Related papers: Alignment-free phylogenetic reconstruction: Sample…

Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…

Clustering is a difficult and widely-studied data mining task, with many varieties of clustering algorithms proposed in the literature. Nearly all algorithms use a similarity measure such as a distance metric (e.g. Euclidean distance) to…

We are facing a real challenge when coping with the continuous acceleration of scientific production and the increasingly changing nature of science. In this article, we extend the classical framework of co-word analysis to the study of…

A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…

Sparse linear regression is a central problem in high-dimensional statistics. We study the correlated random design setting, where the covariates are drawn from a multivariate Gaussian $N(0,\Sigma)$, and we seek an estimator with small…

Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…

We describe a method that will reconstruct an unrooted binary phylogenetic level-1 network on n taxa from the set of all quartets containing a certain fixed taxon, in O(n^3) time. We also present a more general method which can handle more…

We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…

To remove redundant components of large language models (LLMs) without incurring significant computational costs, this work focuses on single-shot pruning without a retraining phase. We simplify the pruning process for Transformer-based…

This work proposes an algorithm for explicitly constructing a pair of neural networks that linearize and reconstruct an embedded submanifold, from finite samples of this manifold. Our such-generated neural networks, called Flattening…

Sampling of sharp posteriors in high dimensions is a challenging problem, especially when gradients of the likelihood are unavailable. In low to moderate dimensions, affine-invariant methods, a class of ensemble-based gradient-free methods,…

When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…

We develop an algorithm for minimizing a function using $n$ batched function value measurements at each of $T$ rounds by using classifiers to identify a function's sublevel set. We show that sufficiently accurate classifiers can achieve…

In recent decades, phylogenetic networks have become a standard tool in modeling evolutionary processes. Nevertheless, basic combinatorial questions about them are still largely open. For instance, even the asymptotic counting problem for…

Grouping elements into families to analyse them separately is a standard analysis procedure in many areas of sciences. We propose herein a new algorithm based on the simple idea that members from a family look like each other, and don't…

Network reconstruction consists in determining the unobserved pairwise couplings between $N$ nodes given only observational data on the resulting behavior that is conditioned on those couplings -- typically a time-series or independent…

We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…

An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…