Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2402.03455

Median and Small Parsimony Problems on RNA trees

Bertrand Marchand·Yoann Anselmetti·Manuel Lafond·Aïda Ouangraoua
View original source ↗Read source document ↗Export metadata ↓

Abstract

Motivation: Non-coding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature of molecular function. Consequently, within an RNA functional family, secondary structures are generally more evolutionarily conserved than sequences. Conversely, homologous RNA families grouped within an RNA clan share ancestors but typically exhibit structural differences. Inferring the evolution of RNA structures within RNA families and clans is crucial for gaining insights into functional adaptations over time and providing clues about the Ancient RNA World Hypothesis. Results: We introduce the median problem and the small parsimony problem for ncRNA families, where secondary structures are represented as leaf-labelled trees. We utilize the Robinson-Foulds (RF) tree distance, which corresponds to a specific edit distance between RNA trees, and a new metric called the Internal-Leafset (IL) distance. While the RF tree distance compares sets of leaves descending from internal nodes of two RNA trees, the IL distance compares the collection of leaf-children of internal nodes. The latter is better at capturing differences in structural elements of RNAs than the RF distance, which is more focused on base pairs. We also consider a more general tree edit distance that allows the mapping of base pairs that are not perfectly aligned. We study the theoretical complexity of the median problem and the small parsimony problem under the three distance metrics and various biologically-relevant constraints, and we present polynomial-time maximum parsimony algorithms for solving some versions of the problems. Our algorithms are applied to ncRNA families from the RFAM database, illustrating their practical utility

Explore related subjects

cs.DS

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Bertrand Marchand, Yoann Anselmetti, Manuel Lafond, Aïda Ouangraoua. 2024-02-05. Median and Small Parsimony Problems on RNA trees. https://arxiv.org/abs/2402.03455

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

Linear-Query Deterministic Approximation for Non-monotone Submodular Maximization under a Knapsack Constraint

Submodular maximization under a knapsack constraint (SMK) is a fundamental combinatorial optimization problem with broad applications across machine learning and data mining. Motivated by large-scale applications where query efficiency is paramount, we study non-monotone SMK and focus on deterministic algorithms with linear query complexity. Prior deterministic linear-query algorithms achieve at best a $1/5-\varepsilon$ approximation, falling short of the $1/4-\varepsilon$ ratio attainable by randomized algorithms. We close this gap by presenting a deterministic $(1/4-\varepsilon)$-approximation with $O(n\log^2(1/\varepsilon)/\varepsilon^2)$ queries. Our approach partitions the analysis based on the cost of the largest optimal element $r$: when the cost of $r$ is moderate, we refine the threshold-twin-greedy framework via residual-budget enumeration to tighten the analysis; when the cost of $r$ is large, we reduce the problem to bicriteria submodular maximization. As a secondary contribution, we obtain a $(1/2-\varepsilon, O(1/\varepsilon))$-bicriteria approximation with $O(n\log(1/\varepsilon)/\varepsilon^2)$ queries, improving over the previous $O(n^2/\varepsilon)$ query bound.

cs.DS↗