Related papers: PhyloGen: Language Model-Enhanced Phylogenetic Inf…
We study the problem of learning a latent tree graphical model where samples are available only from a subset of variables. We propose two consistent and computationally efficient algorithms for learning minimal latent trees, that is, trees…
The advances in variational inference are providing promising paths in Bayesian estimation problems. These advances make variational phylogenetic inference an alternative approach to Markov Chain Monte Carlo methods for approximating the…
Decision trees are a crucial class of models offering robust predictive performance and inherent interpretability across various domains, including healthcare, finance, and logistics. However, current tree induction methods often face…
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
Recent advancements in aligning large language models via reinforcement learning have achieved remarkable gains in solving complex reasoning problems, but at the cost of expensive on-policy rollouts and limited exploration of diverse…
In the last decade, some algebraic tools have been successfully applied to phylogenetic reconstruction. These tools are mainly based on the knowledge of equations describing algebraic varieties associated to phylogenetic trees evolving…
In this article we propose a novel method to estimate the frequency distribution of linguistic variables while controlling for statistical non-independence due to shared ancestry. Unlike previous approaches, our technique uses all available…
A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
Reconstructing the evolutionary history relating a collection of molecular sequences is the main subject of modern Bayesian phylogenetic inference. However, the commonly used Markov chain Monte Carlo methods can be inefficient due to the…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…
Phylogenetic trees are important tools in the study of evolutionary relationships between species. Measures such as the index of Sackin, Colless, and Total Cophenetic have been extensively used to quantify tree balance, one key property of…
This project aims to investigate a novel sequence generation method inspired by the AlphaGo paradigm, adapting it for use with large language models (LLMs). The proposed approach involves creating search trees of different possible…
Bayesian inference has predominantly relied on the Markov chain Monte Carlo (MCMC) algorithm for many years. However, MCMC is computationally laborious, especially for complex phylogenetic models of time trees. This bottleneck has led to…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…
Computational phylogenetics has become an established tool in historical linguistics, with many language families now analyzed using likelihood-based inference. However, standard approaches rely on expert-annotated cognate sets, which are…
We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package…
Open-domain long-form text generation requires generating coherent, comprehensive responses that address complex queries with both breadth and depth. This task is challenging due to the need to accurately capture diverse facets of input…
We introduce phylodyn, an R package for phylodynamic analysis based on gene genealogies. The package main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes…