Related papers: Listing Conflicting Triples in Optimal Time

Consensus is one of the most thoroughly studied problems in distributed computing, yet there are still complexity gaps that have not been bridged for decades. In particular, in the classical message-passing setting with processes' crashes,…

Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree $T$ to vertices and edges of a species tree $S$. The relative timing of the last common…

This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0 <= p <= 1 such that for every input set T of rooted triplets, there…

We consider finding a counterfactual explanation for a classification or regression forest, such as a random forest. This requires solving an optimization problem to find the closest input instance to a given instance for which the forest…

A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favour gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon…

Algorithms for efficiently finding optimal alphabetic decision trees -- such as the Hu-Tucker algorithm -- are well established and commonly used. However, such algorithms generally assume that the cost per decision is uniform and thus…

We consider the problem of exploring an unknown tree with a team of $k$ initially colocated mobile agents. Each agent has limited energy and cannot, as a result, traverse more than $B$ edges. The goal is to maximize the number of nodes…

Semi-labeled trees are phylogenies whose internal nodes may be labeled by higher-order taxa. Thus, a leaf labeled Mus musculus could nest within a subtree whose root node is labeled Rodentia, which itself could nest within a subtree whose…

We study the problem of computing the triplet distance between two rooted unordered trees with $n$ labeled leafs. Introduced by Dobson 1975, the triplet distance is the number of leaf triples that induce different topologies in the two…

We propose an approach for learning optimal tree-based prescription policies directly from data, combining methods for counterfactual estimation from the causal inference literature with recent advances in training globally-optimal decision…

Finding interactions between variables in large and high-dimensional datasets is often a serious computational challenge. Most approaches build up interaction sets incrementally, adding variables in a greedy fashion. The drawback is that…

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…

The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…

Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this…

We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…

In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…

We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…

Nonlinear metrics, such as the F1-score, Matthews correlation coefficient, and Fowlkes-Mallows index, are often used to evaluate the performance of machine learning models, in particular, when facing imbalanced datasets that contain more…

A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…

We consider the problem of sorting $n$ items, given the outcomes of $m$ pre-existing comparisons. We present a simple and natural deterministic algorithm that runs in $O(m + \log T)$ time and does $O(\log T)$ comparisons, where $T$ is the…