Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states

Fitch method for inferring ancestral state

Inducibility of d-ary trees

CITATION: Czabarka, E. et al. 2020. Inducibility of d-ary trees. Discrete Mathematics, 343(2). doi:10.1016/j.disc.2019.111671.The original publication is available at https://www.sciencedirect.com/journal/discrete-mathematicsImitating the binary inducibility, a recently introduced invariant of binary trees (Cz- abarka et al., 2017), we initiate the study of the inducibility of d-ary trees (rooted trees whose vertex outdegrees are bounded from above by d ≥ 2). We determine the exact inducibility for stars and binary caterpillars. For T in the family of strictly d-ary trees (every vertex has 0 or d children), we prove that the difference between the maximum density of a d-ary tree D in T and the inducibility of D is of order O(|T |−1/2) compared to the general case where it is shown that the difference is O(|T |−1) which, in particular, responds positively to a conjecture on the inducibility in binary trees. We also discover that the inducibility of a binary tree in d-ary trees is independent of d. Furthermore, we establish a general lower bound on the inducibility and also provide a bound for some special trees. Moreover, we find that the maximum inducibility is attained for binary caterpillars for every d.https://www.sciencedirect.com/science/article/pii/S0012365X19303498Publishers versio

Rainbow Turan Methods for Trees

The rainbow Turan number, a natural extension of the well-studied traditionalTuran number, was introduced in 2007 by Keevash, Mubayi, Sudakov and Verstraete. The rainbow Tur ́an number of a graph F , ex*(n, F ), is the largest number of edges for an n vertex graph G that can be properly edge colored with no rainbow F subgraph. Chapter 1 of this dissertation gives relevant definitions and a brief history of extremal graph theory. Chapter 2 defines k-unique colorings and the related k-unique Turan number and provides preliminary results on this new variant. In Chapter 3, we explore the reduction method for finding upper bounds on rainbow Turan numbers and use this to inform results for the rainbow Turan numbers of specific families of trees. These results are used in Chapter 4 to prove that the rainbow Turan numbers of all trees are linear in n, which correlates to a well-known property of the traditional Turan numbers of trees. We discuss improvements to the constant term in Chapters 4 and 5, and conclude with a discussion on avenues for future work

A 'stochastic safety radius' for distance-based tree reconstruction

A variety of algorithms have been proposed for reconstructing trees that show the evolutionary relationships between species by comparing differences in genetic data across present-day taxa. If the leaf-to-leaf distances in a tree can be accurately estimated, then it is possible to reconstruct this tree from these estimated distances, using polynomial-time methods such as the popular `Neighbor-Joining' algorithm. There is a precise combinatorial condition under which distance-based methods are guaranteed to return a correct tree (in full or in part) based on the requirement that the input distances all lie within some `safety radius' of the true distances. Here, we explore a stochastic analogue of this condition, and mathematically establish upper and lower bounds on this `stochastic safety radius' for distance-based tree reconstruction methods. Using simulations, we show how this notion provides a new way to compare the performance of distance-based tree reconstruction methods. This may help explain why Neighbor-Joining performs so well, as its stochastic safety radius appears close to optimal (while its more classical safety radius is the same as many other less accurate methods).Comment: 18 pages, 1 figure, 4 table

Limit Laws for Functions of Fringe trees for Binary Search Trees and Recursive Trees

We prove limit theorems for sums of functions of subtrees of binary search trees and random recursive trees. In particular, we give simple new proofs of the fact that the number of fringe trees of size $k=k_n$ in the binary search tree and the random recursive tree (of total size $n$) asymptotically has a Poisson distribution if $k\rightarrow\infty$, and that the distribution is asymptotically normal for $k=o(\sqrt{n})$. Furthermore, we prove similar results for the number of subtrees of size $k$ with some required property $P$, for example the number of copies of a certain fixed subtree $T$. Using the Cram\'er-Wold device, we show also that these random numbers for different fixed subtrees converge jointly to a multivariate normal distribution. As an application of the general results, we obtain a normal limit law for the number of $\ell$-protected nodes in a binary search tree or random recursive tree. The proofs use a new version of a representation by Devroye, and Stein's method (for both normal and Poisson approximation) together with certain couplings