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mouse_thymus_cite_totalvi

scvi-tools
biology
genomics
single-cell
model_cls_name:TOTALVI
scvi_version:1.2.0
anndata_version:0.11.1
modality:rna
modality:protein
tissue:thymus
annotated:True
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  1. mdata.h5mu +2 -2
  2. metrics.json +3 -3
  3. model.pt +2 -2
mdata.h5mu CHANGED
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metrics.json CHANGED
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  {
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- "cell_wise_cv": "Modality: rna\n\n| Metric | Training Value | Validation Value |\n|-------------------------|----------------|------------------|\n| Mean Absolute Error | 2.07 | 2.06 |\n| Pearson Correlation | 0.55 | 0.60 |\n| Spearman Correlation | 0.63 | 0.63 |\n| R\u00b2 (R-Squared) | -3.69 | -4.52 |\n\nModality: protein\n\n| Metric | Training Value | Validation Value |\n|-------------------------|----------------|------------------|\n| Mean Absolute Error | 0.23 | 0.23 |\n| Pearson Correlation | 0.73 | 0.72 |\n| Spearman Correlation | 0.72 | 0.71 |\n| R\u00b2 (R-Squared) | 0.38 | 0.35 |\n\n",
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- "gene_wise_cv": "Modality: rna\n\n| Metric | Training Value |\n|-------------------------|----------------|\n| Mean Absolute Error | 4.91 |\n| Pearson Correlation | 0.88 |\n| Spearman Correlation | 0.98 |\n| R\u00b2 (R-Squared) | 0.77 |\n\nModality: protein\n\n| Metric | Training Value |\n|-------------------------|----------------|\n| Mean Absolute Error | 0.23 |\n| Pearson Correlation | 0.94 |\n| Spearman Correlation | 0.97 |\n| R\u00b2 (R-Squared) | 0.65 |\n\n",
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- "diff_exp": "Modality: rna\n\n| Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |\n| --- | --- | --- | --- | --- | --- | --- | --- |\n| DP (Q2) | 0.90 | 2.04 | 0.52 | 0.84 | 0.09 | 0.02 | 10864.00 |\n| DP (Sig.) | 0.83 | 1.90 | 0.50 | 0.86 | 0.03 | 0.02 | 9824.00 |\n| DP (Q1) | 0.89 | 1.75 | 0.54 | 0.86 | 0.02 | 0.02 | 8556.00 |\n| Mature CD4 | 0.95 | 2.05 | 0.59 | 0.89 | 0.05 | 0.02 | 6525.00 |\n| Immature CD8 | 0.94 | 1.95 | 0.59 | 0.86 | 0.02 | 0.02 | 5686.00 |\n| DP (P) | 0.93 | 1.29 | 0.67 | 0.95 | 0.85 | 0.08 | 5593.00 |\n| Immature CD4 | 0.92 | 2.08 | 0.56 | 0.84 | 0.02 | 0.02 | 5164.00 |\n| Mature CD8 | 0.88 | 1.92 | 0.65 | 0.90 | 0.34 | 0.08 | 4234.00 |\n| DN | 0.80 | 1.48 | 0.63 | 0.93 | 0.69 | 0.14 | 2395.00 |\n| GD T | 0.80 | 2.38 | 0.54 | 0.79 | 0.34 | 0.33 | 2279.00 |\n| Treg | 0.88 | 2.21 | 0.61 | 0.80 | 0.42 | 0.35 | 1966.00 |\n| Neg. sel. (2) | 0.88 | 2.72 | 0.61 | 0.73 | 0.28 | 0.26 | 1560.00 |\n| Dying | 0.70 | 3.28 | 0.54 | 0.52 | 0.02 | 0.01 | 1552.00 |\n| Neg. sel. (1) | 0.80 | 2.62 | 0.65 | 0.76 | 0.21 | 0.14 | 1206.00 |\n| Mature cycling | 0.87 | 2.22 | 0.68 | 0.86 | 0.78 | 0.72 | 992.00 |\n| Interferon sig. | 0.86 | 2.98 | 0.62 | 0.62 | 0.27 | 0.13 | 984.00 |\n| NKT | 0.66 | 2.08 | 0.56 | 0.81 | 0.58 | 0.36 | 928.00 |\n| Myeloid | 0.86 | 1.50 | 0.66 | 0.86 | 0.56 | 0.41 | 908.00 |\n| Doublet | 