Related papers: Succinct Permutation Graphs
Graph similarity search has received considerable attention in many applications, such as bioinformatics, data mining, pattern recognition, and social networks. Existing methods for this problem have limited scalability because of the huge…
Graph problems are troublesome when it comes to MapReduce. Typically, to be able to design algorithms that make use of the advantages of MapReduce, assumptions beyond what the model imposes, such as the density of the input graph, are…
We present new and improved data structures that answer exact node-to-node distance queries in planar graphs. Such data structures are also known as distance oracles. For any directed planar graph on n nodes with non-negative lengths we…
The class of quasi-chain graphs is an extension of the well-studied class of chain graphs. This latter class enjoys many nice and important properties, such as bounded clique-width, implicit representation, well-quasi-ordering by induced…
The study of sorting permutations by block interchanges has recently been stimulated by a phenomenon observed in the genome maintenance of certain ciliate species. The result was the identification of a block interchange operation that…
Quasi-median graphs are a tool commonly used by evolutionary biologists to visualise the evolution of molecular sequences. As with any graph, a quasi-median graph can contain cut vertices, that is, vertices whose removal disconnect the…
We propose a new algorithm for merging succinct representations of de Bruijn graphs introduced in [Bowe et al. WABI 2012]. Our algorithm is based on the lightweight BWT merging approach by Holt and McMillan [Bionformatics 2014, ACM-BCB…
In the recent research of data mining, frequent structures in a sequence of graphs have been studied intensively, and one of the main concern is changing structures along a sequence of graphs that can capture dynamic properties of data. On…
Deterministic finite automata are one of the simplest and most practical models of computation studied in automata theory. Their conceptual extension is the non-deterministic finite automata which also have plenty of applications. In this…
The notion of shortcut partition, introduced recently by Chang, Conroy, Le, Milenkovi\'c, Solomon, and Than [CCLMST23], is a new type of graph partition into low-diameter clusters. Roughly speaking, the shortcut partition guarantees that…
We perform experimental studies on data structures that answer path median, path counting, and path reporting queries in weighted trees. These query problems generalize the well-known range median query problem in arrays, as well as the…
We propose to design data structures called succinct geometric indexes of negligible space (more precisely, o(n) bits) that, by taking advantage of the n points in the data set permuted and stored elsewhere as a sequence, to support…
We survey permutation-based methods for approximate k-nearest neighbor search. In these methods, every data point is represented by a ranked list of pivots sorted by the distance to this point. Such ranked lists are called permutations. The…
Graphs have become increasingly popular in modeling structures and interactions in a wide variety of problems during the last decade. Graph-based clustering and semi-supervised classification techniques have shown impressive performance.…
A permutation $\pi: [n] \rightarrow [n]$ is a Baxter permutation if and only if it does not contain either of the patterns $2-41-3$ and $3-14-2$. Baxter permutations are one of the most widely studied subclasses of general permutation due…
Compact and I/O-efficient data representations play an important role in efficient algorithm design, as memory bandwidth and latency can present a significant performance bottleneck, slowing the computation by orders of magnitude. While…
Given an $n$-bit array $A$, the succinct rank data structure problem asks to construct a data structure using space $n+r$ bits for $r\ll n$, supporting rank queries of form $\mathtt{rank}(x)=\sum_{i=0}^{x-1} A[i]$. In this paper, we design…
Graph-structured data is central to many scientific and industrial domains, where the goal is often to optimize objectives defined over graph structures. Given the combinatorial complexity of graph spaces, such optimization problems are…
We consider the problems of finding optimal identifying codes, (open) locating-dominating sets and resolving sets of an interval or a permutation graph. In these problems, one asks to find a subset of vertices, normally called a…
Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…