22 Result(s)
within
Computer Science
Algorithm Analysis and Problem Complexity
David Fernández-Baca
Conference Paper
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Chapter and Conference Paper
Solving parametric problems on trees
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Chapter and Conference Paper
Augmentation problems on hierarchically defined graphs
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Chapter and Conference Paper
Space-sweep algorithms for parametric optimization
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Chapter and Conference Paper
On matroids and hierarchical graphs
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Chapter and Conference Paper
Optimal parametric search on graphs of bounded tree-width
We give linear-time algorithms for a class of parametric search problems on weighted graphs of bounded tree-width. We also discuss the implications of our results to approximate parametric search on planar gra...
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Chapter and Conference Paper
Linear-time algorithms for parametric minimum spanning tree problems on planar graphs
We give a linear-time algorithm for the minimum-ratio spanning tree problem on planar graphs. The algorithm is based on a new planar minimum spanning tree algorithm. The approach extends to other parametric mi...
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Chapter and Conference Paper
On the approximability of the Steiner tree problem in phylogeny
Three results on the Steiner tree problem are presented: (i) Computing optimum k-restricted Steiner tree is APX-complete for k≥4, (ii) the minimum-cost k-restricted Steiner tree problem in phylogeny is APX-comple...
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Chapter and Conference Paper
Using sparsification for parametric minimum spanning tree problems
Two applications of sparsification to parametric computing are given. The first is a fast algorithm for enumerating all distinct minimum spanning trees in a graph whose edge weights vary linearly with a parame...
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Chapter and Conference Paper
Multi-parameter Minimum Spanning Trees
A framework for solving certain multidimensional parametric search problems in randomized linear time is presented, along with its application to optimization on matroids, including parametric minimum spanning...
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Chapter and Conference Paper
Parametric Multiple Sequence Alignment and Phylogeny Construction
Bounds are given on the size of the parameter-space decomposition induced by multiple sequence alignment problems where phylogenetic information may be given or inferred. It is shown that many of the usual for...
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Chapter and Conference Paper
Supertrees by Flip**
The input to a supertree problem is a collection of phyloge-netic trees that intersect pairwise in their leaf sets; the goal is to construct a single tree that retains as much as possible of the information in...
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Chapter and Conference Paper
Inverse Parametric Sequence Alignment
We consider the inverse parametric sequence alignment problem, where a sequence alignment is given and the task is to determine parameter values such that the given alignment is optimal at that parameter setti...
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Chapter and Conference Paper
Parametric Analysis for Ungapped Markov Models of Evolution
We present efficient sensitivity-analysis algorithms for two problems involving Markov models of sequence evolution: ancestral reconstruction in evolutionary trees and local ungapped alignment under log-odds s...
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Chapter and Conference Paper
Comparing and Aggregating Partially Resolved Trees
We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies the input trees induce on tripl...
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Chapter and Conference Paper
Fast Local Search for Unrooted Robinson-Foulds Supertrees
A Robinson-Foulds (RF) supertree for a collection of input trees is a comprehensive species phylogeny that is at minimum total RF distance to the input trees. Thus, an RF supertree is consistent with the maxim...
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Chapter and Conference Paper
Constructing Large Conservative Supertrees
Generalizations of the strict and loose consensus methods to the supertree setting, recently introduced by McMorris and Wilkinson, are studied. The supertrees these methods produce are conservative in the sens...
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Chapter and Conference Paper
Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters
We study a long standing conjecture on the necessary and sufficient conditions for the compatibility of multi-state characters: There exists a function f(r) such that, for any set C of r-state characters, C is co...
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Chapter and Conference Paper
Fixed-Parameter Algorithms for Finding Agreement Supertrees
We study the agreement supertree approach for combining rooted phylogenetic trees when the input trees do not fully agree on the relative positions of the taxa. Two approaches to dealing with such conflicting ...
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Chapter and Conference Paper
Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms
A rogue taxon in a collection of phylogenetic trees is one whose position varies drastically from tree to tree. The presence of such taxa can greatly reduce the resolution of the consensus tree (e.g., the majo...
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Chapter and Conference Paper
Extracting Conflict-Free Information from Multi-labeled Trees
A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relationships for the same set of ...
