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scvi-tools
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heart-cell-atlas-scvi

scvi-tools
biology
genomics
single-cell
model_cls_name:SCVI
scvi_version:1.2.0
anndata_version:0.11.1
modality:rna
tissue:heart
annotated:True
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@@ -51,10 +51,10 @@ space might still be useful for analysis.
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  | Metric | Training Value | Validation Value |
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  |-------------------------|----------------|------------------|
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- | Mean Absolute Error | 1.24 | 1.31 |
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- | Pearson Correlation | 0.52 | 0.49 |
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- | Spearman Correlation | 0.58 | 0.56 |
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- | R² (R-Squared) | -0.84 | -0.95 |
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  The gene-wise coefficient of variation summarizes how well variation between different genes is
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  preserved by the generated model expression. This value is usually quite high.
@@ -63,10 +63,10 @@ preserved by the generated model expression. This value is usually quite high.
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  | Metric | Training Value |
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  |-------------------------|----------------|
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- | Mean Absolute Error | 2.67 |
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- | Pearson Correlation | 0.85 |
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- | Spearman Correlation | 0.95 |
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- | R² (R-Squared) | 0.03 |
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  </details>
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@@ -83,17 +83,17 @@ cell-type.
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  | Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |
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  | --- | --- | --- | --- | --- | --- | --- | --- |
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- | Ventricular_Cardiomyocyte | 0.96 | 1.33 | 0.65 | 0.96 | 0.29 | 0.91 | 5307.00 |
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- | Endothelial | 0.93 | 0.89 | 0.64 | 0.91 | 0.26 | 0.94 | 4109.00 |
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- | Pericytes | 0.94 | 1.08 | 0.48 | 0.85 | 0.22 | 0.87 | 3204.00 |
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- | Fibroblast | 0.94 | 1.38 | 0.60 | 0.91 | 0.36 | 0.90 | 2446.00 |
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- | Atrial_Cardiomyocyte | 0.95 | 2.28 | 0.49 | 0.84 | 0.38 | 0.84 | 1009.00 |
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- | Myeloid | 0.90 | 2.24 | 0.53 | 0.87 | 0.40 | 0.90 | 957.00 |
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- | Lymphoid | 0.92 | 3.25 | 0.47 | 0.76 | 0.31 | 0.85 | 653.00 |
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- | Smooth_muscle_cells | 0.84 | 2.98 | 0.51 | 0.73 | 0.36 | 0.81 | 641.00 |
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- | Neuronal | 0.51 | 5.32 | 0.44 | 0.46 | 0.38 | 0.67 | 153.00 |
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- | Adipocytes | 0.77 | 4.52 | 0.52 | 0.72 | 0.52 | 0.80 | 145.00 |
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- | Mesothelial | 0.29 | 10.24 | 0.30 | 0.20 | 0.39 | 0.64 | 17.00 |
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  </details>
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@@ -146,17 +146,17 @@ Arguments passed to setup_anndata of the original model:
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  <summary><strong>Data Registry</strong></summary>
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  Registry elements for AnnData manager:
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- | Registry Key | scvi-tools Location |
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- |------------------------|--------------------------------------------|
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- | X | adata.layers['counts'] |
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- | batch | adata.obs['_scvi_batch'] |
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- | extra_categorical_covs | adata.obsm['_scvi_extra_categorical_covs'] |
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- | extra_continuous_covs | adata.obsm['_scvi_extra_continuous_covs'] |
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- | labels | adata.obs['_scvi_labels'] |
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- | latent_qzm | adata.obsm['scvi_latent_qzm'] |
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- | latent_qzv | adata.obsm['scvi_latent_qzv'] |
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- | minify_type | adata.uns['_scvi_adata_minify_type'] |
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- | observed_lib_size | adata.obs['observed_lib_size'] |
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  - **Data is Minified**: False
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@@ -165,16 +165,16 @@ Registry elements for AnnData manager:
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  <details>
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  <summary><strong>Summary Statistics</strong></summary>
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- | Summary Stat Key | Value |
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  |--------------------------|-------|
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- | n_batch | 1 |
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- | n_cells | 18641 |
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- | n_extra_categorical_covs | 2 |
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- | n_extra_continuous_covs | 2 |
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- | n_labels | 1 |
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- | n_latent_qzm | 10 |
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- | n_latent_qzv | 10 |
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- | n_vars | 1200 |
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  </details>
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  | Metric | Training Value | Validation Value |
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  |-------------------------|----------------|------------------|
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+ | Mean Absolute Error | 0.89 | 0.95 |
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+ | Pearson Correlation | 0.79 | 0.76 |
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+ | Spearman Correlation | 0.81 | 0.79 |
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+ | R² (R-Squared) | 0.43 | 0.29 |
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  The gene-wise coefficient of variation summarizes how well variation between different genes is
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  preserved by the generated model expression. This value is usually quite high.
