Related papers: Listing Conflicting Triples in Optimal Time
One of the goals of phylogenetic research is to find the species tree describing the evolutionary history of a set of species. But the trees derived from geneti data with the help of tree inference methods are gene trees that need not…
Decision tree learning is a widely used approach in machine learning, favoured in applications that require concise and interpretable models. Heuristic methods are traditionally used to quickly produce models with reasonably high accuracy.…
We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…
Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…
We present a simple $O(n^4)$-time algorithm for computing optimal search trees with two-way comparisons. The only previous solution to this problem, by Anderson et al., has the same running time, but is significantly more complicated and is…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
We show fast deterministic algorithms for fundamental problems on forests in the challenging low-space regime of the well-known Massive Parallel Computation (MPC) model. A recent breakthrough result by Coy and Czumaj [STOC'22] shows that,…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…
The {Congested Clique} is a distributed-computing model for single-hop networks with restricted bandwidth that has been very intensively studied recently. It models a network by an $n$-vertex graph in which any pair of vertices can…
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 present a complete classification of the deterministic distributed time complexity for a family of graph problems: binary labeling problems in trees. These are locally checkable problems that can be encoded with an alphabet of size two…
THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree $T$ and $\sigma$ an…
Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…
Recent work has shown that not only decision trees (DTs) may not be interpretable but also proposed a polynomial-time algorithm for computing one PI-explanation of a DT. This paper shows that for a wide range of classifiers, globally…
In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
The three-in-a-tree problem is to determine if a simple undirected graph contains an induced subgraph which is a tree connecting three given vertices. Based on a beautiful characterization that is proved in more than twenty pages,…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
Survival analysis studies and predicts the time of death, or other singular unrepeated events, based on historical data, while the true time of death for some instances is unknown. Survival trees enable the discovery of complex nonlinear…