Attention-based network for microbial sequencing data.
IMPORTANT: If installing on a server cluster, spawn an instance with a GPU before proceeding with environment setup. First create a new conda environment with unifrac
conda create --name aam -c conda-forge -c bioconda unifrac python=3.9 cython
conda activate aam
Install CUDA 11.8
conda install nvidia/label/cuda-11.8.0::cuda-toolkit
Verify the NVIDIA GPU drives are on your path
nvidia-smi
Please see Tensorflow for more information
For the latest version
pip install git+https://github.com/kwcantrell/attention-all-microbes.git
or install a specific version
pip install git+https://github.com/kwcantrell/[email protected]
git clone [email protected]:kwcantrell/attention-all-microbes.git
cd attention-all-microbes
pip install -e .
Classifiers and Regressors are trained use cross-validation
attention --help