惯性聚合 高效追踪和阅读你感兴趣的博客、新闻、科技资讯
阅读原文 在惯性聚合中打开

推荐订阅源

奇客Solidot–传递最新科技情报
奇客Solidot–传递最新科技情报
L
LangChain Blog
让小产品的独立变现更简单 - ezindie.com
让小产品的独立变现更简单 - ezindie.com
Recent Announcements
Recent Announcements
大猫的无限游戏
大猫的无限游戏
罗磊的独立博客
MongoDB | Blog
MongoDB | Blog
博客园 - 【当耐特】
博客园 - 叶小钗
I
InfoQ
MyScale Blog
MyScale Blog
H
Help Net Security
月光博客
月光博客
Vercel News
Vercel News
B
Blog
酷 壳 – CoolShell
酷 壳 – CoolShell
D
DataBreaches.Net
Cyber Security Advisories - MS-ISAC
Cyber Security Advisories - MS-ISAC
N
Netflix TechBlog - Medium
宝玉的分享
宝玉的分享
WordPress大学
WordPress大学
GbyAI
GbyAI
Blog — PlanetScale
Blog — PlanetScale
博客园 - Franky

math.CO updates on arXiv.org

Complement Submodular Information Measures for Balanced and Robust Data Selection A Proof of a Conjecture on Positive and Negative Square Energies of Unicyclic Graphs Laplacian Spectrum of the Weakly Zero-Divisor Graph of a Finite Commutative Ring An identity for second Eulerian numbers via lattice-point counting $t$-tone edge coloring of graphs Constructing Maximal Bumpless Pipedreams for Double Grothendieck Polynomials Mubayi's Polynomial-Ideal Conjecture and Cover-Ideal Turán Methods Implicit Binarization via Complex Phase Dynamics in Combinatorial Optimization The limits of Schur multipliers in Pólya conversion problems for the $q$-permanent function Universality theorems for generalized splines Framing Triangulations for Arbitrary Integer Flow Polytopes On the Common Generalization of Gentle Algebras and Framed Directed Acyclic Graphs The complexity of frugal digraph homomorphisms Chaotic and periodic behavior of jeu de taquin on infinite Young tableaux Enumerating Pattern Avoiding Parking Functions Incidence toric ideals and three-point functions Unique Winning Opening Move in Three-Row Chomp Strong majority colorings of graphs A Balancing Theorem for Spanning Trees of Rectangular Grid Graphs Spectral radius and edge-disjoint connected factors of graphs New invariants for rank metric codes, with applications to the classification of rank two semifields of order 256 Flexible DP-4-coloring of planar graphs without 4-cycles and intersecting triangles Balanced intersection size distributions in projective planes List Reconstruction Problem with List Size Two Is Dimensionality a Barrier for Retrieval Models? The INIEP: Irreducible and Positive Realizations The number of Pfaffian orientations on punctured polygonally cellulated surfaces Explicit Construction of Polytopes whose Ehrhart Polynomials Realize any Given Sign Pattern Finite-state enumeration of adjacency-constrained 132-avoiding permutations AMDS and quantum AMDS Constacyclic codes of length $4p^ς$ over $\mathbb{F}_{{p}^{m}}$
Genome assembly, from practice to theory: safe, complete ...
Massimo Cairo, Romeo Rizzi, Alexandru I. Tomescu, Elia C. Zirond · 2020-02-25 · via math.CO updates on arXiv.org

Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Even though it is one of the key problems in Bioinformatics, it is generally lacking major theoretical advances. Its hardness stems both from practical issues (size and errors of real data), and from the fact that problem formulations inherently admit multiple solutions. Given these, at their core, most state-of-the-art assemblers are based on finding non-branching paths (unitigs) in an assembly graph. If one defines a genome assembly solution as a closed arc-covering walk of the graph, then unitigs appear in all solutions, being thus safe partial solutions. All all such safe walks were recently characterized as omnitigs, leading to the first safe and complete genome assembly algorithm. Even if omnitig finding was improved to quadratic time, it remained open whether the crucial linear-time feature of finding unitigs can be attained with omnitigs. We describe a surprising $O(m)$-time algorithm to identify all maximal omnitigs of a graph with $n$ nodes and $m$ arcs, notwithstanding the existence of families of graphs with $Θ(mn)$ total maximal omnitig size. This is based on the discovery of a family of walks (macrotigs) with the property that all the non-trivial omnitigs are univocal extensions of subwalks of a macrotig, with two consequences: (1) A linear-time output-sensitive algorithm enumerating all maximal omnitigs. (2) A compact $O(m)$ representation of all maximal omnitigs, which allows, e.g., for $O(m)$-time computation of various statistics on them. Our results close a long-standing theoretical question inspired by practical genome assemblers, originating with the use of unitigs in 1995. We envision our results to be at the core of a reverse transfer from theory to practical and complete genome assembly programs, as has been the case for other key Bioinformatics problems.