finite state models
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Linguistics ◽  
2019 ◽  
Author(s):  
Jane Chandlee

Much like the term “computational linguistics”, the term “computational phonology” has come to mean different things to different people. Research grounded in a variety of methodologies and formalisms can be included in its scope. The common thread of the research that falls under this umbrella term is the use of computational methods to investigate questions of interest in phonology, primarily how to delimit the set of possible phonological patterns from the larger set of “logically possible” patterns and how those patterns are learned. Computational phonology arguably began with the foundational result that Sound Pattern of English (SPE) rules are regular relations (provided they can’t recursively apply to their own structural change), which means they can be modeled with finite-state transducers (FSTs) and that a system of ordered rules can be composed into a single FST. The significance of this result can be seen in the prominence of finite-state models both in theoretical phonology research and in more applied areas like natural language processing and human language technology. The shift in the field of phonology from rule-based grammars to constraint-based frameworks like Optimality Theory (OT) initially sparked interest in the question of how to model OT with FSTs and thereby preserve the noted restriction of phonology to the complexity level of regular. But an additional point of interest for computational work on OT stemmed from the ways in which its architecture readily lends itself to the development of learning algorithms and models, including statistical approaches that address recognized challenges such as gradient acceptability, process optionality, and the learning of underlying forms and hidden structure. Another line of research has taken on the question of to what extent phonology is not just regular, but subregular, meaning describable with proper subclasses of the regular languages and relations. The advantages of subregular modeling of phonological phenomena are argued to be stronger typological explanations, in that the computational properties that establish the subclasses as properly subregular restrict the kinds of phenomena that can be described in desirable ways. Also, these same restrictions lead directly to provably correct learning algorithms. Once again this work has made extensive use of the finite-state formalism, but it has also employed logical characterizations that more readily extend from strings to non-linear phenomena such as autosegmental representations and syllable structure.


2019 ◽  
Vol 35 (14) ◽  
pp. i360-i369
Author(s):  
Dinithi Sumanaweera ◽  
Lloyd Allison ◽  
Arun S Konagurthu

AbstractThe information criterion of minimum message length (MML) provides a powerful statistical framework for inductive reasoning from observed data. We apply MML to the problem of protein sequence comparison using finite state models with Dirichlet distributions. The resulting framework allows us to supersede the ad hoc cost functions commonly used in the field, by systematically addressing the problem of arbitrariness in alignment parameters, and the disconnect between substitution scores and gap costs. Furthermore, our framework enables the generation of marginal probability landscapes over all possible alignment hypotheses, with potential to facilitate the users to simultaneously rationalize and assess competing alignment relationships between protein sequences, beyond simply reporting a single (best) alignment. We demonstrate the performance of our program on benchmarks containing distantly related protein sequences.Availability and implementationThe open-source program supporting this work is available from: http://lcb.infotech.monash.edu.au/seqmmligner.Supplementary informationSupplementary data are available at Bioinformatics online.


2018 ◽  
Vol 44 (1) ◽  
pp. 17-37 ◽  
Author(s):  
Joan Andreu Sánchez ◽  
Martha Alicia Rocha ◽  
Verónica Romero ◽  
Mauricio Villegas

Probabilistic finite-state automata are a formalism that is widely used in many problems of automatic speech recognition and natural language processing. Probabilistic finite-state automata are closely related to other finite-state models as weighted finite-state automata, word lattices, and hidden Markov models. Therefore, they share many similar properties and problems. Entropy measures of finite-state models have been investigated in the past in order to study the information capacity of these models. The derivational entropy quantifies the uncertainty that the model has about the probability distribution it represents. The derivational entropy in a finite-state automaton is computed from the probability that is accumulated in all of its individual state sequences. The computation of the entropy from a weighted finite-state automaton requires a normalized model. This article studies an efficient computation of the derivational entropy of left-to-right probabilistic finite-state automata, and it introduces an efficient algorithm for normalizing weighted finite-state automata. The efficient computation of the derivational entropy is also extended to continuous hidden Markov models.


10.29007/d336 ◽  
2018 ◽  
Author(s):  
Igor Konnov

We present CheAPS, the checker of asynchronous parameterized communicating systems. It is a set of tools for verification of parameterized families F = M_n of finite-state models against LTL specification S. Each model M_n from a family F is composed of a fixed number of control processes and n processes from a fixed set of prototypes. Given a description of a family CheAPS generates finite-state models M_n and checks if one of such models can be used as an invariant of the family. As soon as an invariant is detected it is model checked by Spin to verify it against a specification S. If Spin completes the verification successfully, then all the models of F satisfy S.We are going to demonstrate an application of CheAPS to several examples: Chandy-Lamport snapshot algorithm, Awerbuch distributed depth-first search algorithm, Milner's scheduler, and the model of RSVP protocol, where invariants were detected successfully on that models by our tools. The project homepage is http://lvk.cs.msu.su/\~konnov/cheaps/. It is available under BSD-like license.The full version of the abstract is uploaded.


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