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Backport PR #2522 on branch 1.1.x (Allow for non-default user params …
…in `POISSONVI`) (#2524) Backport PR #2522: Allow for non-default user params in `POISSONVI` Co-authored-by: Martin Kim <46072231+martinkim0@users.noreply.github.com>
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Original file line number | Diff line number | Diff line change |
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@@ -1,13 +1,69 @@ | ||
from torch.nn import Linear | ||
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from scvi.data import synthetic_iid | ||
from scvi.external import POISSONVI | ||
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def test_poissonvi(): | ||
adata = synthetic_iid(batch_size=100) | ||
POISSONVI.setup_anndata( | ||
adata, | ||
) | ||
POISSONVI.setup_anndata(adata) | ||
model = POISSONVI(adata) | ||
model.train(max_epochs=1) | ||
model.get_latent_representation() | ||
model.get_accessibility_estimates() | ||
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def test_poissonvi_default_params(): | ||
from scvi.model import PEAKVI | ||
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adata = synthetic_iid(batch_size=100) | ||
POISSONVI.setup_anndata(adata) | ||
PEAKVI.setup_anndata(adata) | ||
poissonvi = POISSONVI(adata) | ||
peakvi = PEAKVI(adata) | ||
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assert poissonvi.module.n_latent == peakvi.module.n_latent | ||
assert poissonvi.module.latent_distribution == peakvi.module.latent_distribution | ||
poisson_encoder = poissonvi.module.z_encoder.encoder | ||
poisson_mean_encoder = poissonvi.module.z_encoder.mean_encoder | ||
poisson_decoder = poissonvi.module.decoder.px_decoder | ||
assert len(poisson_encoder.fc_layers) == peakvi.module.n_layers_encoder | ||
assert len(poisson_decoder.fc_layers) == peakvi.module.n_layers_encoder | ||
assert poisson_encoder.fc_layers[-1][0].in_features == peakvi.module.n_hidden | ||
assert poisson_decoder.fc_layers[-1][0].in_features == peakvi.module.n_hidden | ||
assert poisson_mean_encoder.out_features == peakvi.module.n_latent | ||
assert poisson_decoder.fc_layers[0][0].in_features == peakvi.module.n_latent | ||
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def test_poissonvi_non_default_params( | ||
n_hidden: int = 50, | ||
n_latent: int = 5, | ||
n_layers: int = 2, | ||
dropout_rate: float = 0.4, | ||
latent_distribution="ln", | ||
): | ||
adata = synthetic_iid(batch_size=100) | ||
POISSONVI.setup_anndata(adata) | ||
model = POISSONVI( | ||
adata, | ||
n_hidden=n_hidden, | ||
n_latent=n_latent, | ||
n_layers=n_layers, | ||
dropout_rate=dropout_rate, | ||
latent_distribution=latent_distribution, | ||
) | ||
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assert model.module.n_latent == n_latent | ||
assert model.module.latent_distribution == latent_distribution | ||
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encoder = model.module.z_encoder.encoder | ||
assert len(encoder.fc_layers) == n_layers | ||
linear = encoder.fc_layers[-1][0] | ||
assert isinstance(linear, Linear) | ||
assert linear.in_features == n_hidden | ||
mean_encoder = model.module.z_encoder.mean_encoder | ||
assert isinstance(mean_encoder, Linear) | ||
assert mean_encoder.out_features == n_latent | ||
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model.train(max_epochs=1) | ||
assert model.get_latent_representation().shape[1] == n_latent |