45,990 research outputs found
Solving the Canonical Representation and Star System Problems for Proper Circular-Arc Graphs in Log-Space
We present a logspace algorithm that constructs a canonical intersection
model for a given proper circular-arc graph, where `canonical' means that
models of isomorphic graphs are equal. This implies that the recognition and
the isomorphism problems for this class of graphs are solvable in logspace. For
a broader class of concave-round graphs, that still possess (not necessarily
proper) circular-arc models, we show that those can also be constructed
canonically in logspace. As a building block for these results, we show how to
compute canonical models of circular-arc hypergraphs in logspace, which are
also known as matrices with the circular-ones property. Finally, we consider
the search version of the Star System Problem that consists in reconstructing a
graph from its closed neighborhood hypergraph. We solve it in logspace for the
classes of proper circular-arc, concave-round, and co-convex graphs.Comment: 19 pages, 3 figures, major revisio
On Smooth Orthogonal and Octilinear Drawings: Relations, Complexity and Kandinsky Drawings
We study two variants of the well-known orthogonal drawing model: (i) the
smooth orthogonal, and (ii) the octilinear. Both models form an extension of
the orthogonal, by supporting one additional type of edge segments (circular
arcs and diagonal segments, respectively).
For planar graphs of max-degree 4, we analyze relationships between the graph
classes that can be drawn bendless in the two models and we also prove
NP-hardness for a restricted version of the bendless drawing problem for both
models. For planar graphs of higher degree, we present an algorithm that
produces bi-monotone smooth orthogonal drawings with at most two segments per
edge, which also guarantees a linear number of edges with exactly one segment.Comment: Appears in the Proceedings of the 25th International Symposium on
Graph Drawing and Network Visualization (GD 2017
Interval Routing Schemes for Circular-Arc Graphs
Interval routing is a space efficient method to realize a distributed routing
function. In this paper we show that every circular-arc graph allows a shortest
path strict 2-interval routing scheme, i.e., by introducing a global order on
the vertices and assigning at most two (strict) intervals in this order to the
ends of every edge allows to depict a routing function that implies exclusively
shortest paths. Since circular-arc graphs do not allow shortest path 1-interval
routing schemes in general, the result implies that the class of circular-arc
graphs has strict compactness 2, which was a hitherto open question.
Additionally, we show that the constructed 2-interval routing scheme is a
1-interval routing scheme with at most one additional interval assigned at each
vertex and we an outline algorithm to calculate the routing scheme for
circular-arc graphs in O(n^2) time, where n is the number of vertices.Comment: 17 pages, to appear in "International Journal of Foundations of
Computer Science
Subclasses of Normal Helly Circular-Arc Graphs
A Helly circular-arc model M = (C,A) is a circle C together with a Helly
family \A of arcs of C. If no arc is contained in any other, then M is a proper
Helly circular-arc model, if every arc has the same length, then M is a unit
Helly circular-arc model, and if there are no two arcs covering the circle,
then M is a normal Helly circular-arc model. A Helly (resp. proper Helly, unit
Helly, normal Helly) circular-arc graph is the intersection graph of the arcs
of a Helly (resp. proper Helly, unit Helly, normal Helly) circular-arc model.
In this article we study these subclasses of Helly circular-arc graphs. We show
natural generalizations of several properties of (proper) interval graphs that
hold for some of these Helly circular-arc subclasses. Next, we describe
characterizations for the subclasses of Helly circular-arc graphs, including
forbidden induced subgraphs characterizations. These characterizations lead to
efficient algorithms for recognizing graphs within these classes. Finally, we
show how do these classes of graphs relate with straight and round digraphs.Comment: 39 pages, 13 figures. A previous version of the paper (entitled
Proper Helly Circular-Arc Graphs) appeared at WG'0
Unit Grid Intersection Graphs: Recognition and Properties
It has been known since 1991 that the problem of recognizing grid
intersection graphs is NP-complete. Here we use a modified argument of the
above result to show that even if we restrict to the class of unit grid
intersection graphs (UGIGs), the recognition remains hard, as well as for all
graph classes contained inbetween. The result holds even when considering only
graphs with arbitrarily large girth. Furthermore, we ask the question of
representing UGIGs on grids of minimal size. We show that the UGIGs that can be
represented in a square of side length 1+epsilon, for a positive epsilon no
greater than 1, are exactly the orthogonal ray graphs, and that there exist
families of trees that need an arbitrarily large grid
Safe and complete contig assembly via omnitigs
Contig assembly is the first stage that most assemblers solve when
reconstructing a genome from a set of reads. Its output consists of contigs --
a set of strings that are promised to appear in any genome that could have
generated the reads. From the introduction of contigs 20 years ago, assemblers
have tried to obtain longer and longer contigs, but the following question was
never solved: given a genome graph (e.g. a de Bruijn, or a string graph),
what are all the strings that can be safely reported from as contigs? In
this paper we finally answer this question, and also give a polynomial time
algorithm to find them. Our experiments show that these strings, which we call
omnitigs, are 66% to 82% longer on average than the popular unitigs, and 29% of
dbSNP locations have more neighbors in omnitigs than in unitigs.Comment: Full version of the paper in the proceedings of RECOMB 201
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