Related papers: An Algorithm for Consensus Trees
A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications…
The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
This paper presents two new deterministic algorithms for constructing consensus trees. Given an input of k phylogenetic trees with identical leaf label sets and n leaves each, the first algorithm constructs the majority rule (+) consensus…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Given two rooted, ordered, and labeled trees $P$ and $T$ the tree inclusion problem is to determine if $P$ can be obtained from $T$ by deleting nodes in $T$. This problem has recently been recognized as an important query primitive in XML…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
The authors recently gave an $n^{O(\log\log n)}$ time membership query algorithm for properly learning decision trees under the uniform distribution (Blanc et al., 2021). The previous fastest algorithm for this problem ran in $n^{O(\log…
This paper presents a detailed comparison of a recently proposed algorithm for optimizing decision trees, tree alternating optimization (TAO), with other popular, established algorithms. We compare their performance on a number of…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
We give an $n^{O(\log\log n)}$-time membership query algorithm for properly and agnostically learning decision trees under the uniform distribution over $\{\pm 1\}^n$. Even in the realizable setting, the previous fastest runtime was…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
We present an algorithm for computing a maximum agreement subtree of two unrooted evolutionary trees. It takes O(n^{1.5} log n) time for trees with unbounded degrees, matching the best known time complexity for the rooted case. Our…
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
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 present a new approximation algorithm for the treewidth problem which finds an upper bound on the treewidth and constructs a corresponding tree decomposition as well. Our algorithm is a faster variation of Reed's classical algorithm. For…
We consider online algorithms for the $k$-server problem on trees. There is a $k$-competitive algorithm for this problem, and it is the best competitive ratio. M. Chrobak and L. Larmore provided it. At the same time, the existing…
Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP…