Attention All Microbes (AAM)

Attention-based network for microbial sequencing data.

Installation Instructions

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

GPU Support

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

Install AAM

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/attention-all-microbes.git@v0.1.1

Developers

git clone git@github.com:kwcantrell/attention-all-microbes.git

cd attention-all-microbes

pip install -e .

Training

Classifiers and Regressors are trained use cross-validation

attention --help