0.57 | 2.89 | 0.61 | 0.50 | 0.35 | 0.04 | 677.00 |\n| B | 0.86 | 3.95 | 0.65 | 0.63 | 0.30 | 0.02 | 106.00 |\n| Erythrocyte | 0.82 | 4.57 | 0.61 | 0.50 | 0.35 | 0.02 | 43.00 |\n\nModality: protein\n\n| Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |\n| --- | --- | --- | --- | --- | --- | --- | --- |\n| DP (Q2) | 1.00 | 0.04 | 1.00 | 0.99 | 0.12 | 0.15 | 10864.00 |\n| DP (Sig.) | 1.00 | 0.04 | 1.00 | 0.98 | 0.28 | 0.32 | 9824.00 |\n| DP (Q1) | 1.00 | 0.03 | 1.00 | 1.00 | 0.11 | 0.15 | 8556.00 |\n| Mature CD4 | 1.00 | 0.06 | 1.00 | 0.99 | 0.11 | 0.15 | 6525.00 |\n| Immature CD8 | 1.00 | 0.04 | 1.00 | 0.99 | 0.36 | 0.38 | 5686.00 |\n| DP (P) | 1.00 | 0.04 | 1.00 | 0.97 | 0.25 | 0.18 | 5593.00 |\n| Immature CD4 | 1.00 | 0.04 | 1.00 | 0.98 | 0.27 | 0.27 | 5164.00 |\n| Mature CD8 | 1.00 | 0.06 | 1.00 | 0.99 | 0.09 | 0.15 | 4234.00 |\n| DN | 0.82 | 0.07 | 1.00 | 0.99 | 0.43 | 0.23 | 2395.00 |\n| GD T | 0.91 | 0.07 | 0.99 | 0.98 | 0.73 | 0.75 | 2279.00 |\n| Treg | 1.00 | 0.06 | 1.00 | 0.99 | 0.64 | 0.67 | 1966.00 |\n| Neg. sel. (2) | 0.91 | 0.06 | 1.00 | 0.99 | 0.64 | 0.67 | 1560.00 |\n| Dying | 0.91 | 0.06 | 0.98 | 0.97 | 0.55 | 0.58 | 1552.00 |\n| Neg. sel. (1) | 1.00 | 0.07 | 0.99 | 0.98 | 0.64 | 0.66 | 1206.00 |\n| Mature cycling | 1.00 | 0.07 | 0.99 | 0.98 | 0.45 | 0.50 | 992.00 |\n| Interferon sig. | 0.91 | 0.06 | 0.97 | 0.87 | 0.45 | 0.46 | 984.00 |\n| NKT | 1.00 | 0.09 | 0.99 | 0.98 | 0.64 | 0.67 | 928.00 |\n| Myeloid | 1.00 | 0.10 | 0.99 | 0.96 | 0.91 | 0.92 | 908.00 |\n| Doublet | 0.82 | 0.12 | 0.83 | 0.84 | 0.96 | 0.83 | 677.00 |\n| B | 0.91 | 0.25 | 0.99 | 0.92 | 0.82 | 0.84 | 106.00 |\n| Erythrocyte | 0.73 | 0.37 | 0.94 | 0.85 | 0.47 | 0.60 | 43.00 |\n\n"
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  }
 
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  {
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+ "cell_wise_cv": "Modality: rna\n\n| Metric | Training Value | Validation Value |\n|-------------------------|----------------|------------------|\n| Mean Absolute Error | 2.07 | 2.06 |\n| Pearson Correlation | 0.57 | 0.63 |\n| Spearman Correlation | 0.63 | 0.64 |\n| R\u00b2 (R-Squared) | -4.01 | -4.47 |\n\nModality: protein\n\n| Metric | Training Value | Validation Value |\n|-------------------------|----------------|------------------|\n| Mean Absolute Error | 0.23 | 0.23 |\n| Pearson Correlation | 0.74 | 0.72 |\n| Spearman Correlation | 0.72 | 0.70 |\n| R\u00b2 (R-Squared) | 0.39 | 0.36 |\n\n",
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+ "gene_wise_cv": "Modality: rna\n\n| Metric | Training Value |\n|-------------------------|----------------|\n| Mean Absolute Error | 4.88 |\n| Pearson Correlation | 0.88 |\n| Spearman Correlation | 0.98 |\n| R\u00b2 (R-Squared) | 0.76 |\n\nModality: protein\n\n| Metric | Training Value |\n|-------------------------|----------------|\n| Mean Absolute Error | 0.23 |\n| Pearson Correlation | 0.93 |\n| Spearman Correlation | 0.97 |\n| R\u00b2 (R-Squared) | 0.64 |\n\n",
