The Experts below are selected from a list of 294 Experts worldwide ranked by ideXlab platform
Mark Wilkinson - One of the best experts on this subject based on the ideXlab platform.
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Majority Rule supertrees
Systematic Biology, 2007Co-Authors: James Cotton, Mark WilkinsonAbstract:Most supertree methods proposed to date are essentially ad hoc, rather than designed with particular properties in mind. Although the supertree problem remains difficult, one promising avenue is to develop from better understood consensus methods to the more general supertree setting. Here, we generalize the widely used Majority-Rule consensus method to the supertree setting. The Majority-Rule consensus tree is the strict consensus of the median trees under the symmetric-difference metric, so we can generalize the consensus method by generalizing this metric to trees with differing leaf sets. There are two different natural generalizations, based on pruning or grafting leaves to produce comparable trees, and these two generalizations produce two different, but related, Majority-Rule supertree methods.
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Majority Rule reduced consensus trees and their use in bootstrapping
Molecular Biology and Evolution, 1996Co-Authors: Mark WilkinsonAbstract:Bootstrap analyses are usually summarized with Majority-Rule component consensus trees. This consensus method is based on replicated components and, like all component consensus methods, it is insensitive to other kinds of agreement between trees. Recently developed reduced consensus methods can be used to summarize much additional agreement on hypothesised phylogenetic relationships among multiple trees. The new methods are “strict” in the sense that they require agreement among all the trees being compared for any relationships to be represented in a consensus tree. Majority-Rule reduced consensus methods are described and their use in bootstrap analyses is illustrated with a hypothetical and a real example. The new methods provide summaries of the bootstrap proportions of all n-taxon statements/partitions and facilitate the identification of hypotheses of relationships that are supported by high bootstrap proportions, in spite of a lack of support for particular components or clades. In practice MajorityRule reduced consensus profiles may contain many trees. The size of the profile can be reduced by constraints on minimal bootstrap proportions and/or cardinality of the included trees. Majority-Rule reduced consensus trees can also be selected a posteriori from the profile. Surrogates to the Majority-Rule reduced consensus methods using partition tables or tree pruning options provided by widely used phylogenetic inference software are also described. The methods are designed to produce more informative summaries of bootstrap analyses and thereby foster more informed assessment of the strengths and weaknesses of complex phylogenetic hypotheses.
Jianrong Dong - One of the best experts on this subject based on the ideXlab platform.
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an axiomatic study of Majority Rule and associated consensus functions on hierarchies
Discrete Applied Mathematics, 2011Co-Authors: Jianrong Dong, David Fernandezbaca, F R Mcmorris, Robert C PowersAbstract:Consensus trees have been used routinely in systematic biology for over 30 years with the Majority-Rule consensus tree among the most popular. In this paper we give axioms that characterize a new consensus function, called Majority-Rule (+), that is based on a generalization of Majority-Rule to the supertree case. In addition, two other related consensus functions are characterized.
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An axiomatic study of Majority-Rule (+ ) and associated consensus functions on hierarchies
Discrete Applied Mathematics, 2011Co-Authors: Jianrong Dong, David Fernández-baca, Fred R. Mcmorris, Robert C PowersAbstract:Consensus trees have been used routinely in systematic biology for over 30 years with the Majority-Rule consensus tree among the most popular. In this paper we give axioms that characterize a new consensus function, called Majority-Rule (+), that is based on a generalization of Majority-Rule to the supertree case. In addition, two other related consensus functions are characterized.
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Majority Rule consensus trees
Bellman Prize in Mathematical Biosciences, 2010Co-Authors: Jianrong Dong, David Fernandezbaca, F R Mcmorris, Robert C PowersAbstract:The construction of a consensus tree to summarize the information of a given set of phylogenetic trees is now routinely a part of many studies in systematic biology. One popular method is the Majority-Rule consensus tree. In this paper we introduce and characterize a new consensus method that refines the Majority-Rule tree by adding certain compatible clusters satisfying a simple criterion.
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Majority-Rule (+) consensus trees.
Bellman Prize in Mathematical Biosciences, 2010Co-Authors: Jianrong Dong, David Fernández-baca, F R Mcmorris, Robert C PowersAbstract:The construction of a consensus tree to summarize the information of a given set of phylogenetic trees is now routinely a part of many studies in systematic biology. One popular method is the Majority-Rule consensus tree. In this paper we introduce and characterize a new consensus method that refines the Majority-Rule tree by adding certain compatible clusters satisfying a simple criterion.
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constructing Majority Rule supertrees
Algorithms for Molecular Biology, 2010Co-Authors: Jianrong Dong, David Fernandezbaca, F R McmorrisAbstract:Background Supertree methods combine the phylogenetic information from multiple partially-overlapping trees into a larger phylogenetic tree called a supertree. Several supertree construction methods have been proposed to date, but most of these are not designed with any specific properties in mind. Recently, Cotton and Wilkinson proposed extensions of the Majority-Rule consensus tree method to the supertree setting that inherit many of the appealing properties of the former.
Robert C Powers - One of the best experts on this subject based on the ideXlab platform.
