9,345 research outputs found
On Computing the Maximum Parsimony Score of a Phylogenetic Network
Phylogenetic networks are used to display the relationship of different
species whose evolution is not treelike, which is the case, for instance, in
the presence of hybridization events or horizontal gene transfers. Tree
inference methods such as Maximum Parsimony need to be modified in order to be
applicable to networks. In this paper, we discuss two different definitions of
Maximum Parsimony on networks, "hardwired" and "softwired", and examine the
complexity of computing them given a network topology and a character. By
exploiting a link with the problem Multicut, we show that computing the
hardwired parsimony score for 2-state characters is polynomial-time solvable,
while for characters with more states this problem becomes NP-hard but is still
approximable and fixed parameter tractable in the parsimony score. On the other
hand we show that, for the softwired definition, obtaining even weak
approximation guarantees is already difficult for binary characters and
restricted network topologies, and fixed-parameter tractable algorithms in the
parsimony score are unlikely. On the positive side we show that computing the
softwired parsimony score is fixed-parameter tractable in the level of the
network, a natural parameter describing how tangled reticulate activity is in
the network. Finally, we show that both the hardwired and softwired parsimony
score can be computed efficiently using Integer Linear Programming. The
software has been made freely available
Computing Bounds on Network Capacity Regions as a Polytope Reconstruction Problem
We define a notion of network capacity region of networks that generalizes
the notion of network capacity defined by Cannons et al. and prove its notable
properties such as closedness, boundedness and convexity when the finite field
is fixed. We show that the network routing capacity region is a computable
rational polytope and provide exact algorithms and approximation heuristics for
computing the region. We define the semi-network linear coding capacity region,
with respect to a fixed finite field, that inner bounds the corresponding
network linear coding capacity region, show that it is a computable rational
polytope, and provide exact algorithms and approximation heuristics. We show
connections between computing these regions and a polytope reconstruction
problem and some combinatorial optimization problems, such as the minimum cost
directed Steiner tree problem. We provide an example to illustrate our results.
The algorithms are not necessarily polynomial-time.Comment: Appeared in the 2011 IEEE International Symposium on Information
Theory, 5 pages, 1 figur
Parallel Metric Tree Embedding based on an Algebraic View on Moore-Bellman-Ford
A \emph{metric tree embedding} of expected \emph{stretch~}
maps a weighted -node graph to a weighted tree with such that, for all ,
and
. Such embeddings are highly useful for designing
fast approximation algorithms, as many hard problems are easy to solve on tree
instances. However, to date the best parallel -depth algorithm that achieves an asymptotically optimal expected stretch of
requires
work and a metric as input.
In this paper, we show how to achieve the same guarantees using
depth and
work, where and is an arbitrarily small constant.
Moreover, one may further reduce the work to at the expense of increasing the expected stretch to
.
Our main tool in deriving these parallel algorithms is an algebraic
characterization of a generalization of the classic Moore-Bellman-Ford
algorithm. We consider this framework, which subsumes a variety of previous
"Moore-Bellman-Ford-like" algorithms, to be of independent interest and discuss
it in depth. In our tree embedding algorithm, we leverage it for providing
efficient query access to an approximate metric that allows sampling the tree
using depth and work.
We illustrate the generality and versatility of our techniques by various
examples and a number of additional results
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