Description

HNOCA atlas

Model properties

Many model properties are in the model tags. Some more are listed below.

model_init_params:

{
    "hidden_layer_sizes": [
        1024
    ],
    "latent_dim": 10,
    "dr_rate": 0.05,
    "use_mmd": false,
    "mmd_on": "z",
    "mmd_boundary": null,
    "recon_loss": "nb",
    "beta": 1,
    "use_bn": false,
    "use_ln": true,
    "embedding_dims": [
        5
    ],
    "embedding_max_norm": 1.0,
    "inject_condition": [
        "encoder",
        "decoder"
    ],
    "mean": null
}

model_setup_anndata_args:

{
    "condition_keys": [
        "batch"
    ],
    "cell_type_keys": [
        "snapseed_pca_rss_level_1",
        "snapseed_pca_rss_level_12",
        "snapseed_pca_rss_level_123"
    ]
}

model_summary_stats:

[1m [0m[1mSummary Stat Key[0m[1m [0m	[1m [0m[1m Value [0m[1m [0m
[94m [0m[94m n_batch [0m[94m [0m	[35m [0m[35m 396 [0m[35m [0m
[94m [0m[94m n_cells [0m[94m [0m	[35m [0m[35m1770578[0m[35m [0m
[94m [0m[94m n_labels [0m[94m [0m	[35m [0m[35m 28 [0m[35m [0m
[94m [0m[94m n_vars [0m[94m [0m	[35m [0m[35m 3000 [0m[35m [0m

model_data_registry:

[1m [0m[1mRegistry Key[0m[1m [0m	[1m [0m[1mscvi-tools Location[0m[1m [0m

model_parent_module: scarches.model

data_is_minified: True

Training data

This is an optional link to where the training data is stored if it is too large to host on the huggingface Model hub.

Training data url: N/A

Training code

This is an optional link to the code used to train the model.

Training code url: N/A

References

He, Z., Dony, L., Fleck, J.S. et al. An integrated transcriptomic cell atlas of human neural organoids. Nature 635, 690–698 (2024). https://doi.org/10.1038/s41586-024-08172-8