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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 $\mathbb{F}_{{p}^{m}}$
Agreement forests of caterpillar trees: complexity, kerne...
Steven Kelk, Ruben Meuwese · 2023-07-23 · via math.CO updates on arXiv.org

Given a set $X$ of species, a phylogenetic tree is an unrooted binary tree whose leaves are bijectively labelled by $X$. Such trees can be used to show the way species evolve over time. One way of understanding how topologically different two phylogenetic trees are, is to construct a minimum-size agreement forest: a partition of $X$ into the smallest number of blocks, such that the blocks induce homeomorphic, non-overlapping subtrees in both trees. This comparison yields insight into commonalities and differences in the evolution of $X$ across the two trees. Computing a smallest agreement forest is NP-hard (Hein, Jiang, Wang and Zhang, Discrete Applied Mathematics 71(1-3), 1996). In this work we study the problem on caterpillars, which are path-like phylogenetic trees. We will demonstrate that, even if we restrict the input to this highly restricted subclass, the problem remains NP-hard and is in fact APX-hard. Furthermore we show that for caterpillars two standard reductions rules well known in the literature yield a tight kernel of size at most $7k$, compared to $15k$ for general trees (Kelk and Simone, SIAM Journal on Discrete Mathematics 33(3), 2019). Finally we demonstrate that we can determine if two caterpillars have an agreement forest with at most $k$ blocks in $O^*(2.49^k)$ time, compared to $O^*(3^k)$ for general trees (Chen, Fan and Sze, Theoretical Computater Science 562, 2015), where $O^*(.)$ suppresses polynomial factors.