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Temporal Logics for Phylogenetic Analysis via Model Checking

Jose Ignacio Requeno, Gregorio de Miguel Casado, Roberto Blanco, Jose Manuel Colom
2013 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
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

Roberto Blanco, Gregorio de Miguel Casado, Jose Ignacio Requeno, Jose Manuel Colom
2010 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)  
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

José Ignacio Requeno, José Manuel Colom
2014 Journal of Integrative Bioinformatics  
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

José Ignacio Requeno, José Manuel Colom
2014 Journal of Integrative Bioinformatics  
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

José Ignacio Requeno, José Manuel Colom
2016 BMC Bioinformatics  
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

José Ignacio Requeno, José Manuel Colom
2013 Journal of Integrative Bioinformatics  
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

Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen
2009 BMC Bioinformatics  
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

Alisa Yurovsky, Bernard M E Moret
2011 BMC Genomics  
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]

Esra Erdem
2011 Lecture Notes in Computer Science  
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

A. D. Letten, D. A. Keith, M. G. Tozer
2014 Proceedings of the Royal Society of London. Biological Sciences  
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

Arash Shaban-Nejad, Volker Haarslev
2008 2008 8th IEEE International Conference on BioInformatics and BioEngineering  
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]

Anna-Lena Lamprecht, Stefan Naujokat, Bernhard Steffen, Tiziana Margaria
2010 arXiv   pre-print
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  
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

ALESSANDRO DAL PALÙ, PAUL TARAU
2018 Theory and Practice of Logic Programming  
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]

Jose Guadalupe Hernandez, Alexander Lalejini, Emily Dolson
2021 arXiv   pre-print
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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