Related papers: Computing k-mers in Graphs

The inducibility of a graph $H$ measures the maximum number of induced copies of $H$ a large graph $G$ can have. Generalizing this notion, we study how many induced subgraphs of fixed order $k$ and size $\ell$ a large graph $G$ on $n$…

K-core decomposition is a commonly used metric to analyze graph structure or study the relative importance of nodes in complex graphs. Recent years have seen rapid growth in the scale of the graph, especially in industrial settings. For…

Genetic sequencing has become an increasingly affordable and accessible source of genomic data in computational biology. This data is often represented as $k$-mers, i.e., strings of some fixed length $k$ with symbols chosen from a reference…

The Kneser graph $K(n,k)$ is defined for integers $n$ and $k$ with $n \geq 2k$ as the graph whose vertices are all the $k$-subsets of $\{1,2,\ldots,n\}$ where two such sets are adjacent if they are disjoint. A classical result of Lov\'asz…

We present an algorithm that takes as input an $n$-vertex planar graph $G$ and a $k$-vertex pattern graph $P$, and computes the number of (induced) copies of $P$ in $G$ in $2^{O(k/\log k)}n^{O(1)}$ time. If $P$ is a matching, independent…

We consider a the minimum k-way cut problem for unweighted graphs with a size bound s on the number of cut edges allowed. Thus we seek to remove as few edges as possible so as to split a graph into k components, or report that this requires…

Most state-of-the-art graph kernels only take local graph properties into account, i.e., the kernel is computed with regard to properties of the neighborhood of vertices or other small substructures. On the other hand, kernels that do take…

We study the problem of approximating the number of $k$-cliques in a graph when given query access to the graph. We consider the standard query model for general graphs via (1) degree queries, (2) neighbor queries and (3) pair queries. Let…

Let $G$ be a graph on $n$ vertices. We call a subset $A$ of the vertex set $V(G)$ \emph{$k$-small} if, for every vertex $v \in A$, $\deg(v) \le n - |A| + k$. A subset $B \subseteq V(G)$ is called \emph{$k$-large} if, for every vertex $u \in…

Let $G$ be a connected graph. Given an ordered set $W = \{w_1, w_2,\dots w_k\}\subseteq V(G)$ and a vertex $u\in V(G)$, the representation of $u$ with respect to $W$ is the ordered $k$-tuple $(d(u,w_1), d(u,w_2),\dots,$ $d(u,w_k))$, where…

As a generalization of the concept of a metric basis, this article introduces the notion of $k$-metric basis in graphs. Given a connected graph $G=(V,E)$, a set $S\subseteq V$ is said to be a $k$-metric generator for $G$ if the elements of…

The problem of enumerating connected subgraphs of a given size in a graph has been extensively studied in recent years. In this paper, we propose an algorithm with a delay of $O(k\Delta)$ for enumerating all connected induced subgraphs of…

We present a new notion of limits of weighted directed graphs of growing size based on convergence of their random quotients. These limits are specified in terms of random exchangeable measures on the unit square. We call our limits…

We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in…

The de Bruijn graph $G_K$ of a set of strings $S$ is a key data structure in genome assembly that represents overlaps between all the $K$-length substrings of $S$. Construction and navigation of the graph is a space and time bottleneck in…

For an ordered set $W=\{w_1,w_2,...,w_k\}$ of vertices and a vertex $v$ in a connected graph $G$, the ordered $k$-vector $r(v|W):=(d(v,w_1),d(v,w_2),.,d(v,w_k))$ is called the (metric) representation of $v$ with respect to $W$, where…

The $k$-dimensional Weisfeiler-Leman ($k$-WL) algorithm is a simple combinatorial algorithm that was originally designed as a graph isomorphism heuristic. It naturally finds applications in Babai's quasipolynomial time isomorphism…

Let $(X,d)$ be a metric space. A set $S\subseteq X$ is said to be a $k$-metric generator for $X$ if and only if for any pair of different points $u,v\in X$, there exist at least $k$ points $w_1,w_2, \ldots w_k\in S$ such that $d(u,w_i)\ne…

We consider a connected undirected graph $G(n,m)$ with $n$ nodes and $m$ edges. A $k$-dominating set $D$ in $G$ is a set of nodes having the property that every node in $G$ is at most $k$ edges away from at least one node in $D$. Finding a…

In this paper we show lower bounds for a certain large class of algorithms solving the Graph Isomorphism problem, even on expander graph instances. Spielman [25] shows an algorithm for isomorphism of strongly regular expander graphs that…