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 $O(m n)$-time algorithms were known. We use a hierarchical sparsification technique to obtain algorithms that run in time $O(n^2)$. For 2-edge strongly connected components our algorithm gives the first running time improvement in 20 years. Additionally we present an $O(m^2 / \log{n})$-time algorithm for 2-edge strongly connected components, and thus improve over the $O(m n)$ running time also when $m = O(n)$. Our approach extends to k-edge and k-vertex strongly connected components for any constant k with a running time of $O(n^2 \log^2 n)$ for edges and $O(n^3)$ for vertices

Maximum flow and topological structure of complex networks

The problem of sending the maximum amount of flow $q$ between two arbitrary nodes $s$ and $t$ of complex networks along links with unit capacity is studied, which is equivalent to determining the number of link-disjoint paths between $s$ and $t$. The average of $q$ over all node pairs with smaller degree $k_{\rm min}$ is $_{k_{\rm min}} \simeq c k_{\rm min}$ for large $k_{\rm min}$ with $c$ a constant implying that the statistics of $q$ 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 $q$ 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 $c$. The applicability of our results to real world networks is tested for the Internet at the autonomous system level.Comment: 7 pages, 4 figure

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 $\lambda$ be the minimum cut, $n$ be the number of nodes in the network, and $D$ be the network diameter. Our algorithm can compute $\lambda$ exactly in $O((\sqrt{n} \log^{*} n+D)\lambda^4 \log^2 n)$ 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 $\lambda\leq 3$ due to Pritchard and Thurimella's $O(D)$-time and $O(D+n^{1/2}\log^* n)$-time algorithms for computing $2$-edge-connected and $3$-edge-connected components. By using the edge sampling technique of Karger's, we can convert this algorithm into a $(1+\epsilon)$-approximation $O((\sqrt{n}\log^{*} n+D)\epsilon^{-5}\log^3 n)$-time algorithm for any $\epsilon>0$. This improves over the previous $(2+\epsilon)$-approximation $O((\sqrt{n}\log^{*} n+D)\epsilon^{-5}\log^2 n\log\log n)$-time algorithm and $O(\epsilon^{-1})$-approximation $O(D+n^{\frac{1}{2}+\epsilon} \mathrm{poly}\log n)$-time algorithm of Ghaffari and Kuhn. Due to the lower bound of $\Omega(D+n^{1/2}/\log n)$ by Das Sarma et al. which holds for any approximation algorithm, this running time is tight up to a $\mathrm{poly}\log n$ 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 $\epsilon^{-9}\log^{7} n$ 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 rr-Simple kk-Path

An $r$-simple $k$-path is a {path} in the graph of length $k$ that passes through each vertex at most $r$ times. The $r$-SIMPLE $k$-PATH problem, given a graph $G$ as input, asks whether there exists an $r$-simple $k$-path in $G$. We first show that this problem is NP-Complete. We then show that there is a graph $G$ that contains an $r$-simple $k$-path and no simple path of length greater than $4\log k/\log r$. 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 $$\mathrm{poly}(n)\cdot 2^{O( k\cdot \log r/r)}$$ that solves the $r$-SIMPLE $k$-PATH on a graph with $n$ vertices with one-sided error. We also show that a randomized algorithm with running time $\mathrm{poly}(n)\cdot 2^{(c/2)k/ r}$ with $c<1$ 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 $O(\log r)$ 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 $PSB (n)$ 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 $PSB (n)$ is the graph whose vertex set is the vertex set of $PSB (n)$ and the edge set is the set of geometric edges or one-dimensional faces of $PSB (n)$. The main result of the paper is a necessary and sufficient condition for vertex adjacencies in the skeleton of the polytope $PSB (n)$ that can be verified in polynomial time.Comment: in Englis