Temporal Logics for Phylogenetic Analysis via Model Checking

2013 ◽  
Vol 10 (4) ◽  
pp. 1058-1070 ◽  
Author(s):  
Jose Ignacio Requeno ◽  
Gregorio de Miguel Casado ◽  
Roberto Blanco ◽  
Jose Manuel Colom
2013 ◽  
Vol 10 (3) ◽  
pp. 16-30 ◽  
Author(s):  
José Ignacio Requeno ◽  
José Manuel Colom

Summary 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 defined over the phylogenetic tree. This strategy allows us to use generic software tools already present in the industry. 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 first one consists of partitioning the phylogenetic tree into a set of subgraphs each one representing a subproblem to be verified so as to speed up the computation time and distribute the memory consumption. The second strategy is based on uncoupling the information associated to each state of the phylogenetic tree (mainly, the DNA sequence) and exporting it to an external tool for the management of large information systems. The integration of all these approaches outperforms the results of monolithic model checking and helps us to execute the verification of properties in a real phylogenetic tree.


1993 ◽  
Vol 04 (01) ◽  
pp. 31-67 ◽  
Author(s):  
WOJCIECH PENCZEK

We investigate an extension of CTL (Computation Tree Logic) by past modalities, called CTL P, interpreted over Mazurkiewicz’s trace systems. The logic is powerful enough to express most of the partial order properties of distributed systems like serializability of database transactions, snapshots, parallel execution of program segments, or inevitability under concurrency fairness assumption. We show that the model checking problem for the logic is NP-hard, even if past modalities cannot be nested. Then, we give a one exponential time model checking algorithm for the logic without nested past modalities. We show that all the interesting partial order properties can be model checked using our algorithm. Next, we show that is is possible to extend the model checking algorithm to cover the whole language and its extension to [Formula: see text]. Finally, we prove that the logic is undecidable and we discuss consequences of our results on using propositional versions of partial order temporal logics to synthesis of concurrent systems from their specifications.


2014 ◽  
Vol 11 (3) ◽  
pp. 17-31 ◽  
Author(s):  
José Ignacio Requeno ◽  
José Manuel Colom

Summary Model checking is a generic verification technique that allows the phylogeneticist to focus on models and specifications instead of on implementation issues. Phylogenetic trees are considered as transition systems over which we interrogate phylogenetic questions written as formulas of temporal logic. Nonetheless, standard logics become insufficient for certain practices of phylogenetic analysis since they do not allow the inclusion of explicit time and probabilities. The aim of this paper is to extend the application of model checking techniques beyond qualitative phylogenetic properties and adapt the existing logical extensions and tools to the field of phylogeny. The introduction of time and probabilities in phylogenetic specifications is motivated by the study of a real example: the analysis of the ratio of lactose intolerance in some populations and the date of appearance of this phenotype.


2007 ◽  
Vol 50 (4) ◽  
pp. 403-420 ◽  
Author(s):  
Kaile Su ◽  
Abdul Sattar ◽  
Xiangyu Luo

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