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scvi-tools
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tabula-sapiens-lung-scanvi

TensorBoard
scvi-tools
biology
genomics
single-cell
model_cls_name:SCANVI
scvi_version:1.2.0
anndata_version:0.11.1
modality:rna
tissue:various
annotated:True
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@@ -54,10 +54,10 @@ 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 | 1.89 | 1.98 |
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- | Pearson Correlation | 0.81 | 0.80 |
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- | Spearman Correlation | 0.77 | 0.76 |
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- | R² (R-Squared) | 0.54 | 0.49 |
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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.
@@ -66,10 +66,10 @@ 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 | 16.79 |
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  | Pearson Correlation | 0.75 |
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  | Spearman Correlation | 0.84 |
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- | R² (R-Squared) | 0.42 |
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  </details>
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@@ -86,42 +86,42 @@ 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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- | macrophage | 0.95 | 1.11 | 0.82 | 0.95 | 0.23 | 0.92 | 12160.00 |
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- | type II pneumocyte | 0.95 | 0.80 | 0.82 | 0.96 | 0.32 | 0.87 | 9146.00 |
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- | basal cell | 0.91 | 1.41 | 0.71 | 0.87 | 0.43 | 0.82 | 2188.00 |
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- | capillary endothelial cell | 0.97 | 2.85 | 0.62 | 0.82 | 0.26 | 0.78 | 1534.00 |
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- | classical monocyte | 0.87 | 3.29 | 0.60 | 0.74 | 0.22 | 0.81 | 1487.00 |
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- | club cell | 0.93 | 2.86 | 0.64 | 0.73 | 0.29 | 0.78 | 1038.00 |
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- | non-classical monocyte | 0.89 | 3.08 | 0.67 | 0.75 | 0.28 | 0.83 | 1005.00 |
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- | respiratory goblet cell | 0.89 | 2.45 | 0.66 | 0.77 | 0.33 | 0.81 | 762.00 |
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- | basophil | 0.93 | 3.41 | 0.66 | 0.71 | 0.22 | 0.83 | 686.00 |
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- | lung ciliated cell | 0.63 | 2.64 | 0.72 | 0.84 | 0.41 | 0.84 | 602.00 |
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- | CD8-positive, alpha-beta T cell | 0.88 | 3.73 | 0.64 | 0.71 | 0.27 | 0.82 | 552.00 |
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- | CD4-positive, alpha-beta T cell | 0.90 | 4.19 | 0.59 | 0.62 | 0.28 | 0.82 | 543.00 |
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- | vein endothelial cell | 0.94 | 4.01 | 0.55 | 0.67 | 0.34 | 0.78 | 508.00 |
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- | lung microvascular endothelial cell | 0.90 | 3.60 | 0.66 | 0.71 | 0.31 | 0.85 | 485.00 |
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- | adventitial cell | 0.78 | 2.84 | 0.76 | 0.92 | 0.33 | 0.80 | 373.00 |
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- | fibroblast | 0.85 | 4.28 | 0.57 | 0.71 | 0.33 | 0.76 | 336.00 |
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- | dendritic cell | 0.85 | 4.34 | 0.62 | 0.74 | 0.29 | 0.81 | 316.00 |
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- | intermediate monocyte | 0.88 | 3.70 | 0.66 | 0.67 | 0.29 | 0.83 | 252.00 |
