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 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)
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 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)
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,
dataset,
train_size=0.9,
test_size=0.1,
use_cuda=use_cuda,
frequency=1,
data_loader_kwargs={"batch_size": 256, "pin_memory": False},
early_stopping_kwargs=early_stopping_kwargs,
)
trainer.train(lr=lr, n_epochs=500)
# create posterior on full data
full_posterior = trainer.create_posterior(
model, dataset, indices=np.arange(len(dataset)), type_class=TotalPosterior,
)
torch.save(
trainer.model.state_dict(), "differential_expression/saved_models/" + n + ".pt"
)