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dvc.yaml
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stages:
subsample:
cmd: $VAE_PY src/pipeline/subsample.py
params:
- params.toml:
- data.subsampling
deps:
- src/pipeline/subsample.py
- data/raw/covid19.h5ad
outs:
- data/raw/covid19_subsampled.h5ad
test_train_val_split:
cmd: $VAE_PY src/pipeline/test_train_val_split.py
deps:
- data/raw/covid19_subsampled.h5ad
- src/pipeline/test_train_val_split.py
outs:
- data/intermediate/covid_test_data.h5ad
- data/intermediate/covid_train_data.h5ad
- data/intermediate/covid_val_data.h5ad
train_vae:
cmd: $VAE_PY src/pipeline/train_vae.py
params:
- params.toml:
- training.latent_dimensions_initial_guess
- training.newton_temperature
- training.batch_size
- training.vae_trainer.max_epochs
deps:
- src/pipeline/train_vae.py
- data/intermediate/covid_test_data.h5ad
- data/intermediate/covid_train_data.h5ad
outs:
- data/artifacts/vae.pth
- data/artifacts/vae.pth.json
simulation:
cmd: $VAE_PY src/pipeline/simulation.py
params:
- params.toml:
- simulation.minimum_cells_per_class
deps:
- src/pipeline/simulation.py
- data/artifacts/vae.pth
- data/artifacts/vae.pth.json
- data/intermediate/covid_train_data.h5ad
outs:
- data/artifacts/simulation_gene_expression.pq
classifier:
cmd: $VAE_PY src/pipeline/classifier.py
params:
- params.toml:
- classifier.n_hidden_layers
- classifier.training_opts.max_epochs
deps:
- src/pipeline/classifier.py
- data/intermediate/covid_test_data.h5ad
- data/intermediate/covid_train_data.h5ad
- data/intermediate/covid_val_data.h5ad
- data/artifacts/simulation_gene_expression.pq
outs:
- data/artifacts/classifer_w_simulated_data_metrics.json
- data/artifacts/classifer_wout_simulated_data_metrics.json