9,918 research outputs found
Comparing graphs
Graphs are a well-studied mathematical concept, which has become ubiquitous to represent structured data in many application domains like computer vision, social network analysis or chem- and bioinformatics. The ever-increasing amount of data in these domains requires to efficiently organize and extract information from large graph data sets. In this context techniques for comparing graphs are fundamental, e.g., in order to obtain meaningful similarity measures between graphs. These are a prerequisite for the application of a variety of data mining algorithms to the domain of graphs. Hence, various approaches to graph comparison evolved and are wide-spread in practice. This thesis is dedicated to two different strategies for comparing graphs: maximum common subgraph problems and graph kernels.
We study maximum common subgraph problems, which are based on classical graph-theoretical concepts for graph comparison and are NP-hard in the general case. We consider variants of the maximum common subgraph problem in restricted graph classes, which are highly relevant for applications in cheminformatics. We develop a polynomial-time algorithm, which allows to compute a maximum common subgraph under block and bridge preserving isomorphism in series-parallel graphs. This generalizes the problem of computing maximum common biconnected subgraphs in series-parallel graphs. We show that previous approaches to this problem, which are based on the separators represented by standard graph decompositions, fail. We introduce the concept of potential separators to overcome this issue and use them algorithmically to solve the problem in series-parallel graphs. We present algorithms with improved bounds on running time for the subclass of outerplanar graphs. Finally, we establish a sufficient condition for maximum common subgraph variants to allow derivation of graph distance metrics. This leads to polynomial-time computable graph distance metrics in restricted graph classes. This progress constitutes a step towards solving practically relevant maximum common subgraph problems in polynomial time.
The second contribution of this thesis is to graph kernels, which have their origin in specific data mining algorithms. A key property of graph kernels is that they allow to consider a large (possibly infinite) number of features and can support graphs with arbitrary annotation, while being efficiently computable. The main contributions of this part of the thesis are (i) the development of novel graph kernels, which are especially designed for attributed graphs with arbitrary annotations and (ii) the systematic study of implicit and explicit mapping into a feature space for computation of graph kernels w.r.t. its impact on the running time and the ability to consider arbitrary annotations. We propose graph kernels based on bijections between subgraphs and walks of fixed length. In an experimental study we show that these approaches provide a viable alternative to known techniques, in particular for graphs with complex annotations
Faster Algorithms for the Maximum Common Subtree Isomorphism Problem
The maximum common subtree isomorphism problem asks for the largest possible
isomorphism between subtrees of two given input trees. This problem is a
natural restriction of the maximum common subgraph problem, which is -hard in general graphs. Confining to trees renders polynomial time
algorithms possible and is of fundamental importance for approaches on more
general graph classes. Various variants of this problem in trees have been
intensively studied. We consider the general case, where trees are neither
rooted nor ordered and the isomorphism is maximum w.r.t. a weight function on
the mapped vertices and edges. For trees of order and maximum degree
our algorithm achieves a running time of by
exploiting the structure of the matching instances arising as subproblems. Thus
our algorithm outperforms the best previously known approaches. No faster
algorithm is possible for trees of bounded degree and for trees of unbounded
degree we show that a further reduction of the running time would directly
improve the best known approach to the assignment problem. Combining a
polynomial-delay algorithm for the enumeration of all maximum common subtree
isomorphisms with central ideas of our new algorithm leads to an improvement of
its running time from to ,
where is the order of the larger tree, is the number of different
solutions, and is the minimum of the maximum degrees of the input
trees. Our theoretical results are supplemented by an experimental evaluation
on synthetic and real-world instances
Layout of Graphs with Bounded Tree-Width
A \emph{queue layout} of a graph consists of a total order of the vertices,
and a partition of the edges into \emph{queues}, such that no two edges in the
same queue are nested. The minimum number of queues in a queue layout of a
graph is its \emph{queue-number}. A \emph{three-dimensional (straight-line
grid) drawing} of a graph represents the vertices by points in
and the edges by non-crossing line-segments. This paper contributes three main
results:
(1) It is proved that the minimum volume of a certain type of
three-dimensional drawing of a graph is closely related to the queue-number
of . In particular, if is an -vertex member of a proper minor-closed
family of graphs (such as a planar graph), then has a drawing if and only if has O(1) queue-number.
