Related papers: Compressed Tree Canonization
Large language models (LLMs) can now solve complex problems through long chain-of-thought (CoT) reasoning, but the trade-off between performance and token cost remains a central challenge. To address this issue, supervised fine-tuning (SFT)…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
The early development of a zygote can be mathematically described by a developmental tree. To compare developmental trees of different species, we need to define distances on trees. If children cells after a division are not…
Billey et al. [arXiv:1507.04976] have recently discovered a surprisingly simple formula for the number $a_n(\sigma)$ of leaf-labelled rooted non-embedded binary trees (also known as phylogenetic trees) with $n\geq 1$ leaves, fixed (for the…
This paper outlines a method to determine whether two label-regular directed trees, are isomorphic and when they are almost isomorphic. The approach involves reinterpreting label-regular directed trees as universal covers of rooted graphs.…
The finite satisfiability problem for the two-variable fragment of first-order logic interpreted over trees was recently shown to be ExpSpace-complete. We consider two extensions of this logic. We show that adding either additional binary…
Working with generating functions, the combinatorics of a recurrence relation can be expressed in a way that allows for more efficient calculation of the quantity. This is true of the Catalan numbers for an ordered binary tree…
We introduce a new class of straight-line programs (SLPs), named the Lyndon SLP, inspired by the Lyndon trees (Barcelo, 1990). Based on this SLP, we propose a self-index data structure of $O(g)$ words of space that can be built from a…
Linear extended top-down tree transducers (or synchronous tree-substitution grammars) are popular formal models of tree transformations. The expressive power of compositions of such transducers with and without regular look-ahead is…
Linear model trees are regression trees that incorporate linear models in the leaf nodes. This preserves the intuitive interpretation of decision trees and at the same time enables them to better capture linear relationships, which is hard…
Latent tree learning models represent sentences by composing their words according to an induced parse tree, all based on a downstream task. These models often outperform baselines which use (externally provided) syntax trees to drive the…
We prove that a uniform, rooted unordered binary tree with $n$ vertices has the Brownian continuum random tree as its scaling limit for the Gromov-Hausdorff topology. The limit is thus, up to a constant factor, the same as that of uniform…
The main focus of this paper is on bisimulation-invariant MSO, and more particularly on giving a novel model-theoretic approach to it. In model theory, a model companion of a theory is a first-order description of the class of models in…
We consider three bivariate polynomial invariants $P$, $A$, and $S$ for rooted trees, as well as a trivariate polynomial invariant $M$. These invariants are motivated by random destruction processes such as the random cutting model or site…
The modular decomposition of a symmetric map $\delta\colon X\times X \to \Upsilon$ (or, equivalently, a set of symmetric binary relations, a 2-structure, or an edge-colored undirected graph) is a natural construction to capture key features…
Rotation distance between rooted binary trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. We give an efficient,…
Rooted bifurcating trees are mathematical objects used to model evolutionary relationships and arise naturally in both coalescent theory and phylogenetics. Recent numerical representations of tree topologies, known as F-matrices, allow for…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
We present a new method to count unrooted maps on the sphere up to orientation-preserving homeomorphisms. The principle, called tree-decomposition, is to deform a map into an arborescent structure whose nodes are occupied by constrained…