Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2208.14315

Sorting Genomes by Prefix Double-Cut-and-Joins

Guillaume Fertin·Géraldine Jean·Anthony Labarre
View original source ↗Read source document ↗Export metadata ↓

Abstract

In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and recombine the severed endpoints in one of two possible ways: one of these options corresponds to a prefix reversal, which reverses the order of elements between the two cuts (as well as their signs in the signed case). Depending on whether we consider both options or reversals only, our main results are: (1) new structural lower bounds based on the breakpoint graph for sorting by unsigned prefix reversals, unsigned prefix DCJs, or signed prefix DCJs; (2) a polynomial-time algorithm for sorting by signed prefix DCJs, thus answering an open question in [8]; (3) a 3/2-approximation for sorting by unsigned prefix DCJs, which is, to the best of our knowledge, the first sorting by {\em prefix} rearrangements problem that admits an approximation ratio strictly smaller than 2 (with the obvious exception of the polynomial-time solvable problems); and finally, (4) an FPT algorithm for sorting by unsigned prefix DCJs parameterised by the number of breakpoints in the genome.

Explore related subjects

cs.DS

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Guillaume Fertin, Géraldine Jean, Anthony Labarre. 2022-08-30. Sorting Genomes by Prefix Double-Cut-and-Joins. https://arxiv.org/abs/2208.14315

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↗