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

GbyAI
GbyAI
Microsoft Azure Blog
Microsoft Azure Blog
Jina AI
Jina AI
Hugging Face - Blog
Hugging Face - Blog
A
About on SuperTechFans
Y
Y Combinator Blog
D
DataBreaches.Net
I
InfoQ
Recent Announcements
Recent Announcements
Last Week in AI
Last Week in AI
G
Google Developers Blog
博客园_首页
博客园 - 司徒正美
V
V2EX
Stack Overflow Blog
Stack Overflow Blog
博客园 - 叶小钗
Engineering at Meta
Engineering at Meta
Apple Machine Learning Research
Apple Machine Learning Research
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
B
Blog
MongoDB | Blog
MongoDB | Blog
博客园 - 【当耐特】
D
Docker
量子位

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 $\mathbb{F}_{{p}^{m}}$
Relative Timing Information and Orthology in Evolutionary...
David Schaller, Tom Hartmann, Manuel Lafond, Nicolas Wieseke, Pe · 2022-12-05 · via math.CO updates on arXiv.org

Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree $T$ to vertices and edges of a species tree $S$. The relative timing of the last common ancestors of two extant genes (leaves of $T$) and the last common ancestors of the two species (leaves of $S$) in which they reside is indicative of horizontal gene transfers (HGT) and ancient duplications. Orthologous gene pairs, on the other hand, require that their last common ancestors coincides with a corresponding speciation event. The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph. Here we give a complete characterization in terms of informative and forbidden triples that can be read off the three graphs and provide a polynomial time algorithm for constructing an evolutionary scenario that explains the graphs, provided such a scenario exists. We show that every EDT graph is perfect. While the information about LDT and PDT graphs is necessary to recognize EDT graphs in polynomial-time for general scenarios, this extra information can be dropped in the HGT-free case. However, recognition of EDT graphs without knowledge of putative LDT and PDT graphs is NP-complete for general scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We finally connect the EDT graph to the alternative definitions of orthology that have been proposed for scenarios with horizontal gene transfer. With one exception, the corresponding graphs are shown to be colored cographs.