TreeFlow: probabilistic programming and automatic differentiation for phylogenetics

Autor:	Swanepoel, Christiaan, Fourment, Mathieu, Ji, Xiang, Nasif, Hassan, Suchard, Marc A, Matsen IV, Frederick A, Drummond, Alexei
Rok vydání:	2022
Předmět:	Quantitative Biology - Populations and Evolution Statistics - Computation
Druh dokumentu:	Working Paper
Popis:	Probabilistic programming frameworks are powerful tools for statistical modelling and inference. They are not immediately generalisable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object. TreeFlow is a software library for probabilistic programming and automatic differentiation with phylogenetic trees. It implements inference algorithms for phylogenetic tree times and model parameters given a tree topology. We demonstrate how TreeFlow can be used to quickly implement and assess new models. We also show that it provides reasonable performance for gradient-based inference algorithms compared to specialized computational libraries for phylogenetics. Comment: 34 pages, 8 figures
Databáze:	arXiv
Externí odkaz:	http://arxiv.org/abs/2211.05220 Zobrazit plný text záznamu View this record from Arxiv