PhenoScore is an open source, artificial intelligence-based phenomics framework that combines facial recognition technology with Human Phenotype Ontology (HPO) data analysis to quantify phenotypic similarity at both the level of individual patients as well as of cohorts.
To install PhenoScore using conda, it is advisable (but not strictly necessary) to create a new environment first:
conda create -n PhenoScore python=3.9
Then, activate the environment
conda activate PhenoScore
Install PhenoScore and the needed dependencies:
pip install .
To fix some dependency issues, especially on Windows, please then run these commands:
pip install mxnet==1.7.0post2 --no-dependencies
pip install numpy==1.23.5
To use the GPU (about a 10x performance increase when doing the LIME predictions) when CUDA is installed:
conda install cudnn
To run the basic example analysis (looking at the two subgroups in SATB1), take a look at the tutorial in the notebooks directory.