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an axiomatic study of Majority Rule and associated consensus functions on hierarchies
Discrete Applied Mathematics, 2011Co-Authors: Jianrong Dong, David Fernandezbaca, F R Mcmorris, Robert C PowersAbstract:Consensus trees have been used routinely in systematic biology for over 30 years with the Majority-Rule consensus tree among the most popular. In this paper we give axioms that characterize a new consensus function, called Majority-Rule (+), that is based on a generalization of Majority-Rule to the supertree case. In addition, two other related consensus functions are characterized.
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An axiomatic study of Majority-Rule (+ ) and associated consensus functions on hierarchies
Discrete Applied Mathematics, 2011Co-Authors: Jianrong Dong, David Fernández-baca, Fred R. Mcmorris, Robert C PowersAbstract:Consensus trees have been used routinely in systematic biology for over 30 years with the Majority-Rule consensus tree among the most popular. In this paper we give axioms that characterize a new consensus function, called Majority-Rule (+), that is based on a generalization of Majority-Rule to the supertree case. In addition, two other related consensus functions are characterized.
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Majority Rule consensus trees
Bellman Prize in Mathematical Biosciences, 2010Co-Authors: Jianrong Dong, David Fernandezbaca, F R Mcmorris, Robert C PowersAbstract:The construction of a consensus tree to summarize the information of a given set of phylogenetic trees is now routinely a part of many studies in systematic biology. One popular method is the Majority-Rule consensus tree. In this paper we introduce and characterize a new consensus method that refines the Majority-Rule tree by adding certain compatible clusters satisfying a simple criterion.
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Majority-Rule (+) consensus trees.
Bellman Prize in Mathematical Biosciences, 2010Co-Authors: Jianrong Dong, David Fernández-baca, F R Mcmorris, Robert C PowersAbstract:The construction of a consensus tree to summarize the information of a given set of phylogenetic trees is now routinely a part of many studies in systematic biology. One popular method is the Majority-Rule consensus tree. In this paper we introduce and characterize a new consensus method that refines the Majority-Rule tree by adding certain compatible clusters satisfying a simple criterion.
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A Characterization of Majority Rule for Hierarchies
Journal of Classification, 2008Co-Authors: Fred R. Mcmorris, Robert C PowersAbstract:The Majority Rule has been a popular method for producing a consensus classification from several different classifications, when the classifications are all on the same set of objects and are structured as hierarchies. In this note, a new axiomatic characterization is proved for this consensus method on hierarchies.
Mathias Risse - One of the best experts on this subject based on the ideXlab platform.
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Arguing for Majority Rule
Raisons Politiques, 2020Co-Authors: Mathias Risse, Christopher Hamel, Juliette RoussinAbstract:This paper questions Majority Rule’s default status by demonstrating some general deficiencies of classical arguments for Majority Rule. The paper shows that these arguments are either “too narrow” to fully defend Majority Rule or, on the contrary, “too broad” to justify it without justifying other decision Rules as well. To do so, the paper offers a criticism of the most interesting recent defense of Majority Rule, Jeremy Waldron’s original reinterpretation of Locke’s argument in the Second Treatise coupled with his reading of May Theorem. The article concludes with an attempt to provide the beginnings of the work needed to offer a more compelling case for Majority Rule.
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on the philosophy of group decision methods i the non obviousness of Majority Rule
Philosophy Compass, 2009Co-Authors: Mathias RisseAbstract:Majority Rule is often adopted almost by default as a group decision Rule. One might think, therefore, that the conditions under which it applies, and the argument on its behalf, are well-understood. However, the standard arguments in support of Majority Rule display systematic deficiencies. This article explores these weaknesses, and assesses what can be said on behalf of Majority Rule.
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on the philosophy of group decision methods ii alternatives to Majority Rule
Philosophy Compass, 2009Co-Authors: Mathias RisseAbstract:In this companion piece to "On the Philosophy of Group Decision Methods I: the Non-Obviousness of Majority Rule," we take a closer look at some competitors of Majority Rule. This exploration supplements the conclusions of the other piece, as well as offer a further-reaching introduction to some of the challenges this field currently poses to philosophers.
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arguing for Majority Rule
Journal of Political Philosophy, 2004Co-Authors: Mathias RisseAbstract:ALTHOUGH Majority Rule finds ready acceptance whenever groups make decisions, there are surprisingly few philosophically interesting arguments in support of it. Jeremy Waldron’s The Dignity of Legislation contains the most interesting recent defense of Majority Rule. Waldron combines his own argument from respect with May’s influential characterization of Majority Rule, tying both to a reinterpretation of a well-known passage from Locke’s Second Treatise (“the body moves into the direction determined by the Majority of forces”). Despite its impressive resourcefulness, Waldron’s defense is deficient, and one goal of this essay is to show how. Yet our main concern is not to criticize Waldron, but to demonstrate general deficiencies of arguments for Majority Rule and to suggest a strategy for a more adequate and more complete defense. Such arguments tend to have one of two weaknesses: Either they assume that collective decisionmaking is done in terms of ranking options and thus neglect both aggregation methods using more information than the relative standing of options in rankings (such as so-called positional methods) and Rules that are not aggregation methods at all (such as fair-division procedures); or they also constitute arguments for other decision Rules. In the first case, the argument is too narrow, in the second it is too broad. The narrowness problem is bigger than stated so far because arguments for Majority Rule tend to assume not only that decisions are made by ranking options, but also that only two options are to be ranked. Both problems arise for Waldron’s defense and leave it incomplete. Yet such incompleteness also characterizes the state of the art in arguing for Majority Rule. So in addition to The Journal of Political Philosophy: Volume 12, Number 1, 2004, pp. 41–64
Fred R. Mcmorris - One of the best experts on this subject based on the ideXlab platform.
