Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2307.13695

A Compact DAG for Storing and Searching Maximal Common Subsequences

Alessio Conte·Roberto Grossi·Giulia Punzi·Takeaki Uno
View original source ↗Read source document ↗Export metadata ↓

Abstract

Maximal Common Subsequences (MCSs) between two strings X and Y are subsequences of both X and Y that are maximal under inclusion. MCSs relax and generalize the well known and widely used concept of Longest Common Subsequences (LCSs), which can be seen as MCSs of maximum length. While the number both LCSs and MCSs can be exponential in the length of the strings, LCSs have been long exploited for string and text analysis, as simple compact representations of all LCSs between two strings, built via dynamic programming or automata, have been known since the '70s. MCSs appear to have a more challenging structure: even listing them efficiently was an open problem open until recently, thus narrowing the complexity difference between the two problems, but the gap remained significant. In this paper we close the complexity gap: we show how to build DAG of polynomial size-in polynomial time-which allows for efficient operations on the set of all MCSs such as enumeration in Constant Amortized Time per solution (CAT), counting, and random access to the i-th element (i.e., rank and select operations). Other than improving known algorithmic results, this work paves the way for new sequence analysis methods based on MCSs.

Explore related subjects

cs.DS

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Alessio Conte, Roberto Grossi, Giulia Punzi, Takeaki Uno. 2023-07-25. A Compact DAG for Storing and Searching Maximal Common Subsequences. https://arxiv.org/abs/2307.13695

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Beyond Kruskal: Polynomial-Time Tensor Decomposition under the Lovitz-Petrov Condition

Identifiability criteria certify that a given tensor decomposition is a unique rank decomposition. Kruskal's classical condition is one of the best-known deterministic criteria for identifiability. However, no polynomial-time decomposition algorithm is known under the Kruskal condition, and verifying the condition itself is NP-hard. Lovitz and Petrov introduced a strictly more general identifiability condition which, in contrast, is polynomial-time verifiable, but no polynomial-time decomposition algorithm was previously known under this condition. We give a polynomial-time algorithm for tensor decomposition under the Lovitz--Petrov condition. Moreover, combining our algorithm with polynomial-time verification of the Lovitz--Petrov condition yields an efficient end-to-end certification procedure: after computing a decomposition, one can deterministically certify in polynomial time that it is unique and therefore of minimum rank. This contrasts with an arbitrary tensor decomposition, which certifies only an upper bound on the tensor rank, while determining tensor rank is NP-hard in general.

cs.DS↗
arXiv2026

Poisson Exchange Beyond Submodularity: Effective Approximation Algorithms for Offline and Online Subset Selection over Matroids

Over the past decade, a growing body of research has shown that $γ$-weak submodularity broadly arises in numerous subset selection tasks, including feature selection, neural network pruning, and video summarization. Despite its prevalence, maximizing a $γ$-weakly submodular function subject to a general matroid constraint remains challenging. To date, the only known approximation guarantee is the conservative $(1+1/γ)^{-2}$ factor established by \citet{chen2018weakly}. To improve upon this result, this paper proposes a novel algorithm called \MGPE, which repeatedly performs maximum-gain local exchanges through careful control of a non-homogeneous Poisson clock, and proves that this \MGPE\ can attain an approximation ratio arbitrarily close to $ρ_γ=1-\left(γ/(2-γ)\right)^{ \frac{γ^2}{2(1-γ)} }$. In sharp contrast to the previous guarantee, our obtained factor $ρ_γ$ not only strictly improves upon $(1+1/γ)^{-2}$ for every $γ\in(0,1]$, but also can asymptotically approach the optimal $(1-1/e)$-approximation for submodular maximization as $γ\to1$. Furthermore, we surprisingly find that when the matroid constraint reduces to a cardinality or the objective satisfies the stronger notion of $α$-weak DR-submodularity, \MGPE\ can automatically recover the tight approximation ratios of $1-e^{-γ}$ and $1-e^{-α}$, respectively. Here, $α\in(0,1]$ denotes the DR ratio.

cs.DS↗
arXiv2026

Approximating Prize-Collecting TSP below 1.556

The prize-collecting traveling salesperson problem is a variant of the metric traveling salesperson problem in which vertices may be left unvisited by paying their associated penalties. The objective is to minimize the length of the tour plus the total penalty of the unvisited vertices. Blauth, Klein, and Nägele gave the previously best-known LP-relative $1.599$-approximation. We show that a simpler version of their algorithm, obtained by omitting the splitting-off preprocessing before the tree decomposition, has an LP-relative approximation ratio of $1.555761$. The improvement comes entirely from a new analysis of the parity-correction step: a simple analysis already gives $1.56$, and the stated factor follows from a numerical parameter search with exact verification.

cs.DS↗