This repo contains the code to reproduce the results from our Bioinformatics paper 'Biologically informed variational autoencoders allow predictive modeling of genetic and drug induced perturbations': https://academic.oup.com/bioinformatics/article/39/6/btad387/7199588
Preprocessed ontobj and pretrained models were deposited under: https://figshare.com/projects/OntoVAE_Ontology_guided_VAE_manuscript/146727
Our web application that allows interactive exploration of all results related to Fig 1b (pathway activities) and Fig 1f (GO networks) is currently hosted under: http://ontovaemodelexplorer.pythonanywhere.com
Our package OntoVAE is available under https://github.com/hdsu-bioquant/onto-vae