32,654 research outputs found
Maximum common subgraph isomorphism algorithms for the matching of chemical structures
The maximum common subgraph (MCS) problem has become increasingly important in those aspects of chemoinformatics that involve the matching of 2D or 3D chemical structures. This paper provides a classification and a review of the many MCS algorithms, both exact and approximate, that have been described in the literature, and makes recommendations regarding their applicability to typical chemoinformatics tasks
Parameterized Approximation Schemes for Steiner Trees with Small Number of Steiner Vertices
We study the Steiner Tree problem, in which a set of terminal vertices needs
to be connected in the cheapest possible way in an edge-weighted graph. This
problem has been extensively studied from the viewpoint of approximation and
also parametrization. In particular, on one hand Steiner Tree is known to be
APX-hard, and W[2]-hard on the other, if parameterized by the number of
non-terminals (Steiner vertices) in the optimum solution. In contrast to this
we give an efficient parameterized approximation scheme (EPAS), which
circumvents both hardness results. Moreover, our methods imply the existence of
a polynomial size approximate kernelization scheme (PSAKS) for the considered
parameter.
We further study the parameterized approximability of other variants of
Steiner Tree, such as Directed Steiner Tree and Steiner Forest. For neither of
these an EPAS is likely to exist for the studied parameter: for Steiner Forest
an easy observation shows that the problem is APX-hard, even if the input graph
contains no Steiner vertices. For Directed Steiner Tree we prove that
approximating within any function of the studied parameter is W[1]-hard.
Nevertheless, we show that an EPAS exists for Unweighted Directed Steiner Tree,
but a PSAKS does not. We also prove that there is an EPAS and a PSAKS for
Steiner Forest if in addition to the number of Steiner vertices, the number of
connected components of an optimal solution is considered to be a parameter.Comment: 23 pages, 6 figures An extended abstract appeared in proceedings of
STACS 201
Dynamic Graph Stream Algorithms in Space
In this paper we study graph problems in dynamic streaming model, where the
input is defined by a sequence of edge insertions and deletions. As many
natural problems require space, where is the number of
vertices, existing works mainly focused on designing space
algorithms. Although sublinear in the number of edges for dense graphs, it
could still be too large for many applications (e.g. is huge or the graph
is sparse). In this work, we give single-pass algorithms beating this space
barrier for two classes of problems.
We present space algorithms for estimating the number of connected
components with additive error and
-approximating the weight of minimum spanning tree, for any
small constant . The latter improves previous
space algorithm given by Ahn et al. (SODA 2012) for connected graphs with
bounded edge weights.
We initiate the study of approximate graph property testing in the dynamic
streaming model, where we want to distinguish graphs satisfying the property
from graphs that are -far from having the property. We consider
the problem of testing -edge connectivity, -vertex connectivity,
cycle-freeness and bipartiteness (of planar graphs), for which, we provide
algorithms using roughly space, which is
for any constant .
To complement our algorithms, we present space
lower bounds for these problems, which show that such a dependence on
is necessary.Comment: ICALP 201
- …