference. We

Estimation of probabilities from sparse data for the language model component of a speech recognizer

by Slava M. Katz - IEEE Transactions on Acoustics, Speech and Signal Processing , 1987
"... Abstract-The description of a novel type of rn-gram language model is given. The model offers, via a nonlinear recursive procedure, a com-putation and space efficient solution to the problem of estimating prob-abilities from sparse data. This solution compares favorably to other proposed methods. Wh ..."
Abstract - Cited by 799 (2 self) - Add to MetaCart
Abstract-The description of a novel type of rn-gram language model is given. The model offers, via a nonlinear recursive procedure, a com-putation and space efficient solution to the problem of estimating prob-abilities from sparse data. This solution compares favorably to other proposed methods

XM2VTSDB: The Extended M2VTS Database

by K. Messer, J. Matas, J. Kittler, K. Jonsson - In Second International Conference on Audio and Video-based Biometric Person Authentication , 1999
"... In this paper we describe the acquisition and content of a large multi-modal database intended for training and testing of multi-modal verification systems. The XM2VTSDB database offers synchronised video and speech data as well as image sequences allowing multiple views of the face. It consists of ..."
Abstract - Cited by 438 (40 self) - Add to MetaCart
In this paper we describe the acquisition and content of a large multi-modal database intended for training and testing of multi-modal verification systems. The XM2VTSDB database offers synchronised video and speech data as well as image sequences allowing multiple views of the face. It consists

Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests

by David Posada, Thomas R. Buckley , 2004
"... Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the sel ..."
Abstract - Cited by 407 (8 self) - Add to MetaCart
selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. In particular, the latter two methods are able to simultaneously compare multiple nested or nonnested models, assess model selection uncertainty, and allow

SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building

by Manolo Gouy, Olivier Gascuel - Mol Biol Evol , 2010
"... We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous ..."
Abstract - Cited by 319 (0 self) - Add to MetaCart
We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its
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