Torchtree: flexible phylogenetic model development and inference using PyTorch

26 June 2024

Mathieu Fourment

Matthew Macaulay

Christiaan J. Swanepoel

Xiang Ji

M. Suchard

Frederick A Matsen IV

BDL

ArXiv PDF HTML

Papers citing "Torchtree: flexible phylogenetic model development and inference using PyTorch"

22 / 22 papers shown

Title
Random-effects substitution models for phylogenetics via scalable gradient approximations Andrew F. Magee Andrew J Holbrook J. Pekar Itzue W. Caviedes-Solis IV FredrickA.Matsen G. Baele J. Wertheim Xiang Ji P. Lemey M. Suchard 16 5 0 23 Mar 2023
Many-core algorithms for high-dimensional gradients on phylogenetic trees K. Gangavarapu Xiang Ji G. Baele Mathieu Fourment P. Lemey Frederick Albert Matsen IV M. Suchard 18 4 0 08 Mar 2023
TreeFlow: probabilistic programming and automatic differentiation for phylogenetics Christiaan J. Swanepoel Mathieu Fourment Xiang Ji Hassan Nasif M. Suchard IV FrederickAMatsen A. Drummond AI4CE 32 3 0 09 Nov 2022
A Variational Approach to Bayesian Phylogenetic Inference Cheng Zhang IV FrederickA.Matsen BDL 60 17 0 16 Apr 2022
VaiPhy: a Variational Inference Based Algorithm for Phylogeny Hazal Koptagel Oskar Kviman Harald Melin Negar Safinianaini J. Lagergren 21 18 0 01 Mar 2022
Scalable Bayesian divergence time estimation with ratio transformations Xiang Ji Alexander A. Fisher Shuo Su J. Thorne B. Potter P. Lemey G. Baele M. Suchard 19 10 0 25 Oct 2021
Variational Refinement for Importance Sampling Using the Forward Kullback-Leibler Divergence Ghassen Jerfel S. Wang Clara Fannjiang Katherine A. Heller Yi-An Ma Michael I. Jordan BDL 69 40 0 30 Jun 2021
Variational Combinatorial Sequential Monte Carlo Methods for Bayesian Phylogenetic Inference A. Moretti Liyi Zhang C. A. Naesseth Hadiah K Venner David M. Blei I. Pe’er BDL 24 16 0 31 May 2021
Improved Variational Bayesian Phylogenetic Inference with Normalizing Flows Cheng Zhang BDL 42 27 0 01 Dec 2020
Markovian Score Climbing: Variational Inference with KL(p\|\|q) C. A. Naesseth Fredrik Lindsten David M. Blei 137 54 0 23 Mar 2020
Automatic structured variational inference L. Ambrogioni Kate Lin Emily Fertig Sharad Vikram Max Hinne Dave Moore Marcel van Gerven BDL 34 30 0 03 Feb 2020
Shrinkage with shrunken shoulders: Gibbs sampling shrinkage model posteriors with guaranteed convergence rates A. Nishimura M. Suchard 75 9 0 06 Nov 2019
$Gradients do grow on trees: a linear-time ${\cal O}\hspace{-0.2em}\left( N \right)$-dimensional gradient for statistical phylogenetics$ Gradients do grow on trees: a linear-time ${\cal O}\hspace{-0.2em}\left( N \right)$ -dimensional gradient for statistical phylogenetics X. Ji Zhenyu Zhang Andrew J Holbrook A. Nishimura G. Baele A. Rambaut P. Lemey M. Suchard 22 31 0 29 May 2019
19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology Mathieu Fourment Andrew F. Magee Chris Whidden Arman Bilge Frederick Albert Matsen IV V. Minin 36 47 0 28 Nov 2018
Semi-Implicit Variational Inference Mingzhang Yin Mingyuan Zhou BDL 64 123 0 28 May 2018
TensorFlow: A system for large-scale machine learning Martín Abadi P. Barham Jianmin Chen Zhiwen Chen Andy Davis ... Vijay Vasudevan Pete Warden Martin Wicke Yuan Yu Xiaoqiang Zhang GNN AI4CE 324 18,300 0 27 May 2016
Automatic Differentiation Variational Inference A. Kucukelbir Dustin Tran Rajesh Ranganath Andrew Gelman David M. Blei 73 711 0 02 Mar 2016
Variational Inference: A Review for Statisticians David M. Blei A. Kucukelbir Jon D. McAuliffe BDL 174 4,748 0 04 Jan 2016
Variational Inference with Normalizing Flows Danilo Jimenez Rezende S. Mohamed DRL BDL 248 4,143 0 21 May 2015
Reweighted Wake-Sleep J. Bornschein Yoshua Bengio BDL 50 183 0 11 Jun 2014
MCMC using Hamiltonian dynamics Radford M. Neal 282 3,278 0 09 Jun 2012
The Bayesian Bridge Nicholas G. Polson James G. Scott Jesse Windle 48 153 0 11 Sep 2011