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https://github.com/4ment/torchtree-physher
https://github.com/4ment/torchtree-physher
c gradient phylogenetics physher pytorch torchtree
Last synced: about 2 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/4ment/torchtree-physher
- Owner: 4ment
- License: gpl-3.0
- Created: 2022-03-02T11:34:38.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-07-10T05:01:06.000Z (6 months ago)
- Last Synced: 2024-10-14T14:06:34.419Z (3 months ago)
- Topics: c, gradient, phylogenetics, physher, pytorch, torchtree
- Language: Python
- Homepage:
- Size: 207 KB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# torchtree-physher
[](https://github.com/4ment/torchtree-physher/actions/workflows/test_linux.yml)
[](https://www.gnu.org/licenses/gpl-3.0)
## About torchtree-physher
torchtree-physher is a python package providing fast gradient calculation implemented in [physher] for [torchtree].
## Getting Started
A C++ compiler such as ``g++`` or ``clang++`` is required.
On Debian-based systems, this can be installed via ``apt``:
```bash
sudo apt install g++
```
On MacOS, it is recommended to use the latest version of ``clang++``:
```bash
brew install llvm
```
The [pybind11] library is also used for binding the
C++ functionality to Python.
### Dependencies
- [physher]
- [pybind11]
- [PyTorch]
- [torchtree]
[physher] is a phylogenetic program written in C that provides C++ wrappers to compute the tree and coalescent likelihoods and their gradients under different models.
To build physher from source you can run
```bash
git clone https://github.com/4ment/physher
cmake -S physher/ -B physher/build -DBUILD_CPP_WRAPPER=on -DBUILD_TESTING=on
cmake --build physher/build/ --target install
```
Check it works (optional)
```bash
ctest --test-dir physher/build/
```
### Installation
To build `torchtree-physher` from source you can run
```bash
git clone https://github.com/4ment/torchtree-physher
pip install torchtree-physher/
```
### Check install
If the installation was successful, this command should print the version of the `torchtree_physher` library
```bash
python -c "import torchtree_physher;print(torchtree_physher.__version__)"
```
## Command line arguments
The torchtree-physher plugin adds these arguments to the torchtree CLI:
```bash
torchtree-cli advi --help
...
--physher use physher
--physher_include_jacobian
include Jacobian of the node height transform in the node height gradient
--physher_disable_sse
disable SSE in physher
--physher_disable_coalescent
disable coalescent calculation by physher
--physher_site {weibull,gamma}
distribution for rate heterogeneity across sites
```
## Features
### Tree likelihood
Some types in the JSON configuration file have to be replaced in order to use the tree likelihood implementation of physher. You simply need to add `torchtree_physher.` before a model type. Here is a list of models implemented in this plugin:
- `TreeLikelihoodModel`
- Substitution models:
- `JC69`
- `HKY`
- `GTR`
- `GeneralNonSymmetricSubstitutionModel`
- Tree models:
- `UnRootedTreeModel`
- `ReparameterizedTimeTreeModel`
- Clock models (optional):
- `StrictClockModel`
- `SimpleClockModel`
- Site models:
- `ConstantSiteModel`
- `GammaSiteModel`
- `InvariantSiteModel`
- `WeibullSiteModel`
Note that the type of every sub-model of the tree likelihood object (e.g. site, tree models...) has to be replaced.
For example if we want to use ADVI with an unrooted tree and a Weibull site model:
```bash
torchtree-cli advi -i data.fa -t data.tree -C 4 > data.json
sed -i -E 's/TreeLikelihoodModel/torchtree_physher.TreeLikelihoodModel/; s/UnRootedTreeModel/torchtree_physher.UnRootedTreeModel/; s/WeibullSiteModel/torchtree_physher.WeibullSiteModel/' data.json
torchtree data.json
```
The JSON file can be created directly using the `--physher` option:
```bash
torchtree-cli advi -i data.fa -t data.tree -C 4 --physher > data.json
```
### Coalescent models
Here is a list of coalescent models implemented in this plugin:
- `ConstantCoalescentModel`
- `PiecewiseConstantCoalescentGridModel` (aka skygrid)
- `PiecewiseConstantCoalescentModel` (aka skyride)
- `PiecewiseLinearCoalescentGridModel`
## License
Distributed under the GPLv3 License. See [LICENSE](LICENSE) for more information.
## Acknowledgements
torchtree-physher makes use of the following libraries and tools, which are under their own respective licenses:
- [physher]
- [pybind11]
- [PyTorch]
- [torchtree]
[physher]: https://github.com/4ment/physher
[pybind11]: https://pybind11.readthedocs.io/en/stable
[PyTorch]: https://pytorch.org
[torchtree]: https://github.com/4ment/torchtree