Related papers: $r$-indexing Wheeler graphs

Let $T [1..n]$ be a text over an alphabet of size $\sigma \in \mathrm{polylog} (n)$, let $r^*$ be the sum of the numbers of runs in the Burrows-Wheeler Transforms of $T$ and its reverse, and let $z$ be the number of phrases in the LZ77…

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…

Computing the directed path-width of a directed graph is an NP-hard problem. Even for digraphs of maximum semi-degree 3 the problem remains hard. We propose a decomposition of an input digraph G=(V,A) by a number k of sequences with entries…

Let $G$ be a unit disk graph in the plane defined by $n$ disks whose positions are known. For the case when $G$ is unweighted, we give a simple algorithm to compute a shortest path tree from a given source in $O(n\log n)$ time. For the case…

Given a planar graph $G$, we consider drawings of $G$ in the plane where edges are represented by straight line segments (which possibly intersect). Such a drawing is specified by an injective embedding $\pi$ of the vertex set of $G$ into…

In recent years several compressed indexes based on variants of the Burrows-Wheeler transformation have been introduced. Some of these index structures far more complex than a single string, as was originally done with the FM-index…

The Burrows-Wheeler Transform (BWT) is an important technique both in data compression and in the design of compact indexing data structures. It has been generalized from single strings to collections of strings and some classes of labeled…

We show how to merge two run-length compressed Burrows-Wheeler Transforms (RLBWTs) into a run-length compressed extended Burrows-Wheeler Transform (eBWT) in $O (r)$ space and $O ((r + L) \log (m + n))$ time, where $m$ and $n$ are the…

We show how to store a searchable partial-sums data structure with constant query time for a static sequence $S$ of $n$ positive integers in $o \left( \frac{\log n}{(\log \log n)^2} \right)$, in $n H_k (S) + o (n)$ bits for $k \in o \left(…

In this paper, we show that given a weighted, directed planar graph $G$, and any $\epsilon >0$, there exists a polynomial time and $O(n^{\frac{1}{2}+\epsilon})$ space algorithm that computes the shortest path between two fixed vertices in…

We solve the following problem: Can an undirected weighted graph G be parti- tioned into two non-empty induced subgraphs satisfying minimum constraints for the sum of edge weights at vertices of each subgraph? We show that this is possible…

We prove that, up to subpolynomial or polylogarithmic factors, there is no tradeoff between preprocessing time, query time, and size of exact distance oracles for planar graphs. Namely, we show how given an $n$-vertex weighted directed…

We initiate the study of computational problems on $k$-mers (strings of length $k$) in labeled graphs. As a starting point, we consider the problem of counting the number of distinct $k$-mers found on the walks of a graph. We establish that…

Let $P \subset \mathbb{R}^2$ be a planar $n$-point set such that each point $p \in P$ has an associated radius $r_p > 0$. The transmission graph $G$ for $P$ is the directed graph with vertex set $P$ such that for any $p, q \in P$, there is…

We present an algorithm to count the number of occurrences of a pattern graph $H$ as an induced subgraph in a host graph $G$. If $G$ belongs to a bounded expansion class, the algorithm runs in linear time. Our design choices are motivated…

Motivated by longstanding conjectures regarding decompositions of graphs into paths and cycles, we prove the following optimal decomposition results for random graphs. Let $0<p<1$ be constant and let $G\sim G_{n,p}$. Let $odd(G)$ be the…

Variation graphs, which represent genetic variation within a population, are replacing sequences as reference genomes. Path indexes are one of the most important tools for working with variation graphs. They generalize text indexes to…

Given a string $T$ on an alphabet of size $\sigma$, we describe a bidirectional Burrows-Wheeler index that takes $O(|T|\log{\sigma})$ bits of space, and that supports the addition \emph{and removal} of one character, on the left or right…

For a graph G and integer r\geq 1 we denote the collection of independent r-sets of G by I^{(r)}(G). If v\in V(G) then I_v^{(r)}(G) is the collection of all independent r-sets containing v. A graph G, is said to be r-EKR, for r\geq 1, iff…

We consider the following problem for oriented graphs and digraphs: Given an oriented graph (digraph) $G$, does it contain an induced subdivision of a prescribed digraph $D$? The complexity of this problem depends on $D$ and on whether $G$…