def totalvi_benchmark(dataset, n_epochs, use_cuda=True):
totalvae = TOTALVI(dataset.nb_genes,
len(dataset.protein_names),
n_batch=dataset.n_batches)
trainer = TotalTrainer(totalvae,
dataset,
train_size=0.5,
use_cuda=use_cuda,
early_stopping_kwargs=None)
trainer.train(n_epochs=n_epochs)
trainer.test_set.reconstruction_error()
trainer.test_set.marginal_ll()
trainer.test_set.get_protein_background_mean()
trainer.test_set.get_latent()
trainer.test_set.generate()
trainer.test_set.get_sample_dropout()
trainer.test_set.get_normalized_denoised_expression(transform_batch=0)
trainer.test_set.get_normalized_denoised_expression(transform_batch=0)
trainer.test_set.imputation()
trainer.test_set.get_protein_mean()
trainer.test_set.one_vs_all_degenes(n_samples=2, M_permutation=10)
trainer.test_set.generate_feature_correlation_matrix(n_samples=2)
trainer.test_set.generate_feature_correlation_matrix(n_samples=2,
transform_batch=0)
return trainer
def test_special_dataset_size(self):
gene_dataset = GeneExpressionDataset()
x = np.random.randint(1, 100, (17 * 2, 10))
y = np.random.randint(1, 100, (17 * 2, 10))
gene_dataset.populate_from_data(x)
protein_data = CellMeasurement(
name="protein_expression",
data=y,
columns_attr_name="protein_names",
columns=np.arange(10),
)
gene_dataset.initialize_cell_measurement(protein_data)
# Test UnsupervisedTrainer
vae = VAE(
gene_dataset.nb_genes,
n_batch=gene_dataset.n_batches,
n_labels=gene_dataset.n_labels,
)
trainer = UnsupervisedTrainer(
vae,
gene_dataset,
train_size=0.5,
use_cuda=False,
data_loader_kwargs={"batch_size": 8},
)
trainer.train(n_epochs=1)
# Test JVATrainer
jvae = JVAE(
[gene_dataset.nb_genes, gene_dataset.nb_genes],
gene_dataset.nb_genes,
[slice(None)] * 2,
["zinb", "zinb"],
[True, True],
n_batch=1,
)
cls = Classifier(gene_dataset.nb_genes, n_labels=2, logits=True)
trainer = JVAETrainer(
jvae,
cls,
[gene_dataset, gene_dataset],
train_size=0.5,
use_cuda=False,
data_loader_kwargs={"batch_size": 8},
)
trainer.train(n_epochs=1)
totalvae = TOTALVI(gene_dataset.nb_genes,
len(gene_dataset.protein_names))
trainer = TotalTrainer(
totalvae,
gene_dataset,
train_size=0.5,
use_cuda=False,
data_loader_kwargs={"batch_size": 8},
early_stopping_kwargs=None,
)
trainer.train(n_epochs=1)
def test_totalvi(save_path):
synthetic_dataset_one_batch = SyntheticDataset(n_batches=1)
totalvi_benchmark(synthetic_dataset_one_batch,
n_epochs=1,
use_cuda=use_cuda)
synthetic_dataset_two_batches = SyntheticDataset(n_batches=2)
totalvi_benchmark(synthetic_dataset_two_batches,
n_epochs=1,
use_cuda=use_cuda)
# adversarial testing
dataset = synthetic_dataset_two_batches
totalvae = TOTALVI(dataset.nb_genes,
len(dataset.protein_names),
n_batch=dataset.n_batches)
trainer = TotalTrainer(
totalvae,
dataset,
train_size=0.5,
use_cuda=use_cuda,
early_stopping_kwargs=None,
use_adversarial_loss=True,
)
trainer.train(n_epochs=1)
with tempfile.TemporaryDirectory() as temp_dir:
posterior_save_path = os.path.join(temp_dir, "posterior_data")
original_post = trainer.create_posterior(
totalvae,
dataset,
indices=np.arange(len(dataset)),
type_class=TotalPosterior,
)
original_post.save_posterior(posterior_save_path)
new_totalvae = TOTALVI(dataset.nb_genes,
len(dataset.protein_names),
n_batch=dataset.n_batches)
new_post = load_posterior(posterior_save_path,
model=new_totalvae,
use_cuda=False)
assert new_post.posterior_type == "TotalPosterior"
assert np.array_equal(new_post.gene_dataset.protein_expression,
dataset.protein_expression)
def totalvi_benchmark(dataset, n_epochs, use_cuda=True):
totalvae = TOTALVI(
dataset.nb_genes, len(dataset.protein_names), n_batch=dataset.n_batches
)
trainer = TotalTrainer(totalvae, dataset, train_size=0.5, use_cuda=use_cuda)
trainer.train(n_epochs=n_epochs)
trainer.test_set.reconstruction_error()
trainer.test_set.marginal_ll()
trainer.test_set.get_protein_background_mean()
trainer.test_set.get_latent()
trainer.test_set.generate()
trainer.test_set.get_sample_dropout()
trainer.test_set.get_normalized_denoised_expression()
trainer.test_set.imputation()
return trainer
def test_totalvi(save_path):
