Related papers: The motif problem
In this paper, we consider the problem of determining in polynomial time whether a given planar point set $P$ of $n$ points admits 4-connected triangulation. We propose a necessary and sufficient condition for recognizing $P$, and present…
Geometrical objects with integral side lengths have fascinated mathematicians through the ages. We call a set $P=\{p_1,...,p_n\}\subset\mathbb{Z}^2$ a maximal integral point set over $\mathbb{Z}^2$ if all pairwise distances are integral and…
Interpreting a node-link graph is enhanced if similar subgraphs (or motifs) are depicted in a similar manner; that is, they have the same visual form. Small motifs within graphs may be perceived to be identical when they are structurally…
A variant of the well-known Set Covering Problem is studied in this paper, where subsets of a collection have to be selected, and pairwise conflicts among subsets of items exist. The selection of each subset has a cost, and the inclusion of…
Optimistic parallelization is a promising approach for the parallelization of irregular algorithms: potentially interfering tasks are launched dynamically, and the runtime system detects conflicts between concurrent activities, aborting and…
The GRAPH MOTIF problem asks whether a given multiset of colors appears on a connected subgraph of a vertex-colored graph. The fastest known parameterized algorithm for this problem is based on a reduction to the $k$-Multilinear Detection…
In this article we propose a maximal a posteriori (MAP) criterion for model selection in the motif discovery problem and investigate conditions under which the MAP asymptotically gives a correct prediction of model size. We also investigate…
A matching of a graph is a subset of edges no two of which share a common vertex, and a maximum matching is a matching of maximum cardinality. In a $b$-matching every vertex $v$ has an associated bound $b_v$, and a maximum $b$-matching is a…
Three well-studied types of subgraph-restricted matchings are induced matchings, uniquely restricted matchings, and acyclic matchings. While it is hard to determine the maximum size of a matching of each of these types, whether some given…
This note provides a complete solution to a certain version of the edge-isoperimetric problem for powers of a cycle graph. Namely, it shows that the maximum number of edges inside a vertex subset of $C_n^s$ of size $k$ is achieved by a set…
Linear arrangements of graphs are a well-known type of graph labeling and are found in many important computational problems, such as the Minimum Linear Arrangement Problem ($\texttt{minLA}$). A linear arrangement is usually defined as a…
A matching of graph $G$ is maximal if it cannot be expanded by adding any edge to create a larger matching. In this paper, for a hexagonal ring $H$ with $n$ hexagons, we show that the number of maximal matchings of $H$ equals to the trace…
Network motifs can capture basic interaction patterns and inform the functional properties of networks. However, real-world complex systems often have multiple types of relationships, which cannot be represented by a monolayer network. The…
Motifs are the fundamental components of complex systems. The topological structure of networks representing complex systems and the frequency and distribution of motifs in these networks are intertwined. The complexities associated with…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
The aim in packing problems is to decide if a given set of pieces can be placed inside a given container. A packing problem is defined by the types of pieces and containers to be handled, and the motions that are allowed to move the pieces.…
We study the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a…
Hypergraphs naturally represent group interactions, which are omnipresent in many domains: collaborations of researchers, co-purchases of items, and joint interactions of proteins, to name a few. In this work, we propose tools for answering…
A motif is a frequently occurring subgraph of a given directed or undirected graph $G$. Motifs capture higher order organizational structure of $G$ beyond edge relationships, and, therefore, have found wide applications such as in graph…
In the point set embeddability problem, we are given a plane graph $G$ with $n$ vertices and a point set $S$ with $n$ points. Now the goal is to answer the question whether there exists a straight-line drawing of $G$ such that each vertex…