Related papers: Space-time Trade-offs for the LCP Array of Wheeler…
We design a space-efficient algorithm for performing depth-first search traversal(DFS) of a graph in $O(m+n\log^* n)$ time using $O(n)$ bits of space. While a normal DFS algorithm results in a DFS-tree (in case the graph is connected), our…
Imagine that unlabelled tokens are placed on the edges of a graph, such that no two tokens are placed on incident edges. A token can jump to another edge if the edges having tokens remain independent. We study the problem of determining the…
Numerous approximation algorithms for problems on unit disk graphs have been proposed in the literature, exhibiting a sharp trade-off between running times and approximation ratios. We introduce a variation of the known shifting strategy…
Population protocols are a popular model of distributed computing, in which randomly-interacting agents with little computational power cooperate to jointly perform computational tasks. Inspired by developments in molecular computation, and…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
Genome assembly is a fundamental problem in Bioinformatics, where for a given set of overlapping substrings of a genome, the aim is to reconstruct the source genome. The classical approaches to solving this problem use assembly graphs, such…
Finding maximum-cardinality matchings in undirected graphs is arguably one of the most central graph problems. For general m-edge and n-vertex graphs, it is well-known to be solvable in $O(m \sqrt{n})$ time. We develop a linear-time…
In large scale distributed computing systems, communication overhead is one of the major bottlenecks. In the map-shuffle-reduce framework, which is one of the major distributed computing frameworks, the communication load among servers can…
A vertex set $W$ in a graph $G$ is a valid $k$-swap for a vertex cover $S$ of $G$ if $W$ has size at most $k$ and $S'=(S \setminus W) \cup (W \setminus S)$, the symmetric difference of $S$ and $W$, is a vertex cover of $G$. If $|S'| < |S|$,…
A Longest Common Extension (LCE) query on a text $T$ of length $N$ asks for the length of the longest common prefix of suffixes starting at given two positions. We show that the signature encoding $\mathcal{G}$ of size $w = O(\min(z \log N…
This paper shows that a simple algorithm produces the {\em all-prefixes-LCSs-graph} in $O(mn)$ time for two input sequences of size $m$ and $n$. Given any prefix $p$ of the first input sequence and any prefix $q$ of the second input…
In the index coding problem, introduced by Birk and Kol (INFOCOM, 1998), the goal is to broadcast an n bit word to n receivers (one bit per receiver), where the receivers have side information represented by a graph G. The objective is to…
We investigate the limits of one of the fundamental ideas in data structures: fractional cascading. This is an important data structure technique to speed up repeated searches for the same key in multiple lists and it has numerous…
The Positional Burrows--Wheeler Transform (PBWT) is a data structure designed for efficiently representing and querying large collections of sequences, such as haplotype panels in genomics. Forward and backward stepping operations --…
The suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…
We consider the standard message passing model; we assume the system is fully synchronous: all processes start at the same time and time proceeds in synchronised rounds. In each round each vertex can transmit a different message of size…
The de Bruijn graph plays an important role in bioinformatics, especially in the context of de novo assembly. However, the representation of the de Bruijn graph in memory is a computational bottleneck for many assemblers. Recent papers…
We present a faster symbolic algorithm for the following central problem in probabilistic verification: Compute the maximal end-component (MEC) decomposition of Markov decision processes (MDPs). This problem generalizes the SCC…
Efficient decoding is crucial to high-throughput and power-sensitive wireless communication scenarios. A theoretical analysis of the performance-complexity tradeoff toward low-complexity decoding is required for a better understanding of…
Linear nested codes, where two or more sub-codes are nested in a global code, have been proposed as candidates for reliable multi-terminal communication. In this paper, we consider nested array-based spatially coupled low-density…