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- | pericyte | 0.88 | 4.30 | 0.62 | 0.62 | 0.32 | 0.77 | 213.00 |
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- | type I pneumocyte | 0.89 | 3.95 | 0.63 | 0.67 | 0.33 | 0.78 | 211.00 |
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- | endothelial cell of artery | 0.84 | 5.28 | 0.55 | 0.62 | 0.34 | 0.77 | 187.00 |
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- | neutrophil | 0.85 | 4.52 | 0.59 | 0.57 | 0.30 | 0.88 | 174.00 |
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- | plasma cell | 0.80 | 4.34 | 0.60 | 0.57 | 0.28 | 0.85 | 134.00 |
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- | effector CD4-positive, alpha-beta T cell | 0.88 | 4.06 | 0.64 | 0.61 | 0.34 | 0.81 | 132.00 |
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- | mature NK T cell | 0.85 | 5.20 | 0.54 | 0.53 | 0.38 | 0.79 | 132.00 |
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- | B cell | 0.76 | 5.10 | 0.55 | 0.50 | 0.36 | 0.76 | 87.00 |
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- | bronchial smooth muscle cell | 0.77 | 4.88 | 0.61 | 0.61 | 0.31 | 0.77 | 81.00 |
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- | effector CD8-positive, alpha-beta T cell | 0.83 | 4.11 | 0.63 | 0.60 | 0.37 | 0.83 | 80.00 |
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- | vascular associated smooth muscle cell | 0.78 | 4.57 | 0.62 | 0.61 | 0.36 | 0.78 | 80.00 |
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- | endothelial cell of lymphatic vessel | 0.52 | 5.92 | 0.53 | 0.50 | 0.32 | 0.74 | 47.00 |
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- | blood vessel endothelial cell | 0.70 | 3.92 | 0.68 | 0.66 | 0.38 | 0.81 | 47.00 |
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- | smooth muscle cell | 0.66 | 4.11 | 0.64 | 0.61 | 0.33 | 0.79 | 25.00 |
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- | pulmonary ionocyte | 0.41 | 6.66 | 0.43 | 0.29 | 0.36 | 0.72 | 19.00 |
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- | plasmacytoid dendritic cell | 0.55 | 5.51 | 0.48 | 0.48 | 0.34 | 0.83 | 18.00 |
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- | mesothelial cell | 0.53 | 5.97 | 0.52 | 0.46 | 0.37 | 0.73 | 17.00 |
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- | serous cell of epithelium of bronchus | 0.60 | 5.30 | 0.52 | 0.45 | 0.40 | 0.80 | 15.00 |
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  </details>
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  | Metric | Training Value | Validation Value |
56
  |-------------------------|----------------|------------------|
57
+ | Mean Absolute Error | 1.89 | 1.94 |
58
+ | Pearson Correlation | 0.82 | 0.81 |
59
+ | Spearman Correlation | 0.77 | 0.77 |
60
+ | R² (R-Squared) | 0.55 | 0.51 |
61
 
62
  The gene-wise coefficient of variation summarizes how well variation between different genes is
63
  preserved by the generated model expression. This value is usually quite high.
 
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  | Metric | Training Value |
68
  |-------------------------|----------------|
69
+ | Mean Absolute Error | 16.73 |
70
  | Pearson Correlation | 0.75 |
71
  | Spearman Correlation | 0.84 |
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+ | R² (R-Squared) | 0.41 |
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  </details>
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  | Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |
88
  | --- | --- | --- | --- | --- | --- | --- | --- |
89
+ | macrophage | 0.94 | 1.18 | 0.81 | 0.95 | 0.23 | 0.92 | 12160.00 |
90
+ | type II pneumocyte | 0.95 | 0.80 | 0.83 | 0.95 | 0.32 | 0.87 | 9146.00 |
