Related papers: On the locality of the Pr\"ufer code
Canonical distances such as Euclidean distance often fail to capture the appropriate relationships between items, subsequently leading to subpar inference and prediction. Many algorithms have been proposed for automated learning of suitable…
Consider a random real tree whose leaf set, or boundary, is endowed with a finite mass measure. Each element of the tree is further given a type, or allele, inherited from the most recent atom of a random point measure…
We demonstrate that adaptively controlling the size of individual regression trees in a random forest can improve predictive performance, contrary to the conventional wisdom that trees should be fully grown. A fast pruning algorithm,…
The edit distance between two rooted ordered trees with $n$ nodes labeled from an alphabet~$\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling…
Twisted permutation codes, introduced recently by the second and third authors, are frequency permutation arrays. They are similar to repetition permutation codes, in that they are obtained by a repetition construction applied to a smaller…
We study the spectral Tur\'an problem for trees. To avoid limiting our perspective to specific families of trees, we parametrize trees in terms of their unique bipartition. We say $T \in \mathcal{T}_{m,l+1}^{\delta}$ if $T$ is a tree of…
This paper revisits recent code similarity evaluation metrics, particularly focusing on the application of Abstract Syntax Tree (AST) editing distance in diverse programming languages. In particular, we explore the usefulness of these…
We study properties of binary codes with parameters close to the parameters of 1-perfect codes. An arbitrary binary $(n=2^m-3, 2^{n-m-1}, 4)$ code $C$, i.e., a code with parameters of a triply-shortened extended Hamming code, is a cell of…
The Robinson-Foulds (RF) distance is by far the most widely used measure of dissimilarity between trees. Although the distribution of these distances has been investigated for twenty years, an algorithm that is explicitly polynomial time…
Codes over trees were introduced recently to bridge graph theory and coding theory with diverse applications in computer science and beyond. A central challenge lies in determining the maximum number of labelled trees over $n$ nodes with…
Given a pattern string $P$ of length $n$ consisting of $\delta$ distinct characters and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet $\Sigma$ of size $\Delta$, the {\em exact string…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
We study the duplication with transposition distance between strings of length $n$ over a $q$-ary alphabet and their roots. In other words, we investigate the number of duplication operations of the form $x = (abcd) \to y = (abcbd)$, where…
A $B$-tree is a type of search tree where every node (except possibly for the root) contains between $m$ and $2m$ keys for some positive integer $m$, and all leaves have the same distance to the root. We study sequences of $B$-trees that…
`Tree pruning' (TP) is an algorithm for probabilistic inference on binary Markov random fields. It has been recently derived by Dror Weitz and used to construct the first fully polynomial approximation scheme for counting independent sets…
Three standard subtree transfer operations for binary trees, used in particular for phylogenetic trees, are: tree bisection and reconnection ($TBR$), subtree prune and regraft ($SPR$) and rooted subtree prune and regraft ($rSPR$). For a…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
We study approximation algorithms for variants of the \emph{median string} problem, which asks for a string that minimizes the sum of edit distances from a given set of $m$ strings of length $n$. Only the straightforward $2$-approximation…
Tree codes, introduced by Schulman, are combinatorial structures essential to coding for interactive communication. An infinite family of tree codes with both rate and distance bounded by positive constants is called asymptotically good.…
We provide finite sample guarantees for the classical Chow-Liu algorithm (IEEE Trans.~Inform.~Theory, 1968) to learn a tree-structured graphical model of a distribution. For a distribution $P$ on $\Sigma^n$ and a tree $T$ on $n$ nodes, we…