Related papers: Reconstructing Ultrametric Trees from Noisy Experi…
Model trees provide an appealing way to perform interpretable machine learning for both classification and regression problems. In contrast to ``classic'' decision trees with constant values in their leaves, model trees can use linear…
Existing techniques to reconstruct tree models of progression for accumulative processes, such as cancer, seek to estimate causation by combining correlation and a frequentist notion of temporal priority. In this paper, we define a novel…
Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…
Extracting a Construction Tree from potentially noisy point clouds is an important aspect of Reverse Engineering tasks in Computer Aided Design. Solutions based on algorithmic geometry impose constraints on usable model representations…
Tree reconstruction methods are often judged by their accuracy, measured by how close they get to the true tree. Yet most reconstruction methods like ML do not explicitly maximize this accuracy. To address this problem, we propose a…
The ''trace reconstruction'' problem asks, given an unknown binary string $x$ and a channel that repeatedly returns ''traces'' of $x$ with each bit randomly deleted with some probability $p$, how many traces are needed to recover $x$? There…
Given access to the vertex set $V$ of a connected graph $G=(V,E)$ and an oracle that given two vertices $u,v\in V$, returns the shortest path distance between $u$ and $v$, how many queries are needed to reconstruct $E$? Firstly, we show…
This paper is concerned with the approximation of high-dimensional functions in a statistical learning setting, by empirical risk minimization over model classes of functions in tree-based tensor format. These are particular classes of…
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…
The problem of fitting distances by tree-metrics has received significant attention in the theoretical computer science and machine learning communities alike, due to many applications in natural language processing, phylogeny, cancer…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
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…
The number of models shared online has recently skyrocketed, with over one million public models available on Hugging Face. Sharing models allows other users to build on existing models, using them as initialization for fine-tuning,…
It is known that evolution strategies in continuous domains might not converge in the presence of noise. It is also known that, under mild assumptions, and using an increasing number of resamplings, one can mitigate the effect of additive…
The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…
A weighted recursive tree is an evolving tree in which vertices are assigned random vertex-weights and new vertices connect to a predecessor with a probability proportional to its weight. Here, we study the maximum degree and near-maximum…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…
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…