Replacement Paths via Row Minima of Concise Matrices

Matrix $M$ is {\em $k$-concise} if the finite entries of each column of $M$ consist of $k$ or less intervals of identical numbers. We give an $O(n+m)$-time algorithm to compute the row minima of any $O(1)$-concise $n\times m$ matrix. Our algorithm yields the first $O(n+m)$-time reductions from the replacement-paths problem on an $n$-node $m$-edge undirected graph (respectively, directed acyclic graph) to the single-source shortest-paths problem on an $O(n)$-node $O(m)$-edge undirected graph (respectively, directed acyclic graph). That is, we prove that the replacement-paths problem is no harder than the single-source shortest-paths problem on undirected graphs and directed acyclic graphs. Moreover, our linear-time reductions lead to the first $O(n+m)$-time algorithms for the replacement-paths problem on the following classes of $n$-node $m$-edge graphs (1) undirected graphs in the word-RAM model of computation, (2) undirected planar graphs, (3) undirected minor-closed graphs, and (4) directed acyclic graphs.Comment: 23 pages, 1 table, 9 figures, accepted to SIAM Journal on Discrete Mathematic

Alignment based Network Coding for Two-Unicast-Z Networks

In this paper, we study the wireline two-unicast-Z communication network over directed acyclic graphs. The two-unicast-Z network is a two-unicast network where the destination intending to decode the second message has apriori side information of the first message. We make three contributions in this paper: 1. We describe a new linear network coding algorithm for two-unicast-Z networks over directed acyclic graphs. Our approach includes the idea of interference alignment as one of its key ingredients. For graphs of a bounded degree, our algorithm has linear complexity in terms of the number of vertices, and polynomial complexity in terms of the number of edges. 2. We prove that our algorithm achieves the rate-pair (1, 1) whenever it is feasible in the network. Our proof serves as an alternative, albeit restricted to two-unicast-Z networks over directed acyclic graphs, to an earlier result of Wang et al. which studied necessary and sufficient conditions for feasibility of the rate pair (1, 1) in two-unicast networks. 3. We provide a new proof of the classical max-flow min-cut theorem for directed acyclic graphs.Comment: The paper is an extended version of our earlier paper at ITW 201

Directed Acyclic Graphs

This code is copyright (2015) by the University of Hertfordshire and is made available to third parties for research or private study, criticism or review, and for the purpose of reporting the state of the art, under the normal fair use/fair dealing exceptions in Sections 29 and 30 of the Copyright, Designs and Patents Act 1988. Use of the code under this provision is limited to non-commercial use: please contact us if you wish to arrange a licence covering commercial use of the code.This source code implements a unified framework for pre-processing Directed Acyclic Graphs (DAGs) to lookup reachability between two vertices as well as compute the least upper bound of two vertices in constant time. Our framework builds on the adaptive pre-processing algorithm for constant time reachability lookups and extends this to compute the least upper bound of a vertex-pair in constant time. The theoretical details of this work can be found in the research paper which is available at http://uhra.herts.ac.uk/handle/2299/1215

Complete Graphical Characterization and Construction of Adjustment Sets in Markov Equivalence Classes of Ancestral Graphs

We present a graphical criterion for covariate adjustment that is sound and complete for four different classes of causal graphical models: directed acyclic graphs (DAGs), maximum ancestral graphs (MAGs), completed partially directed acyclic graphs (CPDAGs), and partial ancestral graphs (PAGs). Our criterion unifies covariate adjustment for a large set of graph classes. Moreover, we define an explicit set that satisfies our criterion, if there is any set that satisfies our criterion. We also give efficient algorithms for constructing all sets that fulfill our criterion, implemented in the R package dagitty. Finally, we discuss the relationship between our criterion and other criteria for adjustment, and we provide new soundness and completeness proofs for the adjustment criterion for DAGs.Comment: 58 pages, 12 figures, to appear in JML

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

Persistent Homology Over Directed Acyclic Graphs

We define persistent homology groups over any set of spaces which have inclusions defined so that the corresponding directed graph between the spaces is acyclic, as well as along any subgraph of this directed graph. This method simultaneously generalizes standard persistent homology, zigzag persistence and multidimensional persistence to arbitrary directed acyclic graphs, and it also allows the study of more general families of topological spaces or point-cloud data. We give an algorithm to compute the persistent homology groups simultaneously for all subgraphs which contain a single source and a single sink in $O(n^4)$ arithmetic operations, where $n$ is the number of vertices in the graph. We then demonstrate as an application of these tools a method to overlay two distinct filtrations of the same underlying space, which allows us to detect the most significant barcodes using considerably fewer points than standard persistence.Comment: Revised versio