Lower bounds on the number of realizations of rigid graphs

Computing the number of realizations of a minimally rigid graph is a notoriously difficult problem. Towards this goal, for graphs that are minimally rigid in the plane, we take advantage of a recently published algorithm, which is the fastest available method, although its complexity is still exponential. Combining computational results with the theory of constructing new rigid graphs by gluing, we give a new lower bound on the maximal possible number of (complex) realizations for graphs with a given number of vertices. We extend these ideas to rigid graphs in three dimensions and we derive similar lower bounds, by exploiting data from extensive Gr\"obner basis computations

Long Proteins with Unique Optimal Foldings in the H-P Model

It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a simple combinatorial model designed to answer qualitative questions about the protein folding process. In this paper we consider a problem suggested by Brian Hayes in 1998: what proteins in the two-dimensional H-P model have unique optimal (minimum energy) foldings? In particular, we prove that there are closed chains of monomers (amino acids) with this property for all (even) lengths; and that there are open monomer chains with this property for all lengths divisible by four.Comment: 22 pages, 18 figure

A Linear Time Algorithm for Drawing a Graph in 3 Pages within its Isotopy Class in 3-Space

We consider undirected graphs up to an ambient isotopy in 3-space. Such a graph can be represented by a plane diagram or a Gauss code. We recognize in linear time if a Gauss code represents an actual graph in 3-space. We also design a linear time algorithm for drawing a topological 3-page embedding of a graph isotopic to a given graph

Frequent Subgraph Mining in Outerplanar Graphs

In recent years there has been an increased interest in frequent pattern discovery in large databases of graph structured objects. While the frequent connected subgraph mining problem for tree datasets can be solved in incremental polynomial time, it becomes intractable for arbitrary graph databases. Existing approaches have therefore resorted to various heuristic strategies and restrictions of the search space, but have not identified a practically relevant tractable graph class beyond trees. In this paper, we define the class of so called tenuous outerplanar graphs, a strict generalization of trees, develop a frequent subgraph mining algorithm for tenuous outerplanar graphs that works in incremental polynomial time, and evaluate the algorithm empirically on the NCI molecular graph dataset

Frequent Subgraph Mining in Outerplanar Graphs

In recent years there has been an increased interest in frequent pattern discovery in large databases of graph structured objects. While the frequent connected subgraph mining problem for tree datasets can be solved in incremental polynomial time, it becomes intractable for arbitrary graph databases. Existing approaches have therefore resorted to various heuristic strategies and restrictions of the search space, but have not identified a practically relevant tractable graph class beyond trees. In this paper, we define the class of so called tenuous outerplanar graphs, a strict generalization of trees, develop a frequent subgraph mining algorithm for tenuous outerplanar graphs that works in incremental polynomial time, and evaluate the algorithm empirically on the NCI molecular graph dataset

06481 Abstracts Collection -- Geometric Networks and Metric Space Embeddings

The Dagstuhl Seminar 06481 ``Geometric Networks and Metric Space Embeddings\u27\u27 was held from November~26 to December~1, 2006 in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. In this paper we describe the seminar topics, we have compiled a list of open questions that were posed during the seminar, there is a list of all talks and there are abstracts of the presentations given during the seminar. Links to extended abstracts or full papers are provided where available