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An axiomatic study of Majority-Rule (+ ) and associated consensus functions on hierarchies
Discrete Applied Mathematics, 2011Co-Authors: Jianrong Dong, David Fernández-baca, Fred R. Mcmorris, Robert C PowersAbstract:Consensus trees have been used routinely in systematic biology for over 30 years with the Majority-Rule consensus tree among the most popular. In this paper we give axioms that characterize a new consensus function, called Majority-Rule (+), that is based on a generalization of Majority-Rule to the supertree case. In addition, two other related consensus functions are characterized.
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WABI - Constructing Majority-Rule supertrees
Lecture Notes in Computer Science, 2009Co-Authors: Jianrong Dong, David Fernández-baca, Fred R. McmorrisAbstract:Supertree methods combine the phylogenetic information from multiple partially-overlapping trees into a larger phylogenetic tree called a supertree. Several supertree construction methods have been proposed to date, but most of these are not designed with any specific properties in mind. Recently, Cotton and Wilkinson proposed extensions of the Majority-Rule consensus tree method to the supertree setting that inherit many of the appealing properties of the former. Here we study a variant of one of their methods, called Majority-Rule (+) supertrees. After proving that a key underlying problem for constructing Majority-Rule (+) supertrees is NP-hard, we develop a polynomial-size integer linear programming formulation of the problem.We then report on a preliminary computational study of our approach. The results indicate that our method is computationally feasible for moderately large inputs. Perhaps more significantly, our results suggest that the Majority-Rule (+) approach produces biologically meaningful results.
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constructing Majority Rule supertrees
Workshop on Algorithms in Bioinformatics, 2009Co-Authors: Jianrong Dong, David Fernandezbaca, Fred R. McmorrisAbstract:Supertree methods combine the phylogenetic information from multiple partially-overlapping trees into a larger phylogenetic tree called a supertree. Several supertree construction methods have been proposed to date, but most of these are not designed with any specific properties in mind. Recently, Cotton and Wilkinson proposed extensions of the Majority-Rule consensus tree method to the supertree setting that inherit many of the appealing properties of the former. Here we study a variant of one of their methods, called Majority-Rule (+) supertrees. After proving that a key underlying problem for constructing Majority-Rule (+) supertrees is NP-hard, we develop a polynomial-size integer linear programming formulation of the problem.We then report on a preliminary computational study of our approach. The results indicate that our method is computationally feasible for moderately large inputs. Perhaps more significantly, our results suggest that the Majority-Rule (+) approach produces biologically meaningful results.
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Constructing Majority-Rule supertrees
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2009Co-Authors: Jianrong Dong, David Fernández-baca, Fred R. McmorrisAbstract:BACKGROUND: Supertree methods combine the phylogenetic information from multiple partially-overlapping trees into a larger phylogenetic tree called a supertree. Several supertree construction methods have been proposed to date, but most of these are not designed with any specific properties in mind. Recently, Cotton and Wilkinson proposed extensions of the Majority-Rule consensus tree method to the supertree setting that inherit many of the appealing properties of the former.\n\nRESULTS: We study a variant of one of Cotton and Wilkinson's methods, called Majority-Rule (+) supertrees. After proving that a key underlying problem for constructing Majority-Rule (+) supertrees is NP-hard, we develop a polynomial-size exact integer linear programming formulation of the problem. We then present a data reduction heuristic that identifies smaller subproblems that can be solved independently. While this technique is not guaranteed to produce optimal solutions, it can achieve substantial problem-size reduction. Finally, we report on a computational study of our approach on various real data sets, including the 121-taxon, 7-tree Seabirds data set of Kennedy and Page.\n\nCONCLUSIONS: The results indicate that our exact method is computationally feasible for moderately large inputs. For larger inputs, our data reduction heuristic makes it feasible to tackle problems that are well beyond the range of the basic integer programming approach. Comparisons between the results obtained by our heuristic and exact solutions indicate that the heuristic produces good answers. Our results also suggest that the Majority-Rule (+) approach, in both its basic form and with data reduction, yields biologically meaningful phylogenies.
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A Characterization of Majority Rule for Hierarchies
Journal of Classification, 2008Co-Authors: Fred R. Mcmorris, Robert C PowersAbstract:The Majority Rule has been a popular method for producing a consensus classification from several different classifications, when the classifications are all on the same set of objects and are structured as hierarchies. In this note, a new axiomatic characterization is proved for this consensus method on hierarchies.
