相关论文: Partial Data Compression and Text Indexing via Opt…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In the \emph{deterministic} variant the goal is to solve the string…
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…
The Burrows-Wheeler Transform is a string transformation that plays a fundamental role for the design of self-indexing compressed data structures. Over the years, researchers have successfully extended this transformation outside the…
We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…
The real-world effectiveness of deep neural networks often depends on their latency, thereby necessitating optimization techniques that can reduce a model's inference time while preserving its performance. One popular approach is to…
The \Problem{knapsack} problem is a fundamental problem in combinatorial optimization. It has been studied extensively from theoretical as well as practical perspectives as it is one of the most well-known NP-hard problems. The goal is to…
Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for…
Grammar compression is a general compression framework in which a string $T$ of length $N$ is represented as a context-free grammar of size $n$ whose language contains only $T$. In this paper, we focus on studying the limitations of…
The index selection problem (ISP) is an important problem for accelerating the execution of relational queries, and it has received a lot of attention as a combinatorial knapsack problem in the past. Various solutions to this very hard…
We consider the basic problem of learning an unknown partition of $n$ elements into at most $k$ sets using simple queries that reveal information about a small subset of elements. Our starting point is the well-studied pairwise same-set…
In this paper we study lower bounds for the fundamental problem of text indexing with mismatches and differences. In this problem we are given a long string of length $n$, the "text", and the task is to preprocess it into a data structure…
We give an algebraic, determinant-based algorithm for the K-Cycle problem, i.e., the problem of finding a cycle through a set of specified elements. Our approach gives a simple FPT algorithm for the problem, matching the $O^*(2^{|K|})$…
The problem of dictionary matching is a classical problem in string matching: given a set S of d strings of total length n characters over an (not necessarily constant) alphabet of size sigma, build a data structure so that we can match in…
In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…
Stemming or suffix stripping, an important part of the modern Information Retrieval systems, is to find the root word (stem) out of a given cluster of words. Existing algorithms targeting this problem have been developed in a haphazard…
The $r$-index represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude in query time. Its space usage, $O(r)$ where $r$ is the number of runs in the…
The suffix array is a fundamental data structure for many applications that involve string searching and data compression. Designing time/space-efficient suffix array construction algorithms has attracted significant attention and…
We consider compact representations of collections of similar strings that support random access queries. The collection of strings is given by a rooted tree where edges are labeled by an edit operation (inserting, deleting, or replacing a…
An archetypal problem discussed in computer science is the problem of searching for a given number in a given set of numbers. Other than sequential search, the classic solution is to sort the list of numbers and then apply binary search.…
Suffix arrays and LCP arrays are one of the most fundamental data structures widely used for various kinds of string processing. We consider two problems for a read-only string of length $N$ over an integer alphabet $[1, \dots, \sigma]$ for…