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+ "diff_exp": "Modality: rna\n\n| Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |\n| --- | --- | --- | --- | --- | --- | --- | --- |\n| DP (Q2) | 0.90 | 2.14 | 0.49 | 0.85 | 0.09 | 0.02 | 10864.00 |\n| DP (Sig.) | 0.83 | 1.98 | 0.48 | 0.86 | 0.03 | 0.02 | 9824.00 |\n| DP (Q1) | 0.89 | 1.78 | 0.52 | 0.86 | 0.02 | 0.02 | 8556.00 |\n| Mature CD4 | 0.95 | 2.08 | 0.59 | 0.88 | 0.05 | 0.02 | 6525.00 |\n| Immature CD8 | 0.93 | 2.05 | 0.56 | 0.87 | 0.02 | 0.02 | 5686.00 |\n| DP (P) | 0.92 | 1.32 | 0.66 | 0.96 | 0.85 | 0.08 | 5593.00 |\n| Immature CD4 | 0.94 | 1.96 | 0.59 | 0.85 | 0.02 | 0.02 | 5164.00 |\n| Mature CD8 | 0.86 | 1.80 | 0.67 | 0.91 | 0.34 | 0.08 | 4234.00 |\n| DN | 0.79 | 1.47 | 0.63 | 0.94 | 0.69 | 0.14 | 2395.00 |\n| GD T | 0.78 | 2.05 | 0.62 | 0.82 | 0.34 | 0.33 | 2279.00 |\n| Treg | 0.89 | 2.15 | 0.62 | 0.81 | 0.42 | 0.35 | 1966.00 |\n| Neg. sel. (2) | 0.88 | 2.77 | 0.60 | 0.72 | 0.29 | 0.26 | 1560.00 |\n| Dying | 0.66 | 3.17 | 0.56 | 0.54 | 0.02 | 0.01 | 1552.00 |\n| Neg. sel. (1) | 0.80 | 2.66 | 0.63 | 0.76 | 0.20 | 0.13 | 1206.00 |\n| Mature cycling | 0.87 | 2.29 | 0.67 | 0.85 | 0.78 | 0.72 | 992.00 |\n| Interferon sig. | 0.85 | 2.89 | 0.64 | 0.62 | 0.26 | 0.14 | 984.00 |\n| NKT | 0.67 | 2.19 | 0.53 | 0.78 | 0.58 | 0.35 | 928.00 |\n| Myeloid | 0.86 | 1.40 | 0.69 | 0.87 | 0.55 | 0.40 | 908.00 |\n| Doublet | 0.54 | 2.84 | 0.61 | 0.48 | 0.29 | 0.04 | 677.00 |\n| B | 0.86 | 3.86 | 0.66 | 0.64 | 0.22 | 0.01 | 106.00 |\n| Erythrocyte | 0.76 | 4.71 | 0.59 | 0.48 | 0.31 | 0.02 | 43.00 |\n\nModality: protein\n\n| Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |\n| --- | --- | --- | --- | --- | --- | --- | --- |\n| DP (Q2) | 0.91 | 0.04 | 1.00 | 0.99 | 0.12 | 0.15 | 10864.00 |\n| DP (Sig.) | 1.00 | 0.04 | 0.99 | 0.97 | 0.28 | 0.32 | 9824.00 |\n| DP (Q1) | 1.00 | 0.04 | 1.00 | 1.00 | 0.11 | 0.15 | 8556.00 |\n| Mature CD4 | 1.00 | 0.06 | 1.00 | 1.00 | 0.11 | 0.15 | 6525.00 |\n| Immature CD8 | 1.00 | 0.04 | 1.00 | 0.99 | 0.36 | 0.38 | 5686.00 |\n| DP (P) | 1.00 | 0.04 | 1.00 | 0.97 | 0.25 | 0.18 | 5593.00 |\n| Immature CD4 | 1.00 | 0.05 | 1.00 | 0.98 | 0.27 | 0.27 | 5164.00 |\n| Mature CD8 | 1.00 | 0.06 | 1.00 | 0.99 | 0.09 | 0.15 | 4234.00 |\n| DN | 0.82 | 0.08 | 1.00 | 0.98 | 0.43 | 0.23 | 2395.00 |\n| GD T | 1.00 | 0.08 | 0.99 | 0.97 | 0.73 | 0.75 | 2279.00 |\n| Treg | 1.00 | 0.06 | 1.00 | 0.99 | 0.64 | 0.67 | 1966.00 |\n| Neg. sel. (2) | 0.91 | 0.06 | 1.00 | 0.99 | 0.64 | 0.67 | 1560.00 |\n| Dying | 0.91 | 0.07 | 0.98 | 0.97 | 0.55 | 0.58 | 1552.00 |\n| Neg. sel. (1) | 1.00 | 0.07 | 0.99 | 0.98 | 0.63 | 0.63 | 1206.00 |\n| Mature cycling | 0.91 | 0.06 | 0.99 | 0.98 | 0.45 | 0.50 | 992.00 |\n| Interferon sig. | 0.91 | 0.06 | 0.97 | 0.88 | 0.46 | 0.46 | 984.00 |\n| NKT | 1.00 | 0.09 | 0.99 | 0.98 | 0.64 | 0.67 | 928.00 |\n| Myeloid | 0.91 | 0.10 | 0.99 | 0.97 | 0.91 | 0.92 | 908.00 |\n| Doublet | 0.55 | 0.13 | 0.83 | 0.83 | 0.95 | 0.73 | 677.00 |\n| B | 0.91 | 0.23 | 0.99 | 0.94 | 0.82 | 0.84 | 106.00 |\n| Erythrocyte | 0.55 | 0.39 | 0.94 | 0.83 | 0.49 | 0.62 | 43.00 |\n\n"
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  }
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