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pro vyhledávání: '"P. Pissis"'
In many real-world database systems, a large fraction of the data is represented by strings: sequences of letters over some alphabet. This is because strings can easily encode data arising from different sources. It is often crucial to represent such
Externí odkaz:
http://arxiv.org/abs/2407.11819
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 two integer
Externí odkaz:
http://arxiv.org/abs/2405.04052
Strings in the real world are often encoded with some level of uncertainty. In the character-level uncertainty model, an uncertain string $X$ of length $n$ on an alphabet $\Sigma$ is a sequence of $n$ probability distributions over $\Sigma$. Given an
Externí odkaz:
http://arxiv.org/abs/2403.14256
Autor:
Charalampopoulos, Panagiotis, Pissis, Solon P., Radoszewski, Jakub, Rytter, Wojciech, Waleń, Tomasz, Zuba, Wiktor
In the $k$-Edit Circular Pattern Matching ($k$-Edit CPM) problem, we are given a length-$n$ text $T$, a length-$m$ pattern $P$, and a positive integer threshold $k$, and we are to report all starting positions of the substrings of $T$ that are at edi
Externí odkaz:
http://arxiv.org/abs/2402.14550
The weighted ancestor problem on a rooted node-weighted tree $T$ is a generalization of the classic predecessor problem: construct a data structure for a set of integers that supports fast predecessor queries. Both problems are known to require $\Ome
Externí odkaz:
http://arxiv.org/abs/2311.15777
Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for applications in
Externí odkaz:
http://arxiv.org/abs/2310.09023
Autor:
Bille, Philip, Gørtz, Inge Li, Lewenstein, Moshe, Pissis, Solon P., Rotenberg, Eva, Steiner, Teresa Anna
In Gapped String Indexing, the goal is to compactly represent a string $S$ of length $n$ such that for any query consisting of two strings $P_1$ and $P_2$, called patterns, and an integer interval $[\alpha, \beta]$, called gap range, we can quickly f
Externí odkaz:
http://arxiv.org/abs/2211.16860
Autor:
Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba
Publikováno v:
Frontiers in Bioinformatics, Vol 4 (2024)
IntroductionAn elastic-degenerate (ED) string is a sequence of sets of strings. It can also be seen as a directed acyclic graph whose edges are labeled by strings. The notion of ED strings was introduced as a simple alternative to variation and seque
Externí odkaz:
https://doaj.org/article/0fbb0868164048a0936e75501aa9841c
Autor:
Bernardini, Giulia, Gabory, Estéban, Pissis, Solon P., Stougie, Leen, Sweering, Michelle, Zuba, Wiktor
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all occurrenc
Externí odkaz:
http://arxiv.org/abs/2209.01095
Autor:
Charalampopoulos, Panagiotis, Kociumaka, Tomasz, Radoszewski, Jakub, Pissis, Solon P., Rytter, Wojciech, Waleń, Tomasz, Zuba, Wiktor
We consider approximate circular pattern matching (CPM, in short) under the Hamming and edit distance, in which we are given a length-$n$ text $T$, a length-$m$ pattern $P$, and a threshold $k>0$, and we are to report all starting positions of fragme
Externí odkaz:
http://arxiv.org/abs/2208.08915