(2) It is proved that queue-number is bounded by tree-width, thus resolving
an open problem due to Ganley and Heath (2001), and disproving a conjecture of
Pemmaraju (1992). This result provides renewed hope for the positive resolution
of a number of open problems in the theory of queue layouts.
(3) It is proved that graphs of bounded tree-width have three-dimensional
drawings with O(n) volume. This is the most general family of graphs known to
admit three-dimensional drawings with O(n) volume.
The proofs depend upon our results regarding \emph{track layouts} and
\emph{tree-partitions} of graphs, which may be of independent interest.Comment: This is a revised version of a journal paper submitted in October
2002. This paper incorporates the following conference papers: (1) Dujmovic',
Morin & Wood. Path-width and three-dimensional straight-line grid drawings of
graphs (GD'02), LNCS 2528:42-53, Springer, 2002. (2) Wood. Queue layouts,
tree-width, and three-dimensional graph drawing (FSTTCS'02), LNCS
2556:348--359, Springer, 2002. (3) Dujmovic' & Wood. Tree-partitions of
-trees with applications in graph layout (WG '03), LNCS 2880:205-217, 200
Graph Treewidth and Geometric Thickness Parameters
Consider a drawing of a graph in the plane such that crossing edges are
coloured differently. The minimum number of colours, taken over all drawings of
, is the classical graph parameter "thickness". By restricting the edges to
be straight, we obtain the "geometric thickness". By further restricting the
vertices to be in convex position, we obtain the "book thickness". This paper
studies the relationship between these parameters and treewidth.
Our first main result states that for graphs of treewidth , the maximum
thickness and the maximum geometric thickness both equal .
This says that the lower bound for thickness can be matched by an upper bound,
even in the more restrictive geometric setting. Our second main result states
that for graphs of treewidth , the maximum book thickness equals if and equals if . This refutes a conjecture of Ganley and
Heath [Discrete Appl. Math. 109(3):215-221, 2001]. Analogous results are proved
for outerthickness, arboricity, and star-arboricity.Comment: A preliminary version of this paper appeared in the "Proceedings of
the 13th International Symposium on Graph Drawing" (GD '05), Lecture Notes in
Computer Science 3843:129-140, Springer, 2006. The full version was published
in Discrete & Computational Geometry 37(4):641-670, 2007. That version
contained a false conjecture, which is corrected on page 26 of this versio
Approximately Counting Embeddings into Random Graphs
Let H be a graph, and let C_H(G) be the number of (subgraph isomorphic)
copies of H contained in a graph G. We investigate the fundamental problem of
estimating C_H(G). Previous results cover only a few specific instances of this
general problem, for example, the case when H has degree at most one
(monomer-dimer problem). In this paper, we present the first general subcase of
the subgraph isomorphism counting problem which is almost always efficiently
approximable. The results rely on a new graph decomposition technique.
Informally, the decomposition is a labeling of the vertices such that every
edge is between vertices with different labels and for every vertex all
neighbors with a higher label have identical labels. The labeling implicitly
generates a sequence of bipartite graphs which permits us to break the problem
of counting embeddings of large subgraphs into that of counting embeddings of
small subgraphs. Using this method, we present a simple randomized algorithm
for the counting problem. For all decomposable graphs H and all graphs G, the
algorithm is an unbiased estimator. Furthermore, for all graphs H having a
decomposition where each of the bipartite graphs generated is small and almost
all graphs G, the algorithm is a fully polynomial randomized approximation
scheme.
We show that the graph classes of H for which we obtain a fully polynomial
randomized approximation scheme for almost all G includes graphs of degree at
most two, bounded-degree forests, bounded-length grid graphs, subdivision of
bounded-degree graphs, and major subclasses of outerplanar graphs,
series-parallel graphs and planar graphs, whereas unbounded-length grid graphs
are excluded.Comment: Earlier version appeared in Random 2008. Fixed an typo in Definition
3.
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