378 research outputs found

    Temporal Phylogenetic Networks and Logic Programming

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    The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities are in contact, and also that a contact is only possible when the languages are spoken at the same time. We show how computational methods of answer set programming and constraint logic programming can be used to generate plausible conjectures about contacts between prehistoric linguistic communities, and illustrate our approach by applying it to the evolutionary history of Indo-European languages. To appear in Theory and Practice of Logic Programming (TPLP)

    Optimization of morphological data in numerical taxonomy analysis using genetic algorithms feature selection method

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    Studies in Numerical Taxonomy are carried out by measuring characters as much as possible. The workload over scientists and labor to perform measurements will increase proportionally with the number of variables (or characters) to be used in the study. However, some part of the data may be irrelevant or sometimes meaningless. Here in this study, we introduce an algorithm to obtain a subset of data with minimum characters that can represent original data. Morphological characters were used in optimization of data by Genetic Algorithms Feature Selection method. The analyses were performed on an 18 character*11 taxa data matrix with standardized continuous characters. The analyses resulted in a minimum set of 2 characters, which means the original tree based on the complete data can also be constructed by those two characters

    Design of an expert system to perform cladistic analysis

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    Biodiversity: Its Measurement and Metaphysics

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    Biodiversity is a concept that plays a key role in both scientific theories such as the species-area law and conservation politics. Currently, however, little agreement exists on how biodiversity should be defined, let alone measured. This has led to suggestions that biodiversity is not a metaphysically robust concept, with major implications for its usefulness in formulating scientific theories and making conservation decisions. A general discussion of biodiversity is presented, highlighting its application both in scientific and conservation contexts, its relationship with environmental ethics, and existing approaches to its measurement. To overcome the limitations of existing biodiversity concepts, a new concept of biocomplexity is proposed. This concept equates the biodiversity of any biological system with its effective complexity. Biocomplexity is shown to be the only feasible measure of biodiversity that captures the essential features desired of a general biodiversity concept. In particular, it is a well-defined, measurable and strongly intrinsic property of any biological system. Finally, the practical application of biocomplexity is discussed

    Biodiversity: Its Measurement and Metaphysics

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    Biodiversity is a concept that plays a key role in both scientific theories such as the species-area law and conservation politics. Currently, however, little agreement exists on how biodiversity should be defined, let alone measured. This has led to suggestions that biodiversity is not a metaphysically robust concept, with major implications for its usefulness in formulating scientific theories and making conservation decisions. A general discussion of biodiversity is presented, highlighting its application both in scientific and conservation contexts, its relationship with environmental ethics, and existing approaches to its measurement. To overcome the limitations of existing biodiversity concepts, a new concept of biocomplexity is proposed. This concept equates the biodiversity of any biological system with its effective complexity. Biocomplexity is shown to be the only feasible measure of biodiversity that captures the essential features desired of a general biodiversity concept. In particular, it is a well-defined, measurable and strongly intrinsic property of any biological system. Finally, the practical application of biocomplexity is discussed

    Cmodels for Tight Disjunctive Logic Programs

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    Disjunctive logic programming under the stable model semantics [GL91] is a new answer set programming (ASP) methodology for solving combinatorial search problems. It is a form of declarative programming related to logic programming languages, such as Prolog, where the solutions to a problem are represented by answer sets, and not by answer substitutions produced in response to a query as in convential logic programming. Instead of Prolog systems, this programming method uses answer set solvers, such as smodels1, smodelscc2, cmodels3, dlv4, and gnt1. These systems made it possible for ASP to be successfully applied in such areas as planning, bounded model checking, and space shuttle control. dlv and gnt are more general as they work with the class of disjunctive logic programs, while other systems cover nondisjunctive programs. System cmodels uses SAT solvers as search engines, which allows it to take advantage of rapid progress in the area of SAT. cmodels proved to be an efficient system in providing the solution to the wire-routing problem [EW04], and to the problem of reconstructing probable phylogenies in the area of historical linguistics [BEMR05]. In this work we extend cmodels [GLM04] to tight disjunctive programs. Complexity of finding a solution for such programs is NP, as in the case of nondisjunctive programs. Extending the syntax of the input language of cmodels to tight disjunctive programs permits the knowledge engineer to be more flexible with the encoding of the problems in the NP complexity class. Experimental analyses demonstrate that the approach is computationally promising and may advance applications of disjunctive logic programming

    PHYLO-ASP: Phylogenetic Systematics with Answer Set Programming

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    This note summarizes the use of Answer Set Programming to solve various computational problems to infer phylogenetic trees and phylogenetic networks, and discusses its applicability and effectiveness on some real taxa

    ESTimating plant phylogeny: lessons from partitioning

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    BACKGROUND: While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies. RESULTS: A maximum parsimony (MP) analysis resulted in a single tree with relatively high support at all nodes in the tree despite rampant conflict among trees generated from the separate analysis of individual partitions. In a comparison of broader-scale groupings based on cellular compartment (ie: chloroplast, mitochondrial or nuclear) or function, only the nuclear partition tree (based largely on EST data) was found to be topologically identical to the tree based on the simultaneous analysis of all data. Despite topological conflict among the broader-scale groupings examined, only the tree based on morphological data showed statistically significant differences. CONCLUSION: Based on the amount of character support contributed by EST data which make up a majority of the nuclear data set, and the lack of conflict of the nuclear data set with the simultaneous analysis tree, we conclude that the inclusion of EST data does provide a viable and efficient approach to address phylogenetic questions within a parsimony framework on a genomic scale, if problems of orthology determination and potential sequencing errors can be overcome. In addition, approaches that examine conflict and support in a simultaneous analysis framework allow for a more precise understanding of the evolutionary history of individual process partitions and may be a novel way to understand functional aspects of different kinds of cellular classes of gene products

    AN EVOLUTIONARY APPROACH TO BIBLIOGRAPHIC CLASSIFICATION

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    This dissertation is research in the domain of information science and specifically, the organization and representation of information. The research has implications for classification of scientific books, especially as dissemination of information becomes more rapid and science becomes more diverse due to increases in multi-, inter-, trans-disciplinary research, which focus on phenomena, in contrast to traditional library classification schemes based on disciplines.The literature review indicates 1) human socio-cultural groups have many of the same properties as biological species, 2) output from human socio-cultural groups can be and has been the subject of evolutionary relationship analyses (i.e., phylogenetics), 3) library and information science theorists believe the most favorable and scientific classification for information packages is one based on common origin, but 4) library and information science classification researchers have not demonstrated a book classification based on evolutionary relationships of common origin.The research project supports the assertion that a sensible book classification method can be developed using a contemporary biological classification approach based on common origin, which has not been applied to a collection of books until now. Using a sample from a collection of earth-science digitized books, the method developed includes a text-mining step to extract important terms, which were converted into a dataset for input into the second step—the phylogenetic analysis. Three classification trees were produced and are discussed. Parsimony analysis, in contrast to distance and likelihood analyses, produced a sensible book classification tree. Also included is a comparison with a classification tree based on a well-known contemporary library classification scheme (the Library of Congress Classification).Final discussions connect this research with knowledge organization and information retrieval, information needs beyond science, and this type of research in context of a unified science of cultural evolution
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