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Temporal Logics for Phylogenetic Analysis via Model Checking
2013
IEEE/ACM Transactions on Computational Biology & Bioinformatics
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To this end, model checking, a mature automated verification technique from computer science, is proposed for phylogenetic analysis. ...
Three cornerstones found our approach: modelling evolution dynamics with transition systems; specifying phylogenetic properties using temporal logic formulae; and verifying the latter by means of automated ...
by means of computational logics (CTL), and system verification via model checking. ...
doi:10.1109/tcbb.2013.87
pmid:24334397
fatcat:vlkqd7zabfh6be77iwotupcgjm
Temporal logics for phylogenetic analysis via model checking
2010
2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
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To this end, model checking, a mature automated verification technique from computer science, is proposed for phylogenetic analysis. ...
Three cornerstones found our approach: modelling evolution dynamics with transition systems; specifying phylogenetic properties using temporal logic formulae; and verifying the latter by means of automated ...
by means of computational logics (CTL), and system verification via model checking. ...
doi:10.1109/bibmw.2010.5703790
fatcat:alwxox5565dwrcn4t45hco42wi
Analyzing phylogenetic trees with timed and probabilistic model checking: the lactose persistence case study
2014
Journal of Integrative Bioinformatics
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Nonetheless, standard logics become insufficient for certain practices of phylogenetic analysis since they do not allow the inclusion of explicit time and probabilities. ...
Phylogenetic trees are considered as transition systems over which we interrogate phylogenetic questions written as formulas of temporal logic. ...
Mainly, we have motivated the extension of model checking for phylogenetic analysis using quantitative data. ...
doi:10.2390/biecoll-jib-2014-248
pmid:25339082
fatcat:m76d54tlsnhhfk7t7b6gwvtu5e
Analyzing Phylogenetic Trees with Timed and Probabilistic Model Checking: The Lactose Persistence Case Study
2014
Journal of Integrative Bioinformatics
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Nonetheless, standard logics become insufficient for certain practices of phylogenetic analysis since they do not allow the inclusion of explicit time and probabilities. ...
Phylogenetic trees are considered as transition systems over which we interrogate phylogenetic questions written as formulas of temporal logic. ...
Mainly, we have motivated the extension of model checking for phylogenetic analysis using quantitative data. ...
doi:10.1515/jib-2014-248
fatcat:c5byw44cvzbqpdbd2krpkv7yua
Evaluation of properties over phylogenetic trees using stochastic logics
2016
BMC Bioinformatics
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Model checking has been recently introduced as an integrated framework for extracting information of the phylogenetic trees using temporal logics as a querying language, an extension of modal logics that ...
Conclusions: We have shown that probabilistic model checking is a competitive framework for describing and analyzing quantitative properties over phylogenetic trees. ...
to thank the Spanish Ministry of Economy (SPE) under the program "Programa de I+D+i Estatal de Investigación, Desarrollo e innovación Orientada a los Retos de la Sociedad", project id TIN2013-40809-R, for ...
doi:10.1186/s12859-016-1077-7
pmid:27301397
pmcid:PMC4908722
fatcat:b3fhnt35offnragtsgo27ux5pu
Model checking software for phylogenetic trees using distribution and database methods
2013
Journal of Integrative Bioinformatics
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Model checking, a generic and formal paradigm stemming from computer science based on temporal logics, has been proposed for the study of biological properties that emerge from the labeling of the states ...
However, the performance of traditional model checking is penalized when scaling the system for large phylogenies. To this end, two strategies are presented here. ...
The introduction of model checking techniques for the automated verification of phylogenetic properties expressed as temporal logic formulas over phylogenetic trees, interpreted as Kripke structures, is ...
doi:10.2390/biecoll-jib-2013-229
pmid:24231143
fatcat:xslrev5pbvebjd3clfyugb6joq
Bio-jETI: a framework for semantics-based service composition
2009
BMC Bioinformatics
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These issues are taken care of at the semantic level by Bio-jETl's model checking and synthesis features. ...
The success of this method strongly depends on a careful semantic annotation of the provided services and on its cOllsequent exploitation for analysis, validation, and synthesis. ...
to be realizable via model checking [54, 55) . ...
doi:10.1186/1471-2105-10-s10-s8
pmid:19796405
pmcid:PMC2755829
fatcat:cxje3kun4banhoocelv6p56uvq
FluReF, an automated flu virus reassortment finder based on phylogenetic trees
2011
BMC Genomics
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Conclusions: FluReF demonstrates robustness of prediction for geographically and temporally expanded datasets, and is not limited to finding reassortments with previously collected sequences. ...
Methods: FluReF finds reassortments by a bottom-up search of the full-genome and segment-based phylogenetic trees for candidate clades-groups of one or more sampled viruses that are separated from the ...