 
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  | Metric | Training Value |
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  |-------------------------|----------------|
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+ | Mean Absolute Error | 1.48 |
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+ | Pearson Correlation | 0.93 |
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+ | Spearman Correlation | 0.99 |
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+ | R² (R-Squared) | 0.86 |
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  </details>
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  | Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |
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  | --- | --- | --- | --- | --- | --- | --- | --- |
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+ | Ventricular_Cardiomyocyte | 0.97 | 0.74 | 0.83 | 0.98 | 0.29 | 0.91 | 5307.00 |
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+ | Endothelial | 0.95 | 0.61 | 0.83 | 0.95 | 0.25 | 0.94 | 4109.00 |
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+ | Pericytes | 0.97 | 0.85 | 0.68 | 0.93 | 0.18 | 0.86 | 3204.00 |
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+ | Fibroblast | 0.96 | 0.79 | 0.81 | 0.97 | 0.34 | 0.89 | 2446.00 |
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+ | Atrial_Cardiomyocyte | 0.97 | 1.28 | 0.79 | 0.93 | 0.34 | 0.84 | 1009.00 |
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+ | Myeloid | 0.95 | 1.69 | 0.69 | 0.93 | 0.39 | 0.90 | 957.00 |
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+ | Lymphoid | 0.97 | 2.34 | 0.66 | 0.89 | 0.30 | 0.85 | 653.00 |
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+ | Smooth_muscle_cells | 0.94 | 2.54 | 0.64 | 0.83 | 0.32 | 0.80 | 641.00 |
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+ | Neuronal | 0.87 | 4.03 | 0.61 | 0.68 | 0.37 | 0.68 | 153.00 |
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+ | Adipocytes | 0.91 | 2.53 | 0.75 | 0.86 | 0.46 | 0.79 | 145.00 |
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+ | Mesothelial | 0.61 | 6.27 | 0.57 | 0.55 | 0.36 | 0.65 | 17.00 |
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  </details>
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  <summary><strong>Data Registry</strong></summary>
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  Registry elements for AnnData manager:
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+ | Registry Key | scvi-tools Location |
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+ |--------------------------|--------------------------------------|
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+ | X | adata.layers['counts'] |
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+ | batch | adata.obs['_scvi_batch'] |
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+ | extra_categorical_covs | adata.obsm['_scvi_extra_categorical_covs'] |
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+ | extra_continuous_covs | adata.obsm['_scvi_extra_continuous_covs'] |
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+ | labels | adata.obs['_scvi_labels'] |
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+ | latent_qzm | adata.obsm['scvi_latent_qzm'] |
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+ | latent_qzv | adata.obsm['scvi_latent_qzv'] |
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+ | minify_type | adata.uns['_scvi_adata_minify_type'] |
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+ | observed_lib_size | adata.obs['observed_lib_size'] |
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  - **Data is Minified**: False
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  <details>
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  <summary><strong>Summary Statistics</strong></summary>
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+ | Summary Stat Key | Value |
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  |--------------------------|-------|
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+ | n_batch | 1 |
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+ | n_cells | 18641 |
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+ | n_extra_categorical_covs | 2 |
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+ | n_extra_continuous_covs | 2 |
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+ | n_labels | 1 |
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+ | n_latent_qzm | 10 |
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+ | n_latent_qzv | 10 |
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+ | n_vars | 1200 |
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  </details>
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