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dvc.lock
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subsample:
cmd: $VAE_PY src/pipeline/subsample.py
deps:
- path: data/raw/covid19.h5ad
md5: c3e66ea8d17fcef1dec63de51893af80
size: 2293697930
- path: src/pipeline/subsample.py
md5: 2cff5fa14532b511b290232468a7d07e
size: 383
params:
params.toml:
data.subsampling: 0.25
outs:
- path: data/raw/covid19_subsampled.h5ad
md5: 8327ef5f07470c4b72771bce5adc5fc1
size: 428636349
test_train_val_split:
cmd: $VAE_PY src/pipeline/test_train_val_split.py
deps:
- path: data/raw/covid19_subsampled.h5ad
md5: 8327ef5f07470c4b72771bce5adc5fc1
size: 428636349
- path: src/pipeline/test_train_val_split.py
md5: eb65ff293bf0fb58c870ba0847f60d51
size: 946
outs:
- path: data/intermediate/covid_test_data.h5ad
md5: cfec609f2ced75b83fab86e7d26062c3
size: 46284484
- path: data/intermediate/covid_train_data.h5ad
md5: 5f658531816b042805334e5248dca7ec
size: 344165415
- path: data/intermediate/covid_val_data.h5ad
md5: 3404d3dcae95d8519f202d86570dbf92
size: 46229075
train_vae:
cmd: $VAE_PY src/pipeline/train_vae.py
deps:
- path: data/intermediate/covid_test_data.h5ad
md5: cfec609f2ced75b83fab86e7d26062c3
size: 46284484
- path: data/intermediate/covid_train_data.h5ad
md5: 5f658531816b042805334e5248dca7ec
size: 344165415
- path: src/pipeline/train_vae.py
md5: cb3f4661f9a9c0abe969c0ef782b58ed
size: 7463
params:
params.toml:
training.batch_size: 256
training.latent_dimensions_initial_guess: 32
training.newton_temperature: 1
training.vae_trainer.max_epochs: 10
outs:
- path: data/artifacts/vae.pth
md5: b1cf824d1f0ceafca3f6399ce314d856
size: 8486773
- path: data/artifacts/vae.pth.json
md5: 93f187aa73f8fd31bdfd5ff0da40523d
size: 69
simulation:
cmd: $VAE_PY src/pipeline/simulation.py
deps:
- path: data/artifacts/vae.pth
md5: b1cf824d1f0ceafca3f6399ce314d856
size: 8486773
- path: data/artifacts/vae.pth.json
md5: 93f187aa73f8fd31bdfd5ff0da40523d
size: 69
- path: data/intermediate/covid_train_data.h5ad
md5: 5f658531816b042805334e5248dca7ec
size: 344165415
- path: src/pipeline/simulation.py
md5: 35155c4c2f1e5278f7160a8c4fdbb3fc
size: 3943
params:
params.toml:
simulation.minimum_cells_per_class: 100
outs:
- path: data/artifacts/simulation_gene_expression.pq
md5: d9631898b98fe93121368c57245988be
size: 189434274
classifier:
cmd: $VAE_PY src/pipeline/classifier.py
deps:
- path: data/artifacts/simulation_gene_expression.pq
md5: d9631898b98fe93121368c57245988be
size: 189434274
- path: data/intermediate/covid_test_data.h5ad
md5: cfec609f2ced75b83fab86e7d26062c3
size: 46284484
- path: data/intermediate/covid_train_data.h5ad
md5: 5f658531816b042805334e5248dca7ec
size: 344165415
- path: data/intermediate/covid_val_data.h5ad
md5: 3404d3dcae95d8519f202d86570dbf92
size: 46229075
- path: src/pipeline/classifier.py
md5: bf5377f89bcd10ee1b53207d900ef86d
size: 4331
params:
params.toml:
classifier.n_hidden_layers: 2
classifier.training_opts.max_epochs: 10
outs:
- path: data/artifacts/classifer_w_simulated_data_metrics.json
md5: 3352e12194ae292bb0150d49b731b162
size: 361
- path: data/artifacts/classifer_wout_simulated_data_metrics.json
md5: f15f836d0f47953309f8b103533df20e
size: 361