$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

29 May 2019

Andrew J Holbrook

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Papers citing "Gradients do grow on trees: a linear-time ${\cal O}\hspace{-0.2em}\left( N \right)$-dimensional gradient for statistical phylogenetics"

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Title
Torchtree: flexible phylogenetic model development and inference using PyTorch Mathieu Fourment Matthew Macaulay Christiaan J. Swanepoel Xiang Ji M. Suchard Frederick A Matsen IV BDL 91 0 0 26 Jun 2024
Leveraging graphical model techniques to study evolution on phylogenetic networks Benjamin Teo P. Bastide Cécile Ané 44 1 0 15 May 2024
On the surprising effectiveness of a simple matrix exponential derivative approximation, with application to global SARS-CoV-2 G. Didier N. Glatt-Holtz Andrew J Holbrook Andrew F. Magee M. Suchard 47 4 0 28 Jun 2023
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 31 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 35 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 34 3 0 09 Nov 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 31 10 0 25 Oct 2021
Additive stacking for disaggregate electricity demand forecasting Christian Capezza B. Palumbo Y. Goude S. Wood Matteo Fasiolo AI4TS 76 7 0 20 May 2020
Zig-zag sampling for discrete structures and non-reversible phylogenetic MCMC Jere Koskela 49 7 0 19 Apr 2020