├── .gitignore ├── LICENSE ├── README.md ├── __init__.py ├── bme_jax ├── data.py ├── loss.py ├── main.py ├── optim.py └── test.py ├── cfg └── bme_config_v3.yml ├── core.py ├── data └── primates.fa ├── demo.ipynb ├── env.yml ├── pyproject.toml └── utils ├── __init__.py ├── data.py └── tree.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/README.md -------------------------------------------------------------------------------- /__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /bme_jax/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/bme_jax/data.py -------------------------------------------------------------------------------- /bme_jax/loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/bme_jax/loss.py -------------------------------------------------------------------------------- /bme_jax/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/bme_jax/main.py -------------------------------------------------------------------------------- /bme_jax/optim.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/bme_jax/optim.py -------------------------------------------------------------------------------- /bme_jax/test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/bme_jax/test.py -------------------------------------------------------------------------------- /cfg/bme_config_v3.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/cfg/bme_config_v3.yml -------------------------------------------------------------------------------- /core.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/core.py -------------------------------------------------------------------------------- /data/primates.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/data/primates.fa -------------------------------------------------------------------------------- /demo.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/demo.ipynb -------------------------------------------------------------------------------- /env.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/env.yml -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/pyproject.toml -------------------------------------------------------------------------------- /utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /utils/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/utils/data.py -------------------------------------------------------------------------------- /utils/tree.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Neclow/GradME/HEAD/utils/tree.py --------------------------------------------------------------------------------