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human-scanvi
brickmanlab/human-scanvi
human-scanvi is a machine learning model from brickmanlab. Use it for the machine learning task on the model card, and read the license before you ship it in a product. It is set up for scvi-tools. The card lists the license as cc-by-4.0.
Human preimplantation development model spanning early stages of development. The model was trained utilizing single‐cell ANnotation using Variational Inference (scANVI, [Xu et al., 2021]) implemented in [scvi-tools].…
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Updated Jan 17, 2025
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At a glance
- Library
- scvi-tools
- License
- cc-by-4.0
- Access
- Public
- Created
- Feb 16, 2024
- Updated
- Jan 17, 2025
- SHA
- 98c55695
Model card
From the Hugging Face model README
Description
Human preimplantation development model spanning early stages of development. The model was trained utilizing single‐cell ANnotation using Variational Inference (scANVI, Xu et al., 2021) implemented in scvi-tools. In short, scANVI raw single-cell RNA sequencing (scRNA-seq) count matrix - cell by gene, where values represent gene expression measured by counting number of transcribed RNA.
Model Training
Metrics
Cell type (ct) prediction
| Metric | Score |
|---|---|
| Accuracy score | 0.7968144640551011 |
| Balanced accuracy | 0.8502734650790613 |
| F1 (micro) | 0.7968144640551011 |
| F1 (macro) | 0.8150578255414443 |
Model parameters
Below we provide settings for scANVI setup
lvae.init_params_["non_kwargs"]
{
"n_hidden": 128,
"n_latent": 10,
"n_layers": 2,
"dropout_rate": 0.1,
"dispersion": "gene",
"gene_likelihood": "nb",
"linear_classifier": false
}
lvae.adata_manager.registry['setup_args']
{
"labels_key": "ct",
"unlabeled_category": "Unknown",
"layer": "counts",
"batch_key": "batch",
"size_factor_key": null,
"categorical_covariate_keys": null,
"continuous_covariate_keys": null
}
References
Proks, M., Salehin, N. & Brickman, J.M. Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing. Nat Methods 22, 207–216 (2025). https://doi.org/10.1038/s41592-024-02511-3
- Library
- scvi-tools
- License
- cc-by-4.0
- Created
- Feb 16, 2024
- Updated
- Jan 17, 2025