PhenoScore

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.

Installing PhenoScore

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

Optional:

To use the GPU (about a 10x performance increase when doing the LIME predictions) when CUDA is installed:

conda install cudnn

Running PhenoScore

To run the basic example analysis (looking at the two subgroups in SATB1), take a look at the tutorial in the notebooks directory.