91
+ | basal cell | 0.92 | 1.43 | 0.70 | 0.88 | 0.42 | 0.81 | 2188.00 |
92
+ | capillary endothelial cell | 0.98 | 2.75 | 0.64 | 0.83 | 0.25 | 0.78 | 1534.00 |
93
+ | classical monocyte | 0.90 | 3.24 | 0.61 | 0.75 | 0.22 | 0.81 | 1487.00 |
94
+ | club cell | 0.94 | 2.88 | 0.64 | 0.73 | 0.30 | 0.78 | 1038.00 |
95
+ | non-classical monocyte | 0.87 | 3.09 | 0.67 | 0.75 | 0.28 | 0.83 | 1005.00 |
96
+ | respiratory goblet cell | 0.90 | 2.47 | 0.66 | 0.78 | 0.32 | 0.80 | 762.00 |
97
+ | basophil | 0.91 | 3.61 | 0.64 | 0.69 | 0.24 | 0.84 | 686.00 |
98
+ | lung ciliated cell | 0.61 | 2.71 | 0.71 | 0.83 | 0.41 | 0.84 | 602.00 |
99
+ | CD8-positive, alpha-beta T cell | 0.87 | 3.70 | 0.64 | 0.71 | 0.28 | 0.82 | 552.00 |
100
+ | CD4-positive, alpha-beta T cell | 0.88 | 4.10 | 0.60 | 0.65 | 0.25 | 0.81 | 543.00 |
101
+ | vein endothelial cell | 0.92 | 3.92 | 0.57 | 0.68 | 0.34 | 0.77 | 508.00 |
102
+ | lung microvascular endothelial cell | 0.90 | 3.54 | 0.67 | 0.71 | 0.31 | 0.85 | 485.00 |
103
+ | adventitial cell | 0.77 | 2.89 | 0.77 | 0.92 | 0.33 | 0.80 | 373.00 |
104
+ | fibroblast | 0.87 | 4.03 | 0.61 | 0.73 | 0.31 | 0.76 | 336.00 |
105
+ | dendritic cell | 0.87 | 4.17 | 0.64 | 0.74 | 0.30 | 0.81 | 316.00 |
106
+ | intermediate monocyte | 0.87 | 3.61 | 0.67 | 0.67 | 0.31 | 0.83 | 252.00 |
107
+ | pericyte | 0.87 | 4.48 | 0.60 | 0.61 | 0.34 | 0.78 | 213.00 |
108
+ | type I pneumocyte | 0.90 | 3.80 | 0.64 | 0.68 | 0.33 | 0.78 | 211.00 |
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+ | endothelial cell of artery | 0.87 | 5.32 | 0.55 | 0.61 | 0.35 | 0.78 | 187.00 |
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+ | neutrophil | 0.84 | 4.58 | 0.59 | 0.57 | 0.29 | 0.88 | 174.00 |
111
+ | plasma cell | 0.80 | 4.34 | 0.60 | 0.57 | 0.29 | 0.86 | 134.00 |
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+ | effector CD4-positive, alpha-beta T cell | 0.87 | 4.12 | 0.63 | 0.60 | 0.33 | 0.81 | 132.00 |
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+ | mature NK T cell | 0.84 | 5.11 | 0.55 | 0.54 | 0.37 | 0.79 | 132.00 |
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+ | B cell | 0.77 | 5.20 | 0.54 | 0.50 | 0.34 | 0.76 | 87.00 |
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+ | bronchial smooth muscle cell | 0.74 | 4.90 | 0.60 | 0.61 | 0.31 | 0.77 | 81.00 |
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+ | effector CD8-positive, alpha-beta T cell | 0.77 | 4.16 | 0.63 | 0.61 | 0.37 | 0.83 | 80.00 |
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+ | vascular associated smooth muscle cell | 0.80 | 4.63 | 0.62 | 0.60 | 0.35 | 0.78 | 80.00 |
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+ | endothelial cell of lymphatic vessel | 0.51 | 6.13 | 0.52 | 0.48 | 0.33 | 0.75 | 47.00 |
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+ | blood vessel endothelial cell | 0.66 | 4.07 | 0.66 | 0.65 | 0.38 | 0.81 | 47.00 |
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+ | smooth muscle cell | 0.67 | 4.08 | 0.64 | 0.62 | 0.31 | 0.79 | 25.00 |
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+ | pulmonary ionocyte | 0.46 | 6.75 | 0.42 | 0.28 | 0.36 | 0.73 | 19.00 |
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+ | plasmacytoid dendritic cell | 0.57 | 5.75 | 0.46 | 0.45 | 0.35 | 0.84 | 18.00 |
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+ | mesothelial cell | 0.50 | 5.80 | 0.53 | 0.47 | 0.36 | 0.73 | 17.00 |
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+ | serous cell of epithelium of bronchus | 0.61 | 5.22 | 0.54 | 0.46 | 0.38 | 0.79 | 15.00 |
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  </details>
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