Related papers: A bijection for the evolution of $B$-trees
The Baxter number can be written as $B_n = \sum_0^n \Theta_{k,n-k-1}$. These numbers have first appeared in the enumeration of so-called Baxter permutations; $B_n$ is the number of Baxter permutations of size $n$, and $\Theta_{k,l}$ is the…
B-slack trees, a subclass of B-trees that have substantially better worst-case space complexity, are introduced. They store $n$ keys in height $O(\log_b n)$, where $b$ is the maximum node degree. Updates can be performed in $O(\log_{\frac b…
We construct a refined bijection $\phi$ between alternating permutations and 0-1-2 increasing trees with degree at most 2. It satisfies that the first element of alternating permutation $\pi$ is equal to the first vertex in $\phi(\pi)$ in…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
We propose BS-tree, an in-memory implementation of the B+-tree that adopts the structure of the disk-based index (i.e., a balanced, multiway tree), setting the node size to a memory block that can be processed fast and in parallel using…
The Binary Search Tree (BST) is average in computer science which supports a compact data structure in memory and oneself even conducts a row of quick algorithms, by which people often apply it in dynamical circumstance. Besides these…
Augmented B-trees (aB-trees) are a broad class of data structures. The seminal work "succincter" by Patrascu showed that any aB-tree can be stored using only two bits of redundancy, while supporting queries to the tree in time proportional…
Binary trait data record the presence or absence of distinguishing traits in individuals. We treat the problem of estimating ancestral trees with time depth from binary trait data. Simple analysis of such data is problematic. Each homology…
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
We present an algorithmic mapping from permutations of length dn to labeled n-node d-ary trees and back again. Given such a bijection, one can interpret each of the factorials in the formula for the Catalan numbers as a count of…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
A data structure, called a biased range tree, is presented that preprocesses a set S of n points in R^2 and a query distribution D for 2-sided orthogonal range counting queries. The expected query time for this data structure, when queries…
We consider random binary trees that appear as the output of certain standard algorithms for sorting and searching if the input is random. We introduce the subtree size metric on search trees and show that the resulting metric spaces…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
We consider the counting problem of the number of \textit{leaf-labeled increasing trees}, where internal nodes may have an arbitrary number of descendants. The set of all such trees is a discrete representation of the genealogies obtained…
We recall the occupancy problem introduced by Konheim & Weiss in 1966 and we consider parking functions as hash maps. Each car $c_i$ prefers parking space $p_i$ (the hash map $c_i \mapsto p_i$ with $c_i$ is a key and $p_i$ an index into an…