Example Usage for NeST VNN

This tool can be used to run the NeST VNN model. The inputs needed for training the model and performing predictions are described in the NeST VNN inputs section and are located in examples directory in cellmaps_vnn repository.

Training

The flow of training NeST VNN

Example run of NeST VNN training using example data provided in examples directory:

cellmaps_vnncmd.py train ./outdir_training --inputdir examples --gene2id examples/gene2ind.txt \
    --cell2id examples/cell2ind.txt --training_data examples/training_data.txt --mutations examples/cell2mutation.txt \
    --cn_deletions examples/cell2cndeletion.txt --cn_amplifications examples/cell2cnamplification.txt --epoch 20

Same example, but using configuration file set via –config_file

cellmaps_vnncmd.py train ./outdir_training --inputdir examples --config_file examples/config.yaml

Prediction

The flow of prediction and interpretation process using NeST VNN

Example run of NeST VNN prediction and interpretation:

cellmaps_vnncmd.py predict ./outdir_prediction --inputdir ./outdir_training --gene2id examples/gene2ind.txt \
    --cell2id examples/cell2ind.txt --predict_data examples/test_data.txt --mutations examples/cell2mutation.txt \
    --cn_deletions examples/cell2cndeletion.txt --cn_amplifications examples/cell2cnamplification.txt

Same example, but using configuration file set via –config_file

cellmaps_vnncmd.py predict ./outdir_prediction --inputdir ./outdir_training --config_file examples/config.yaml

Annotation

The flow of annotation process from NeST VNN

cellmaps_vnncmd.py annotate ./outdir_annotation --model_predictions ./outdir_prediction

Same example but with upload to NDEx:

If using NeST hierarchy provided in examples directory in the GitHub repo, you can upload it with its interactome that is available on ndexbio.org with this uuid: 0b7b8aee-332f-11ef-9621-005056ae23aa.

cellmaps_vnncmd.py annotate ./outdir_annotation --model_predictions ./outdir_prediction --ndexuser USERNAME --ndexpassword - --parent_network 0b7b8aee-332f-11ef-9621-005056ae23aa --visibility