synthetic_dataset_one_batch = SyntheticDataset(n_batches=1)
totalvi_benchmark(synthetic_dataset_one_batch, n_epochs=1, use_cuda=use_cuda)
synthetic_dataset_two_batches = SyntheticDataset(n_batches=2)
totalvi_benchmark(synthetic_dataset_two_batches, n_epochs=1, use_cuda=use_cuda)
# adversarial testing
dataset = synthetic_dataset_two_batches
totalvae = TOTALVI(
dataset.nb_genes, len(dataset.protein_names), n_batch=dataset.n_batches
)
trainer = TotalTrainer(
totalvae,
dataset,
train_size=0.5,
use_cuda=use_cuda,
early_stopping_kwargs=None,
use_adversarial_loss=True,
)
trainer.train(n_epochs=1)
for n, adata in zip(names, adatas):
hvg = adata.var["hvg_encode"]
dataset = AnnDatasetFromAnnData(ad=adata[:, hvg])
protein_data = CellMeasurement(
name="protein_expression",
data=adata.obsm["protein_expression"].astype(np.float32),
columns_attr_name="protein_names",
columns=adata.uns["protein_names"],
)
dataset.initialize_cell_measurement(protein_data)
dataset.gene_names = adata[:, hvg].var_names.values
set_seed(0)
model = TOTALVI(dataset.nb_genes, dataset.protein_expression.shape[1], n_latent=20,)
use_cuda = True
lr = 4e-3
early_stopping_kwargs = {
"early_stopping_metric": "elbo",
"save_best_state_metric": "elbo",
"patience": 45,
"threshold": 0,
"reduce_lr_on_plateau": True,
"lr_patience": 30,
"lr_factor": 0.6,
"posterior_class": TotalPosterior,
}
trainer = TotalTrainer(
model,
def test_differential_expression(save_path):
dataset = CortexDataset(save_path=save_path)
n_cells = len(dataset)
all_indices = np.arange(n_cells)
vae = VAE(dataset.nb_genes, dataset.n_batches)
trainer = UnsupervisedTrainer(vae, dataset, train_size=0.5, use_cuda=use_cuda)
trainer.train(n_epochs=2)
post = trainer.create_posterior(vae, dataset, shuffle=False, indices=all_indices)
with tempfile.TemporaryDirectory() as temp_dir:
posterior_save_path = os.path.join(temp_dir, "posterior_data")
post.save_posterior(posterior_save_path)
new_vae = VAE(dataset.nb_genes, dataset.n_batches)
new_post = load_posterior(posterior_save_path, model=new_vae, use_cuda=False)
assert np.array_equal(new_post.indices, post.indices)
assert np.array_equal(new_post.gene_dataset.X, post.gene_dataset.X)
# Sample scale example
px_scales = post.scale_sampler(
n_samples_per_cell=4, n_samples=None, selection=all_indices
)["scale"]
assert (
px_scales.shape[1] == dataset.nb_genes
), "posterior scales should have shape (n_samples, n_genes)"
# Differential expression different models
idx_1 = [1, 2, 3]
idx_2 = [4, 5, 6, 7]
de_dataframe = post.differential_expression_score(
idx1=idx_1,
idx2=idx_2,
n_samples=10,
mode="vanilla",
use_permutation=True,
M_permutation=100,
)
de_dataframe = post.differential_expression_score(
idx1=idx_1,
idx2=idx_2,
n_samples=10,
mode="change",
use_permutation=True,
M_permutation=100,
cred_interval_lvls=[0.5, 0.95],
)
print(de_dataframe.keys())
assert (
de_dataframe["confidence_interval_0.5_min"]
<= de_dataframe["confidence_interval_0.5_max"]
).all()
assert (
de_dataframe["confidence_interval_0.95_min"]
<= de_dataframe["confidence_interval_0.95_max"]
).all()
# DE estimation example
de_probabilities = de_dataframe.loc[:, "proba_de"]
assert ((0.0 <= de_probabilities) & (de_probabilities <= 1.0)).all()
# Test totalVI DE
sp = os.path.join(save_path, "10X")
dataset = Dataset10X(dataset_name="pbmc_10k_protein_v3", save_path=sp)
n_cells = len(dataset)
all_indices = np.arange(n_cells)
vae = TOTALVI(
dataset.nb_genes, len(dataset.protein_names), n_batch=dataset.n_batches
)
trainer = TotalTrainer(
vae, dataset, train_size=0.5, use_cuda=use_cuda, early_stopping_kwargs=None
)
trainer.train(n_epochs=2)
post = trainer.create_posterior(
vae, dataset, shuffle=False, indices=all_indices, type_class=TotalPosterior
)
# Differential expression different models
idx_1 = [1, 2, 3]
idx_2 = [4, 5, 6, 7]
de_dataframe = post.differential_expression_score(
idx1=idx_1,
idx2=idx_2,
n_samples=10,
mode="vanilla",
use_permutation=True,
M_permutation=100,
)
de_dataframe = post.differential_expression_score(
idx1=idx_1,
idx2=idx_2,
n_samples=10,
mode="change",
use_permutation=True,
M_permutation=100,
)