Related papers: Computing k-mers in Graphs

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…

We consider parameterised subgraph-counting problems of the following form: given a graph G, how many k-tuples of its vertices have a given property? A number of such problems are known to be #W[1]-complete; here we substantially generalise…

We consider the problem of enumerating all instances of a given pattern graph in a large data graph. Our focus is on determining the input/output (I/O) complexity of this problem. Let $E$ be the number of edges in the data graph, $k=O(1)$…

Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…

We consider the (exact, minimum) $k$-cut problem: given a graph and an integer $k$, delete a minimum-weight set of edges so that the remaining graph has at least $k$ connected components. This problem is a natural generalization of the…

Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…

This paper deals with the maximum value of the difference between the determining number and the metric dimension of a graph as a function of its order. Our technique requires to use locating-dominating sets, and perform an independent…

A set of vertices $S$ is a \emph{determining set} of a graph $G$ if every automorphism of $G$ is uniquely determined by its action on $S$. The \emph{determining number} of $G$ is the minimum cardinality of a determining set of $G$. This…

Graph spanners are fundamental graph structures with a wide range of applications in distributed networks. We consider a standard synchronous message passing model where in each round $O(\log n)$ bits can be transmitted over every edge (the…

Most of the literature on spanners focuses on building the graph from scratch. This paper instead focuses on adding edges to improve an existing graph. A major open problem in this field is: given a graph embedded in a metric space, and a…

Twin-width is a graph parameter introduced in the context of first-order model checking, and has since become a central parameter in algorithmic graph theory. While many algorithmic problems become easier on arbitrary classes of bounded…

Graph kernels based on the $1$-dimensional Weisfeiler-Leman algorithm and corresponding neural architectures recently emerged as powerful tools for (supervised) learning with graphs. However, due to the purely local nature of the…

We determine the size of $k$-core in a large class of dense graph sequences. Let $G_n$ be a sequence of undirected, $n$-vertex graphs with edge weights $\{a^n_{i,j}\}_{i,j \in [n]}$ that converges to a kernel $W:[0,1]^2\to [0,+\infty)$ in…

We discuss the recently introduced concept of k-in-out graphs, and provide a construction for k-in-out graphs for any positive integer k. We derive a lower bound for the number of vertices of a k-in-out graph for any positive integer k, and…

The Weisfeiler-Leman (WL) algorithms form a family of incomplete approaches to the graph isomorphism problem. They recently found various applications in algorithmic group theory and machine learning. In fact, the algorithms form a…

There is substantial literature dealing with fixed parameter algorithms for the dominating set problem on various families of graphs. In this paper, we give a $k^{O(dk)} n$ time algorithm for finding a dominating set of size at most $k$ in…

In the minimum $k$-cut problem, we want to find the minimum number of edges whose deletion breaks the input graph into at least $k$ connected components. The classic algorithm of Karger and Stein runs in $\tilde O(n^{2k-2})$ time, and…

Motivation: Building the histogram of occurrences of every $k$-symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name of $k$-mer counting. Its applications include developing de…

The problem of subgraph counting asks for the number of occurrences of a pattern graph $H$ as a subgraph of a host graph $G$ and is known to be computationally challenging: it is $\#W[1]$-hard even when $H$ is restricted to simple…

In order to support the real-time interaction with LLMs and the instant search or the instant recommendation on social media, it becomes an imminent problem to build a k-NN graph or an indexing graph for the massive number of vectorized…