Various metrics for the path from the candidate group to the LCA_-Without, via the LCA, are checked to ensure that the separation distance is nontrivial and that the three path has strong support. ...
doi:10.1186/1471-2164-12-s2-s3
pmid:21989112
pmcid:PMC3194234
fatcat:nbwfacqmhjgwffc23jjuygh6ua
Applications of Answer Set Programming in Phylogenetic Systematics
[chapter]
2011
Lecture Notes in Computer Science
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methods/tools both from the point of view of phylogenetic systematics and from the point of view of ASP. ...
We summarize some applications of Answer Set Programming (ASP) in phylogenetics systematics, focusing on the challenges, how they are handled using computational methods of ASP, the usefulness of the ASP-based ...
Acknowledgments Our work on the use of ASP in phylogenetic systematics has involved, at various stages, close collaborations with Yasin Bakis, Balkiz Ozturk Basaran, Dan Brooks, Duygu Cakmak, Thomas Eiter ...
doi:10.1007/978-3-642-20832-4_26
fatcat:5ridsmxnxjgifnyfjgl6zod2tq
Phylogenetic and functional dissimilarity does not increase during temporal heathland succession
2014
Proceedings of the Royal Society of London. Biological Sciences
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Succession has been a focal point of ecological research for over a century, but thus far has been poorly explored through the lens of modern phylogenetic and trait-based approaches to community assembly ...
However, relative to the observed temporal rate of taxonomic turnover, both phylogenetic and functional turnover were comparatively low, suggesting a degree of functional redundancy among close relatives ...
Thanks to Will Pearse for assistance with PHYLO-GENERATOR, Nate Swenson for providing code for the analysis of phylogenetic and functional beta diversity, and Jodi Price, Will Cornwell and two anonymous ...
doi:10.1098/rspb.2014.2102
pmid:25377459
pmcid:PMC4240997
fatcat:ecuo5vqohvea3fkt7qkzhnovle
Ontology-inferred phylogeny reconstruction for analyzing the evolutionary relationships between species: Ontological inference versus cladistics
2008
2008 8th IEEE International Conference on BioInformatics and BioEngineering
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For this experiment, we focused on the phylogeny of fungi. Lexical chaining technique has been used for incremental population of evolving ontological elements. ...
Also category theory has been employed to provide an underlying formalism for capturing and analyzing the evolutionary behavior of the system. ...
One can identify the common lineage for these fungal species by using the description logic reasoner, RACER, via the command instance types, which retrieves the concepts that instantiate each fungal species ...
doi:10.1109/bibe.2008.4696848
dblp:conf/bibe/Shaban-NejadH08
fatcat:lyu6hr6335diva2yq2actpnb2q
Constraint-Guided Workflow Composition Based on the EDAM Ontology
[article]
2010
arXiv
pre-print
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In this paper we discuss how the EMBRACE data and methods ontology (EDAM) can be used as background knowledge for the composition of bioinformatics workflows. ...
Methods for the automatic composition of services into executable workflows need detailed knowledge about the application domain,in particular about the available services and their behavior in terms of ...
model, non-formal specification of constraints using natural language templates, and automatic generation of model checking formulas (to check global properties of workflows). ...
arXiv:1012.1640v1
fatcat:j3iuowcz7ja43l6m4ab4ba4eia
Page 5860 of Mathematical Reviews Vol. , Issue 98I
[page]
1998
Mathematical Reviews
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Ross, Process calcu- lus based upon: evaluation to committed form (155-182); Doron Peled, Thomas Wilke and Pierre Wolper, An algorithmic ap- proach for checking closure properties of temporal logic spec ...
specifications: an overview (19-37); Ming Li [Ming Li'] and Paul Vitanyi, Average-case analysis via incom- ...
Introduction to the 34-th international conference on logic programming special issue
2018
Theory and Practice of Logic Programming
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This special issue of Theory and Practice of Logic Programming (TPLP) contains the regular papers accepted for presentation at the 34-th International Conference on Logic Programming (ICLP 2018), held ...
Cautious Reasoning in ASP via Minimal models and Unsatisfiable Cores • Joaquín Arias, Manuel Carro, Elmer Salazar, Kyle Marple and Gopal Gupta. ...
for Logic Programming. ...
doi:10.1017/s1471068418000352
fatcat:npib57qunzgzvhp4grx2fsavae
What can phylogenetic metrics tell us about useful diversity in evolutionary algorithms?
[article]
2021
arXiv
pre-print
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Moreover, our results suggest that phylogenetic diversity is indeed a better predictor of success. ...
We find that, in most cases, phylogenetic metrics behave meaningfully differently from other diversity metrics. ...
Michigan State University provided computational resources through the Institute for Cyber-Enabled Research. ...
arXiv:2108.12586v1
fatcat:hqm6o2su4zatzkoipdcyhytjua
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