inVAE

inVAE is a conditionally invariant variational autoencoder that identifies both spurious (distractors) and invariant features. It leverages domain variability to learn conditionally invariant representations. We show that inVAE captures biological variations in single-cell datasets obtained from diverse conditions and labs. inVAE incorporates biological covariates and mechanisms such as disease states, to learn an invariant data representation. This improves cell classification accuracy significantly.

Installation

PyPI only
pip install invae
Development Version (latest version on github)
git clone https://github.com/theislab/inVAE.git
cd inVAE
pip install .

Example

Integration of Human Lung Cell Atlas using both healthy and disease samples

Usage

Load the data:
adata = sc.read(path/to/data)
Optional - Split the data into train, val, test (in supervised case for training classifier as well)
Initialize the model, either Factorized or Non-Factorized:

from inVAE import FinVAE, NFinVAE`

inv_covar_keys = {
    'cont': [],
    'cat': ['cell_type', 'disease'] #set to the keys in the adata
}

spur_covar_keys = {
    'cont': [],
    'cat': ['batch'] #set to the keys in the adata
}

model = FinVAE(
    adata = adata_train,
    layer = 'counts', # The layer where the raw counts are stored in adata (None for adata.X: default)
    inv_covar_keys = inv_covar_keys,
    spur_covar_keys = spur_covar_keys,
    latent_dim_inv = 20, 
    latent_dim_spur = 5,
    device = 'cpu',
    decoder_dist = 'nb'
)

Set inject_covar_in_latent= True if you wish to add the spurious conditions directly to the latent (instead of learning the spurious latents). This gives you the most compatible version to SCVI.

For non-factorized model, use:

model = NFinVAE(
    adata = adata_train,
    layer = 'counts', # The layer where the raw counts are stored in adata (None for adata.X: default)
    inv_covar_keys = inv_covar_keys,
    spur_covar_keys = spur_covar_keys,
    latent_dim_inv = 20, 
    latent_dim_spur = 5,
    device = 'cpu',
    decoder_dist = 'nb'
)

Train the generative model:
model.train(n_epochs=500, lr_train=0.001, weight_decay=0.0001)
Get the latent representation:
latent = model.get_latent_representation(adata)
Optional - Train the classifer (for cell types):

model.train_classifier(
    adata_val,
    batch_key = 'batch',
    label_key = 'cell_type',
)

Optional - Predict cell types:
pred_test = model.predict(adata_test, dataset_type='test')
Optional - Saving and loading model:

model.save('./checkpoints/path.pt')
model.load('./checkpoints/path.pt')

Dependencies

scanpy==1.9.3
torch==2.0.1
tensorboard==2.13.0
anndata==0.8.0

Citation