Related papers: Computing Matching Statistics on Repetitive Texts
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…
We study various models of associative memories with sparse information, i.e. a pattern to be stored is a random string of $0$s and $1$s with about $\log N$ $1$s, only. We compare different synaptic weights, architectures and retrieval…
Maximal repetition of a string is the maximal length of a repeated substring. This paper investigates maximal repetition of strings drawn from stochastic processes. Strengthening previous results, two new bounds for the almost sure growth…
It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In…
We present CREST (Compact Retrieval-Based Speculative Decoding), a redesign of REST that allows it to be effectively "compacted". REST is a drafting technique for speculative decoding based on retrieving exact n-gram matches of the most…
Lempel-Ziv (LZ77 or, briefly, LZ) is one of the most effective and widely-used compressors for repetitive texts. However, the existing efficient methods computing the exact LZ parsing have to use linear or close to linear space to index the…
In this paper we revisit the classical regular expression matching problem, namely, given a regular expression $R$ and a string $Q$, decide if $Q$ matches one of the strings specified by $R$. Let $m$ and $n$ be the length of $R$ and $Q$,…
We consider the classical exact multiple string matching problem. Our solution is based on $q$-grams combined with pattern superimposition, bit-parallelism and alphabet size reduction. We discuss the pros and cons of the various…
The LZ-End parsing [Kreft & Navarro, 2011] of an input string yields compression competitive with the popular Lempel-Ziv 77 scheme, but also allows for efficient random access. Kempa and Kosolobov showed that the parsing can be computed in…
In this paper we present $LCSk$++: a new metric for measuring the similarity of long strings, and provide an algorithm for its efficient computation. With ever increasing size of strings occuring in practice, e.g. large genomes of plants…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…
In this paper, we explore worst-case solutions for the problems of single and multiple matching on strings in the word RAM model with word length w. In the first problem, we have to build a data structure based on a pattern p of length m…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
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…
Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to…
Systems often repeat the same prompt to large language models (LLMs) and aggregate responses to improve reliability. This short note analyzes an estimator of the self-consistency of LLMs and the tradeoffs it induces under a fixed compute…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
The Cartesian tree of a sequence captures the relative order of the sequence's elements. In recent years, Cartesian tree matching has attracted considerable attention, particularly due to its applications in time series analysis. Consider a…
Park et al. [TCS 2020] observed that the similarity between two (numerical) strings can be captured by the Cartesian trees: The Cartesian tree of a string is a binary tree recursively constructed by picking up the smallest value of the…