Related papers: On Locating Paths in Compressed Tries
The Burrows-Wheeler Transform (BWT) of a string is an invertible permutation of the string, which can be used for data compression and compact indexes for string pattern matching. Ganguly et al. [SODA, 2017] introduced the parameterized BWT…
Given a pattern $P$ and a text $T$, both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of $P$ occurs in $T$. The indexed version of this problem, i.e., preprocessing a…
Due to the exponential growth of genomic data, constructing dedicated data structures has become the principal bottleneck in common bioinformatics applications. In particular, the Burrows-Wheeler Transform (BWT) is the basis of some of the…
We introduce space- and time-efficient algorithms and data structures for the offline set intersection problem. We show that a sorted integer set $S \subseteq [0{..}u)$ of $n$ elements can be represented using compressed space while…
This paper addresses the problem of collaborative navigation in an unknown environment, where two robots, referred to in the sequel as the Seeker and the Supporter, traverse the space simultaneously. The Supporter assists the Seeker by…
We address the problem of summarizing embedded tree patterns extracted from large data trees. We do so by defining and mining closed and maximal embedded unordered tree patterns from a single large data tree. We design an embedded frequent…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…
Stochastic resetting has attracted significant attention in recent years due to its wide-ranging applications across physics, biology, and search processes. In most existing studies, however, resetting events are governed by an external…
In this paper we investigate the problem of partitioning an input string T in such a way that compressing individually its parts via a base-compressor C gets a compressed output that is shorter than applying C over the entire T at once.…
We consider the well-studied pattern counting problem: given a permutation $\pi \in \mathbb{S}_n$ and an integer $k > 1$, count the number of order-isomorphic occurrences of every pattern $\tau \in \mathbb{S}_k$ in $\pi$. Our first result…
The most fundamental problem considered in algorithms for text processing is pattern matching: given a pattern $p$ of length $m$ and a text $t$ of length $n$, does $p$ occur in $t$? Multiple versions of this basic question have been…
We consider the problem of augmenting an $n$-vertex tree with one shortcut in order to minimize the diameter of the resulting graph. The tree is embedded in an unknown space and we have access to an oracle that, when queried on a pair of…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
In this paper we consider the following modification of the iterative search problem. We are given a tree $T$, so that a dynamic catalog $C(v)$ is associated with every tree node $v$. For any $x$ and for any node-to-root path $\pi$ in $T$,…
We address the problem of efficiently gathering correlated data from a wired or a wireless sensor network, with the aim of designing algorithms with provable optimality guarantees, and understanding how close we can get to the known…
We introduce exponential search trees as a novel technique for converting static polynomial space search structures for ordered sets into fully-dynamic linear space data structures. This leads to an optimal bound of O(sqrt(log n/loglog n))…
We show how to represent sets in a linear space data structure such that expressions involving unions and intersections of sets can be computed in a worst-case efficient way. This problem has applications in e.g. information retrieval and…
Permutation patterns and pattern avoidance have been intensively studied in combinatorics and computer science, going back at least to the seminal work of Knuth on stack-sorting (1968). Perhaps the most natural algorithmic question in this…
We consider the replica placement problem: given a graph with clients and nodes, place replicas on a minimum set of nodes to serve all the clients; each client is associated with a request and maximum distance that it can travel to get…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…