The Ramsey Theory of Henson graphs

Analogues of Ramsey's Theorem for infinite structures such as the rationals or the Rado graph have been known for some time. In this context, one looks for optimal bounds, called degrees, for the number of colors in an isomorphic substructure rather than one color, as that is often impossible. Such theorems for Henson graphs however remained elusive, due to lack of techniques for handling forbidden cliques. Building on the author's recent result for the triangle-free Henson graph, we prove that for each $k\ge 4$, the $k$-clique-free Henson graph has finite big Ramsey degrees, the appropriate analogue of Ramsey's Theorem. We develop a method for coding copies of Henson graphs into a new class of trees, called strong coding trees, and prove Ramsey theorems for these trees which are applied to deduce finite big Ramsey degrees. The approach here provides a general methodology opening further study of big Ramsey degrees for ultrahomogeneous structures. The results have bearing on topological dynamics via work of Kechris, Pestov, and Todorcevic and of Zucker.Comment: 75 pages. Substantial revisions in the presentation. Submitte

Classical and consecutive pattern avoidance in rooted forests

Following Anders and Archer, we say that an unordered rooted labeled forest avoids the pattern $\sigma\in\mathcal{S}_k$ if in each tree, each sequence of labels along the shortest path from the root to a vertex does not contain a subsequence with the same relative order as $\sigma$. For each permutation $\sigma\in\mathcal{S}_{k-2}$, we construct a bijection between $n$-vertex forests avoiding $(\sigma)(k-1)k=\sigma(1)\cdots\sigma(k-2)(k-1)k$ and $n$-vertex forests avoiding $(\sigma)k(k-1)=\sigma(1)\cdots\sigma(k-2)k(k-1)$, giving a common generalization of results of West on permutations and Anders--Archer on forests. We further define a new object, the forest-Young diagram, which we use to extend the notion of shape-Wilf equivalence to forests. In particular, this allows us to generalize the above result to a bijection between forests avoiding $\{(\sigma_1)k(k-1), (\sigma_2)k(k-1), \dots, (\sigma_\ell) k(k-1)\}$ and forests avoiding $\{(\sigma_1)(k-1)k, (\sigma_2)(k-1)k, \dots, (\sigma_\ell) (k-1)k\}$ for $\sigma_1, \dots, \sigma_\ell \in \mathcal{S}_{k-2}$. Furthermore, we give recurrences enumerating the forests avoiding $\{123\cdots k\}$, $\{213\}$, and other sets of patterns. Finally, we extend the Goulden--Jackson cluster method to study consecutive pattern avoidance in rooted trees as defined by Anders and Archer. Using the generalized cluster method, we prove that if two length-$k$ patterns are strong-c-forest-Wilf equivalent, then up to complementation, the two patterns must start with the same number. We also prove the surprising result that the patterns $1324$ and $1423$ are strong-c-forest-Wilf equivalent, even though they are not c-Wilf equivalent with respect to permutations.Comment: 39 pages, 11 figure

Trees and Markov convexity

We show that an infinite weighted tree admits a bi-Lipschitz embedding into Hilbert space if and only if it does not contain arbitrarily large complete binary trees with uniformly bounded distortion. We also introduce a new metric invariant called Markov convexity, and show how it can be used to compute the Euclidean distortion of any metric tree up to universal factors

Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.Comment: Version submitted to Algorithms for Molecular Biology. A number of fixes from previous versio

Positional Games

Positional games are a branch of combinatorics, researching a variety of two-player games, ranging from popular recreational games such as Tic-Tac-Toe and Hex, to purely abstract games played on graphs and hypergraphs. It is closely connected to many other combinatorial disciplines such as Ramsey theory, extremal graph and set theory, probabilistic combinatorics, and to computer science. We survey the basic notions of the field, its approaches and tools, as well as numerous recent advances, standing open problems and promising research directions.Comment: Submitted to Proceedings of the ICM 201

Coherence for indexed symmetric monoidal categories

Indexed symmetric monoidal categories are an important refinement of bicategories -- this structure underlies several familiar bicategories, including the homotopy bicategory of parametrized spectra, and its equivariant and fiberwise generalizations. In this paper, we extend existing coherence theorems to the setting of indexed symmetric monoidal categories. The most central theorem states that a large family of operations on a bicategory defined from an indexed symmetric monoidal category are all canonically isomorphic. As a part of this theorem, we introduce a rigorous graphical calculus that specifies when two such operations admit a canonical isomorphism.Comment: 100 pages, 64 figures, 13 table