Related papers: Optimal Phylogenetic Reconstruction from Sampled Q…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
The Cartesian tree of a sequence captures the relative order of the sequence's elements. In recent years, Cartesian tree matching has attracted considerable attention, particularly due to its applications in time series analysis. Consider a…
We introduce and initiate the study of a new model of reductions called the random noise model. In this model, the truth table $T_f$ of the function $f$ is corrupted on a randomly chosen $\delta$-fraction of instances. A randomized…
Motivation: The construction of statistics for summarizing posterior samples returned by a Bayesian phylogenetic study has so far been hindered by the poor geometric insights available into the space of phylogenetic trees, and ad hoc…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…
We present a method for the reconstruction of networks, based on the order of nodes visited by a stochastic branching process. Our algorithm reconstructs a network of minimal size that ensures consistency with the data. Crucially, we show…
In the trace reconstruction problem our goal is to learn an unknown string $x\in \{0,1\}^n$ given independent traces of $x$. A trace is obtained by independently deleting each bit of $x$ with some probability $\delta$ and concatenating the…
Data reconstruction attacks on trained neural networks aim to recover the data on which the network has been trained and pose a significant threat to privacy, especially if the training dataset contains sensitive information. Here, we…
The mutational heterogeneity of tumours can be described with a tree representing the evolutionary history of the tumour. With noisy sequencing data there may be uncertainty in the inferred tree structure, while we may also wish to study…
The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…
We consider learning Ising tree models when the observations from the nodes are corrupted by independent but non-identically distributed noise with unknown statistics. Katiyar et al. (2020) showed that although the exact tree structure…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…
The goal of trace reconstruction is to reconstruct an unknown $n$-bit string $x$ given only independent random traces of $x$, where a random trace of $x$ is obtained by passing $x$ through a deletion channel. A Statistical Query (SQ)…
Given a set of n data objects and their pairwise dissimilarities, the goal of the minimum quartet tree cost (MQTC) problem is to construct an optimal tree from the total number of possible combinations of quartet topologies on n, where…