Arithmetic for Rooted Trees

We propose a new arithmetic for non-empty rooted unordered trees simply called trees. After discussing tree representation and enumeration, we define the operations of tree addition, multiplication and stretch, prove their properties, and show that all trees can be generated from a starting tree of one vertex. We then show how a given tree can be obtained as the sum or product of two trees, thus defining prime trees with respect to addition and multiplication. In both cases we show how primality can be decided in time polynomial in the number of vertices and we prove that factorization is unique. We then define negative trees and suggest dealing with tree equations, giving some preliminary results. Finally we comment on how our arithmetic might be useful, and discuss preceding studies that have some relations with our. To the best of our knowledge our approach and results are completely new aside for an earlier version of this work submitte as an arXiv manuscript.Comment: 18 pages, 8 figure

UPGMA and the normalized equidistant minimum evolution problem

UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a widely used clustering method. Here we show that UPGMA is a greedy heuristic for the normalized equidistant minimum evolution (NEME) problem, that is, finding a rooted tree that minimizes the minimum evolution score relative to the dissimilarity matrix among all rooted trees with the same leaf-set in which all leaves have the same distance to the root. We prove that the NEME problem is NP-hard. In addition, we present some heuristic and approximation algorithms for solving the NEME problem, including a polynomial time algorithm that yields a binary, rooted tree whose NEME score is within O(log2n) of the optimum

Algorithms for Combinatorial Systems: Well-Founded Systems and Newton Iterations

We consider systems of recursively defined combinatorial structures. We give algorithms checking that these systems are well founded, computing generating series and providing numerical values. Our framework is an articulation of the constructible classes of Flajolet and Sedgewick with Joyal's species theory. We extend the implicit species theorem to structures of size zero. A quadratic iterative Newton method is shown to solve well-founded systems combinatorially. From there, truncations of the corresponding generating series are obtained in quasi-optimal complexity. This iteration transfers to a numerical scheme that converges unconditionally to the values of the generating series inside their disk of convergence. These results provide important subroutines in random generation. Finally, the approach is extended to combinatorial differential systems.Comment: 61 page