Related papers: Linear-size CDAWG: new repetition-aware indexing a…
Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
Two important similarity measures between sequences are the longest common subsequence (LCS) and the dynamic time warping distance (DTWD). The computations of these measures for two given sequences are central tasks in a variety of…
Palindromes are strings that read the same forward and backward. The computation of palindromic structures within strings is a fundamental problem in string algorithms, being motivated by potential applications in formal language theory and…
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 --…
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…
Given strings $P$ of length $m$ and $T$ of length $n$ over an alphabet of size $\sigma$, the string matching with $k$-mismatches problem is to find the positions of all the substrings in $T$ that are at Hamming distance at most $k$ from…
We present an efficient algorithm for computing the LZ78 factorization of a text, where the text is represented as a straight line program (SLP), which is a context free grammar in the Chomsky normal form that generates a single string.…
We revisit the fundamental problem of dictionary look-up with mismatches. Given a set (dictionary) of $d$ strings of length $m$ and an integer $k$, we must preprocess it into a data structure to answer the following queries: Given a query…
We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm…
The sensitivity of a string compression algorithm $C$ asks how much the output size $C(T)$ for an input string $T$ can increase when a single character edit operation is performed on $T$. This notion enables one to measure the robustness of…
We introduce the first self-index based on the Lempel-Ziv 1977 compression format (LZ77). It is particularly competitive for highly repetitive text collections such as sequence databases of genomes of related species, software repositories,…
We introduce a new approach to LZ77 factorization that uses O(n/d) words of working space and O(dn) time for any d >= 1 (for polylogarithmic alphabet sizes). We also describe carefully engineered implementations of alternative approaches to…
We present a novel compressed dynamic self-index for highly repetitive text collections. Signature encoding is a compressed dynamic self-index for highly repetitive texts and has a large disadvantage that the pattern search for short…
Conventional representation learning algorithms for knowledge graphs (KG) map each entity to a unique embedding vector. Such a shallow lookup results in a linear growth of memory consumption for storing the embedding matrix and incurs high…
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…
Structural measures of graphs, such as treewidth, are central tools in computational complexity resulting in efficient algorithms when exploiting the parameter. It is even known that modern SAT solvers work efficiently on instances of small…
This study presents a novel deterministic optimization algorithm based on a special variant of the Linear Congruential Generator (LCG). While conventional algorithms generally operate within the search space, the introduced technique…
The identification of repeating patterns in discrete grids is rudimentary within symbolic reasoning, algorithm synthesis and structural optimization across diverse computational domains. Although statistical approaches targeting noisy data…
A constant weight binary code consists of $n$-bit binary codewords, each with exactly $w$ bits equal to 1, such that any two codewords are at least Hamming distance $d$ apart. $A(n,d,w)$ is the maximum size of a constant weight binary code…