Finding Diverse Strings and Longest Common Subsequences in a Graph
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| Format: | Preprint |
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2024
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| author | Shida, Yuto Punzi, Giulia Kobayashi, Yasuaki Uno, Takeaki Arimura, Hiroki |
| author_facet | Shida, Yuto Punzi, Giulia Kobayashi, Yasuaki Uno, Takeaki Arimura, Hiroki |
| contents | In this paper, we study for the first time the Diverse Longest Common Subsequences (LCSs) problem under Hamming distance. Given a set of a constant number of input strings, the problem asks to decide if there exists some subset $\mathcal X$ of $K$ longest common subsequences whose diversity is no less than a specified threshold $Δ$, where we consider two types of diversities of a set $\mathcal X$ of strings of equal length: the Sum diversity and the Min diversity defined as the sum and the minimum of the pairwise Hamming distance between any two strings in $\mathcal X$, respectively. We analyze the computational complexity of the respective problems with Sum- and Min-diversity measures, called the Max-Sum and Max-Min Diverse LCSs, respectively, considering both approximation algorithms and parameterized complexity. Our results are summarized as follows. When $K$ is bounded, both problems are polynomial time solvable. In contrast, when $K$ is unbounded, both problems become NP-hard, while Max-Sum Diverse LCSs problem admits a PTAS. Furthermore, we analyze the parameterized complexity of both problems with combinations of parameters $K$ and $r$, where $r$ is the length of the candidate strings to be selected. Importantly, all positive results above are proven in a more general setting, where an input is an edge-labeled directed acyclic graph (DAG) that succinctly represents a set of strings of the same length. Negative results are proven in the setting where an input is explicitly given as a set of strings. The latter results are equipped with an encoding such a set as the longest common subsequences of a specific input string set. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2405_00131 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Finding Diverse Strings and Longest Common Subsequences in a Graph Shida, Yuto Punzi, Giulia Kobayashi, Yasuaki Uno, Takeaki Arimura, Hiroki Data Structures and Algorithms Computational Complexity Formal Languages and Automata Theory In this paper, we study for the first time the Diverse Longest Common Subsequences (LCSs) problem under Hamming distance. Given a set of a constant number of input strings, the problem asks to decide if there exists some subset $\mathcal X$ of $K$ longest common subsequences whose diversity is no less than a specified threshold $Δ$, where we consider two types of diversities of a set $\mathcal X$ of strings of equal length: the Sum diversity and the Min diversity defined as the sum and the minimum of the pairwise Hamming distance between any two strings in $\mathcal X$, respectively. We analyze the computational complexity of the respective problems with Sum- and Min-diversity measures, called the Max-Sum and Max-Min Diverse LCSs, respectively, considering both approximation algorithms and parameterized complexity. Our results are summarized as follows. When $K$ is bounded, both problems are polynomial time solvable. In contrast, when $K$ is unbounded, both problems become NP-hard, while Max-Sum Diverse LCSs problem admits a PTAS. Furthermore, we analyze the parameterized complexity of both problems with combinations of parameters $K$ and $r$, where $r$ is the length of the candidate strings to be selected. Importantly, all positive results above are proven in a more general setting, where an input is an edge-labeled directed acyclic graph (DAG) that succinctly represents a set of strings of the same length. Negative results are proven in the setting where an input is explicitly given as a set of strings. The latter results are equipped with an encoding such a set as the longest common subsequences of a specific input string set. |
| title | Finding Diverse Strings and Longest Common Subsequences in a Graph |
| topic | Data Structures and Algorithms Computational Complexity Formal Languages and Automata Theory |
| url | https://arxiv.org/abs/2405.00131 |