A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics

Paper title: Gradients do grow on trees: a linear-time O(N)-dimensional gradient for statistical phylogenetics ^[1]

Reproduce the analyses

Follow the instruction on ^[2]:

Setting up BEAGLE

Using Linux system, do the following ^[3] but get the hmc-clock branch.

sudo apt-get install cmake build-essential autoconf automake libtool git pkg-config openjdk-11-jdk
git clone -b hmc-clock https://github.com/beagle-dev/beagle-lib.git
cd beagle-lib
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX:PATH=$HOME ..
make install
cmake ..
export LD_LIBRARY_PATH=$HOME/lib:$LD_LIBRARY_PATH
make test

Setting up BEAST

git clone -b hmc-clock https://github.com/beast-dev/beast-mcmc.git
cd beast-mcmc
ant

Reproducing the analyses

Prepare files and folders:

git clone https://github.com/suchard-group/hmc_clock_manuscript_supplement.git

mkdir test_results
cd test_results
beast_path=/media/XLStorage/ybao2/gradient_paper/
xml_path=/media/XLStorage/ybao2/gradient_paper/hmc_clock_manuscript_supplement

West Nile Virus

• Optimization
  • Analytic gradient

     java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/WNV/WNV_skyline_optimization_save -seed 666 -overwrite where_this_repository_is_stored/xmls/WNV/WNV_HMC_skyline_MLE_Analytic.xml
    

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1. Ji X, Zhang Z, Holbrook A, Nishimura A, Baele G, Rambaut A, Lemey P, Suchard MA. 2019. Gradients do grow on trees: a linear-time O(N)-dimensional gradient for statistical phylogenetics. Available from: https://arxiv.org/pdf/1905.12146.pdf. ↩︎

2. https://github.com/suchard-group/hmc_clock_manuscript_supplement ↩︎

3. https://github.com/beagle-dev/beagle-lib/wiki/LinuxInstallInstructions ↩︎