340 research outputs found
Covering Pairs in Directed Acyclic Graphs
The Minimum Path Cover problem on directed acyclic graphs (DAGs) is a
classical problem that provides a clear and simple mathematical formulation for
several applications in different areas and that has an efficient algorithmic
solution. In this paper, we study the computational complexity of two
constrained variants of Minimum Path Cover motivated by the recent introduction
of next-generation sequencing technologies in bioinformatics. The first problem
(MinPCRP), given a DAG and a set of pairs of vertices, asks for a minimum
cardinality set of paths "covering" all the vertices such that both vertices of
each pair belong to the same path. For this problem, we show that, while it is
NP-hard to compute if there exists a solution consisting of at most three
paths, it is possible to decide in polynomial time whether a solution
consisting of at most two paths exists. The second problem (MaxRPSP), given a
DAG and a set of pairs of vertices, asks for a path containing the maximum
number of the given pairs of vertices. We show its NP-hardness and also its
W[1]-hardness when parametrized by the number of covered pairs. On the positive
side, we give a fixed-parameter algorithm when the parameter is the maximum
overlapping degree, a natural parameter in the bioinformatics applications of
the problem
Finding 2-Edge and 2-Vertex Strongly Connected Components in Quadratic Time
We present faster algorithms for computing the 2-edge and 2-vertex strongly
connected components of a directed graph, which are straightforward
generalizations of strongly connected components. While in undirected graphs
the 2-edge and 2-vertex connected components can be found in linear time, in
directed graphs only rather simple -time algorithms were known. We use
a hierarchical sparsification technique to obtain algorithms that run in time
. For 2-edge strongly connected components our algorithm gives the
first running time improvement in 20 years. Additionally we present an -time algorithm for 2-edge strongly connected components, and thus
improve over the running time also when . Our approach
extends to k-edge and k-vertex strongly connected components for any constant k
with a running time of for edges and for vertices
Maximum flow and topological structure of complex networks
The problem of sending the maximum amount of flow between two arbitrary
nodes and of complex networks along links with unit capacity is
studied, which is equivalent to determining the number of link-disjoint paths
between and . The average of over all node pairs with smaller degree
is for large with a constant implying that the statistics of is related to the
degree distribution of the network. The disjoint paths between hub nodes are
found to be distributed among the links belonging to the same edge-biconnected
component, and can be estimated by the number of pairs of edge-biconnected
links incident to the start and terminal node. The relative size of the giant
edge-biconnected component of a network approximates to the coefficient .
The applicability of our results to real world networks is tested for the
Internet at the autonomous system level.Comment: 7 pages, 4 figure
Recommended from our members
Forests, Frames and Games: Algorithms for Matroid Sums and Applications ; CU-CS-446-89
Almost-Tight Distributed Minimum Cut Algorithms
We study the problem of computing the minimum cut in a weighted distributed
message-passing networks (the CONGEST model). Let be the minimum cut,
be the number of nodes in the network, and be the network diameter. Our
algorithm can compute exactly in time. To the best of our knowledge, this is the first paper that
explicitly studies computing the exact minimum cut in the distributed setting.
Previously, non-trivial sublinear time algorithms for this problem are known
only for unweighted graphs when due to Pritchard and
Thurimella's -time and -time algorithms for
computing -edge-connected and -edge-connected components.
By using the edge sampling technique of Karger's, we can convert this
algorithm into a -approximation -time algorithm for any . This improves
over the previous -approximation -time algorithm and
-approximation -time algorithm of Ghaffari and Kuhn. Due to the lower
bound of by Das Sarma et al. which holds for any
approximation algorithm, this running time is tight up to a factor.
To get the stated running time, we developed an approximation algorithm which
combines the ideas of Thorup's algorithm and Matula's contraction algorithm. It
saves an factor as compared to applying Thorup's tree
packing theorem directly. Then, we combine Kutten and Peleg's tree partitioning
algorithm and Karger's dynamic programming to achieve an efficient distributed
algorithm that finds the minimum cut when we are given a spanning tree that
crosses the minimum cut exactly once
On -Simple -Path
An -simple -path is a {path} in the graph of length that passes
through each vertex at most times. The -SIMPLE -PATH problem, given a
graph as input, asks whether there exists an -simple -path in . We
first show that this problem is NP-Complete. We then show that there is a graph
that contains an -simple -path and no simple path of length greater
than . So this, in a sense, motivates this problem especially
when one's goal is to find a short path that visits many vertices in the graph
while bounding the number of visits at each vertex.
We then give a randomized algorithm that runs in time that solves the -SIMPLE -PATH on a graph with
vertices with one-sided error. We also show that a randomized algorithm
with running time with gives a
randomized algorithm with running time \poly(n)\cdot 2^{cn} for the
Hamiltonian path problem in a directed graph - an outstanding open problem. So
in a sense our algorithm is optimal up to an factor
Balancing Minimum Spanning and Shortest Path Trees
This paper give a simple linear-time algorithm that, given a weighted
digraph, finds a spanning tree that simultaneously approximates a shortest-path
tree and a minimum spanning tree. The algorithm provides a continuous
trade-off: given the two trees and epsilon > 0, the algorithm returns a
spanning tree in which the distance between any vertex and the root of the
shortest-path tree is at most 1+epsilon times the shortest-path distance, and
yet the total weight of the tree is at most 1+2/epsilon times the weight of a
minimum spanning tree. This is the best tradeoff possible. The paper also
describes a fast parallel implementation.Comment: conference version: ACM-SIAM Symposium on Discrete Algorithms (1993
Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees
Background: The Maximal Pairing Problem (MPP) is the prototype of a class of combinatorial optimization problems that are of considerable interest in bioinformatics: Given an arbitrary phylogenetic tree T and weights ωxy for the paths between any two pairs of leaves (x, y), what is the collection of edge-disjoint paths between pairs of leaves that maximizes the total weight? Special cases of the MPP for binary trees and equal weights have been described previously; algorithms to solve the general MPP are still missing, however. Results: We describe a relatively simple dynamic programming algorithm for the special case of binary trees. We then show that the general case of multifurcating trees can be treated by interleaving solutions to certain auxiliary Maximum Weighted Matching problems with an extension of this dynamic programming approach, resulting in an overall polynomial-time solution of complexity (n^4 log n) w.r.t. the number n of leaves. The source code of a C implementation can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/Targeting. For binary trees, we furthermore discuss several constrained variants of the MPP as well as a partition function approach to the probabilistic version of the MPP. Conclusions: The algorithms introduced here make it possible to solve the MPP also for large trees with high-degree vertices. This has practical relevance in the field of comparative phylogenetics and, for example, in the context of phylogenetic targeting, i.e., data collection with resource limitations.Human Evolutionary Biolog
Diagnosis of autosomal dominant polycystic kidney disease in utero and in the young infant.
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135563/1/jum198765249.pd
On vertex adjacencies in the polytope of pyramidal tours with step-backs
We consider the traveling salesperson problem in a directed graph. The
pyramidal tours with step-backs are a special class of Hamiltonian cycles for
which the traveling salesperson problem is solved by dynamic programming in
polynomial time. The polytope of pyramidal tours with step-backs is
defined as the convex hull of the characteristic vectors of all possible
pyramidal tours with step-backs in a complete directed graph. The skeleton of
is the graph whose vertex set is the vertex set of and the
edge set is the set of geometric edges or one-dimensional faces of .
The main result of the paper is a necessary and sufficient condition for vertex
adjacencies in the skeleton of the polytope that can be verified in
polynomial time.Comment: in Englis
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