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--- |
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license: cc-by-4.0 |
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library_name: scvi-tools |
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tags: |
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- biology |
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- genomics |
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- single-cell |
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- model_cls_name:SCANVI |
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- modality:rna |
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- annotated:True |
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--- |
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# Description |
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Mouse preimplantation development model spanning early stages of development. The |
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model was trained utilizing single‐cell ANnotation using Variational Inference |
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(scANVI, [Xu et al., 2021]) implemented in [scvi-tools]. In short, scANVI raw |
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single-cell RNA sequencing (scRNA-seq) count matrix - cell by gene, where values |
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represent gene expression measured by counting number of transcribed RNA. |
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# Model Training |
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- [raw dataset](https://zenodo.org/records/13749348/files/01_mouse_reprocessed.h5ad) |
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- [notebook analysis](https://github.com/brickmanlab/proks-salehin-et-al/blob/master/notebooks/15_mouse_scANVI_fix.ipynb) |
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# Metrics |
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Cell type (`ct`) prediction |
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| Metric | Score | |
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|-------------------|---------------------| |
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| Accuracy score | 0.9126746506986028 | |
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| Balanced accuracy | 0.9572872718187365 | |
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| F1 (micro) | 0.9126746506986028 | |
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| F1 (macro) | 0.9201654923575322 | |
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# Model parameters |
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Below we provide settings for scANVI setup |
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`lvae.init_params_["non_kwargs"]` |
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```json |
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{ |
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"n_hidden": 128, |
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"n_latent": 10, |
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"n_layers": 2, |
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"dropout_rate": 0.1, |
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"dispersion": "gene", |
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"gene_likelihood": "nb", |
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"linear_classifier": false |
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} |
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``` |
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`lvae.adata_manager.registry['setup_args']` |
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```json |
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{ |
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"labels_key": "ct", |
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"unlabeled_category": "Unknown", |
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"layer": "counts", |
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"batch_key": "batch", |
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"size_factor_key": null, |
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"categorical_covariate_keys": null, |
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"continuous_covariate_keys": null |
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} |
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``` |
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# References |
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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](https://doi.org/10.1038/s41592-024-02511-3) |
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[Xu et al., 2021]: https://www.embopress.org/doi/full/10.15252/msb.20209620 |
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[scvi-tools]: http://scvi-tools.org |
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