The Experts below are selected from a list of 300 Experts worldwide ranked by ideXlab platform
A. Lien - One of the best experts on this subject based on the ideXlab platform.
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A detailed derivation of extended Jones Matrix Representation for twisted nematic liquid crystal displays
Liquid Crystals, 1997Co-Authors: A. LienAbstract:A detailed derivation of the extended Jones Matrix Representation for twisted nematic liquid crystal displays at oblique incidence (which was previously published by the author) is given. It is shown that this Representation reduces to the well-known ordinary Jones Matrix Representation at normal incidence.
Sebastian Böcker - One of the best experts on this subject based on the ideXlab platform.
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COCOON - FlipCut supertrees: towards Matrix Representation accuracy in polynomial time
Lecture Notes in Computer Science, 2011Co-Authors: Malte Brinkmeyer, Thasso Griebel, Sebastian BöckerAbstract:In computational phylogenetics, supertree methods provide a way to reconstruct larger clades of the Tree of Life. The supertree problem can be formalized in different ways, to cope with contradictory information in the input. In particular, there exist methods based on encoding the input trees in a Matrix, and methods based on finding minimum cuts in some graph. Matrix Representation methods compute supertrees of superior quality, but the underlying optimization problems are computationally hard. In contrast, graph-based methods have polynomial running time, but supertrees are inferior in quality. In this paper, we present a novel approach for the computation of supertrees called FlipCut supertree. Our method combines the computation of minimum cuts from graph-based methods with a Matrix Representation method, namely Minimum Flip Supertrees. Here, the input trees are encoded in a 0/1/?-Matrix. We present a heuristic to search for a minimum set of 0/1-flips such that the resulting Matrix admits a directed perfect phylogeny. We then extend our approach by using edge weights to weight the columns of the 0/1/?-Matrix. In our evaluation, we show that our method is extremely swift in practice, and orders of magnitude faster than the runner up. Concerning supertree quality, our method is sometimes on par with the "gold standard" Matrix Representation with Parsimony.
William S.-y. Wang - One of the best experts on this subject based on the ideXlab platform.
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A Matrix Representation of phylogenetic trees
Lecture Notes in Computer Science, 1997Co-Authors: Sanzheng Qiao, William S.-y. WangAbstract:In this paper we begin by describing two currently used methods for evaluating phylogenetic trees, one proposed by Fitch and Margoliash [5] and the other proposed by Saitou and Nei [7]. Both methods are heuristic in the sense that not all possible trees are tested to ensure that the best solution has been reached. We develop a Matrix Representation of unrooted binary trees. The problem of evaluating phylogenetic trees is then transformed into the standard linear least squares problem. Then we propose a Matrix decomposition method for evaluating phylogenetic trees.
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COCOON - A Matrix Representation of Polygenetic Trees
Lecture Notes in Computer Science, 1997Co-Authors: Sanzheng Qiao, William S.-y. WangAbstract:In this paper we begin by describing two currently used methods for evaluating phylogenetic trees, one proposed by Fitch and Margoliash [5] and the other proposed by Saitou and Nei [7]. Both methods are heuristic in the sense that not all possible trees are tested to ensure that the best solution has been reached. We develop a Matrix Representation of unrooted binary trees. The problem of evaluating phylogenetic trees is then transformed into the standard linear least squares problem. Then we propose a Matrix decomposition method for evaluating phylogenetic trees.
Malte Brinkmeyer - One of the best experts on this subject based on the ideXlab platform.
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COCOON - FlipCut supertrees: towards Matrix Representation accuracy in polynomial time
Lecture Notes in Computer Science, 2011Co-Authors: Malte Brinkmeyer, Thasso Griebel, Sebastian BöckerAbstract:In computational phylogenetics, supertree methods provide a way to reconstruct larger clades of the Tree of Life. The supertree problem can be formalized in different ways, to cope with contradictory information in the input. In particular, there exist methods based on encoding the input trees in a Matrix, and methods based on finding minimum cuts in some graph. Matrix Representation methods compute supertrees of superior quality, but the underlying optimization problems are computationally hard. In contrast, graph-based methods have polynomial running time, but supertrees are inferior in quality. In this paper, we present a novel approach for the computation of supertrees called FlipCut supertree. Our method combines the computation of minimum cuts from graph-based methods with a Matrix Representation method, namely Minimum Flip Supertrees. Here, the input trees are encoded in a 0/1/?-Matrix. We present a heuristic to search for a minimum set of 0/1-flips such that the resulting Matrix admits a directed perfect phylogeny. We then extend our approach by using edge weights to weight the columns of the 0/1/?-Matrix. In our evaluation, we show that our method is extremely swift in practice, and orders of magnitude faster than the runner up. Concerning supertree quality, our method is sometimes on par with the "gold standard" Matrix Representation with Parsimony.
Sanzheng Qiao - One of the best experts on this subject based on the ideXlab platform.
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A Matrix Representation of phylogenetic trees
Lecture Notes in Computer Science, 1997Co-Authors: Sanzheng Qiao, William S.-y. WangAbstract:In this paper we begin by describing two currently used methods for evaluating phylogenetic trees, one proposed by Fitch and Margoliash [5] and the other proposed by Saitou and Nei [7]. Both methods are heuristic in the sense that not all possible trees are tested to ensure that the best solution has been reached. We develop a Matrix Representation of unrooted binary trees. The problem of evaluating phylogenetic trees is then transformed into the standard linear least squares problem. Then we propose a Matrix decomposition method for evaluating phylogenetic trees.
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COCOON - A Matrix Representation of Polygenetic Trees
Lecture Notes in Computer Science, 1997Co-Authors: Sanzheng Qiao, William S.-y. WangAbstract:In this paper we begin by describing two currently used methods for evaluating phylogenetic trees, one proposed by Fitch and Margoliash [5] and the other proposed by Saitou and Nei [7]. Both methods are heuristic in the sense that not all possible trees are tested to ensure that the best solution has been reached. We develop a Matrix Representation of unrooted binary trees. The problem of evaluating phylogenetic trees is then transformed into the standard linear least squares problem. Then we propose a Matrix decomposition method for evaluating phylogenetic trees.
