Related papers: Succincter Text Indexing with Wildcards
Suffixient sets are a novel prefix array (PA) compression technique based on subsampling PA (rather than compressing the entire array like previous techniques used to do): by storing very few entries of PA (in fact, a compressed number of…
We consider the problem of designing succinct data structures for interval graphs with $n$ vertices while supporting degree, adjacency, neighborhood and shortest path queries in optimal time in the $\Theta(\log n)$-bit word RAM model. The…
One of the important factors that make a search engine fast and accurate is a concise and duplicate free index. In order to remove duplicate and near-duplicate documents from the index, a search engine needs a swift and reliable duplicate…
We give a new successor data structure which improves upon the index size of the P\v{a}tra\c{s}cu-Thorup data structures, reducing the index size from $O(n w^{4/5})$ bits to $O(n \log w)$ bits, with optimal probe complexity. Alternatively,…
Minimizers sampling is one of the most widely-used mechanisms for sampling strings [Roberts et al., Bioinformatics 2004]. Let $S=S[1]\ldots S[n]$ be a string over a totally ordered alphabet $\Sigma$. Further let $w\geq 2$ and $k\geq 1$ be…
Since the release of human genome sequences, one of the most important research issues is about indexing the genome sequences, and the suffix tree is most widely adopted for that purpose. The traditional suffix tree construction algorithms…
This paper presents a general technique for optimally transforming any dynamic data structure that operates on atomic and indivisible keys by constant-time comparisons, into a data structure that handles unbounded-length keys whose…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
We revisit the exact shortest unique substring (SUS) finding problem, and propose its approximate version where mismatches are allowed, due to its applications in subfields such as computational biology. We design a generic in-place…
We revisit the classic problem of simplex range searching and related problems in computational geometry. We present a collection of new results which improve previous bounds by multiple logarithmic factors that were caused by the use of…
Bille and G{\o}rtz (2011) recently introduced the problem of substring range counting, for which we are asked to store compactly a string $S$ of $n$ characters with integer labels in ([0, u]), such that later, given an interval ([a, b]) and…
Suppose that we are given a string $s$ of length $n$ over an alphabet $\{0,1,\ldots,n^{O(1)}\}$ and $\delta$ is the string complexity of $s$, a known compression measure. We describe an index on $s$ with $O(\delta\log\frac{n}{\delta})$…
The fully-functional succinct tree representation of Navarro and Sadakane (ACM Transactions on Algorithms, 2014) supports a large number of operations in constant time using $2n+o(n)$ bits. However, the full idea is hard to implement. Only…
To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on grammars. In this paper we show how, given a straight-line program with $r$ rules for a string (S [1..n]) whose…
In the search with wildcards problem [Ambainis, Montanaro, Quantum Inf.~Comput.'14], one's goal is to learn an unknown bit-string $x \in \{-1,1\}^n$. An algorithm may, at unit cost, test equality of any subset of the hidden string with a…
Approximate dictionary matching is a classic string matching problem (checking if a query string occurs in a collection of strings) with applications in, e.g., spellchecking, online catalogs, geolocation, and web searchers. We present a…
We propose new succinct representations of ordinal trees, which have been studied extensively. It is known that any $n$-node static tree can be represented in $2n + o(n)$ bits and a number of operations on the tree can be supported in…
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…
We consider how to assign labels to any undirected graph with n nodes such that, given the labels of two nodes and no other information regarding the graph, it is possible to determine the distance between the two nodes. The challenge in…
Pliable index coding considers a server with m messages, and n clients where each has as side information a subset of the messages. We seek to minimize the number of transmissions the server should make, so that each client receives (any)…