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scvi-tools
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tabula-sapiens-lung-scvi

TensorBoard
scvi-tools
biology
genomics
single-cell
model_cls_name:SCVI
scvi_version:1.2.0
anndata_version:0.11.1
modality:rna
tissue:various
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 | 1.85 | 1.99 |
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  | Pearson Correlation | 0.82 | 0.79 |
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- | Spearman Correlation | 0.78 | 0.76 |
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- | R² (R-Squared) | 0.58 | 0.51 |
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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.
@@ -63,9 +63,9 @@ 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 | 17.34 |
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- | Pearson Correlation | 0.73 |
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- | Spearman Correlation | 0.82 |
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  | R² (R-Squared) | 0.29 |
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  </details>
@@ -83,42 +83,42 @@ 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 | 0.94 | 1.12 | 0.82 | 0.94 | 0.24 | 0.92 | 12160.00 |
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- | type II pneumocyte | 0.95 | 0.85 | 0.80 | 0.95 | 0.32 | 0.87 | 9146.00 |
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- | basal cell | 0.91 | 1.46 | 0.69 | 0.85 | 0.43 | 0.82 | 2188.00 |
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- | capillary endothelial cell | 0.95 | 2.67 | 0.66 | 0.81 | 0.27 | 0.79 | 1534.00 |
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- | classical monocyte | 0.92 | 3.19 | 0.62 | 0.75 | 0.22 | 0.81 | 1487.00 |
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- | club cell | 0.93 | 2.92 | 0.63 | 0.72 | 0.29 | 0.78 | 1038.00 |
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- | non-classical monocyte | 0.90 | 3.17 | 0.65 | 0.73 | 0.29 | 0.83 | 1005.00 |
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- | respiratory goblet cell | 0.90 | 2.44 | 0.67 | 0.77 | 0.33 | 0.81 | 762.00 |
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- | basophil | 0.92 | 3.46 | 0.66 | 0.70 | 0.24 | 0.84 | 686.00 |
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- | lung ciliated cell | 0.64 | 2.31 | 0.76 | 0.85 | 0.41 | 0.84 | 602.00 |
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- | CD8-positive, alpha-beta T cell | 0.87 | 3.67 | 0.64 | 0.69 | 0.29 | 0.82 | 552.00 |
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- | CD4-positive, alpha-beta T cell | 0.86 | 4.18 | 0.59 | 0.62 | 0.27 | 0.82 | 543.00 |
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- | vein endothelial cell | 0.91 | 3.65 | 0.61 | 0.70 | 0.33 | 0.77 | 508.00 |
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- | lung microvascular endothelial cell | 0.90 | 3.63 | 0.66 | 0.71 | 0.30 | 0.85 | 485.00 |
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- | adventitial cell | 0.78 | 2.85 | 0.76 | 0.91 | 0.34 | 0.80 | 373.00 |
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- | fibroblast | 0.84 | 4.10 | 0.59 | 0.70 | 0.34 | 0.76 | 336.00 |
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- | dendritic cell | 0.88 | 4.12 | 0.63 | 0.72 | 0.30 | 0.81 | 316.00 |
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- | intermediate monocyte | 0.89 | 3.97 | 0.64 | 0.63 | 0.32 | 0.83 | 252.00 |
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- | pericyte | 0.86 | 4.74 | 0.57 | 0.58 | 0.32 | 0.77 | 213.00 |
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- | type I pneumocyte | 0.90 | 4.00 | 0.62 | 0.66 | 0.33 | 0.77 | 211.00 |
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- | endothelial cell of artery | 0.87 | 5.20 | 0.55 | 0.63 | 0.35 | 0.77 | 187.00 |
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- | neutrophil | 0.86 | 4.53 | 0.59 | 0.56 | 0.32 | 0.88 | 174.00 |
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- | plasma cell | 0.76 | 4.50 | 0.59 | 0.56 | 0.29 | 0.86 | 134.00 |
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- | effector CD4-positive, alpha-beta T cell | 0.85 | 4.03 | 0.64 | 0.61 | 0.32 | 0.80 | 132.00 |
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- | mature NK T cell | 0.87 | 5.16 | 0.54 | 0.52 | 0.39 | 0.79 | 132.00 |
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- | B cell | 0.78 | 5.04 | 0.55 | 0.51 | 0.33 | 0.75 | 87.00 |
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- | bronchial smooth muscle cell | 0.71 | 4.91 | 0.61 | 0.61 | 0.29 | 0.76 | 81.00 |
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- | effector CD8-positive, alpha-beta T cell | 0.79 | 4.01 | 0.64 | 0.62 | 0.33 | 0.82 | 80.00 |
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- | vascular associated smooth muscle cell | 0.79 | 4.79 | 0.59 | 0.58 | 0.37 | 0.79 | 80.00 |
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- | endothelial cell of lymphatic vessel | 0.51 | 5.85 | 0.54 | 0.50 | 0.33 | 0.74 | 47.00 |
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- | blood vessel endothelial cell | 0.66 | 3.96 | 0.67 | 0.66 | 0.38 | 0.81 | 47.00 |
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- | smooth muscle cell | 0.66 | 4.39 | 0.61 | 0.59 | 0.36 | 0.80 | 25.00 |
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- | pulmonary ionocyte | 0.40 | 6.39 | 0.45 | 0.32 | 0.34 | 0.72 | 19.00 |
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- | plasmacytoid dendritic cell | 0.57 | 5.31 | 0.48 | 0.48 | 0.34 | 0.83 | 18.00 |
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- | mesothelial cell | 0.49 | 5.88 | 0.52 | 0.45 | 0.38 | 0.74 | 17.00 |
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- | serous cell of epithelium of bronchus | 0.60 | 5.26 | 0.53 | 0.46 | 0.34 | 0.78 | 15.00 |
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  </details>
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  | Metric | Training Value | Validation Value |
53
  |-------------------------|----------------|------------------|
54
+ | Mean Absolute Error | 1.86 | 1.98 |
55
  | Pearson Correlation | 0.82 | 0.79 |
56
+ | Spearman Correlation | 0.77 | 0.76 |
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+ | R² (R-Squared) | 0.58 | 0.48 |
58
 
59
  The gene-wise coefficient of variation summarizes how well variation between different genes is
60
  preserved by the generated model expression. This value is usually quite high.
 
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  | Metric | Training Value |
65
  |-------------------------|----------------|
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+ | Mean Absolute Error | 17.10 |
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+ | Pearson Correlation | 0.74 |
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+ | Spearman Correlation | 0.83 |
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  | R² (R-Squared) | 0.29 |
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  </details>
 
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  | Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |
85
  | --- | --- | --- | --- | --- | --- | --- | --- |
86
+ | macrophage | 0.94 | 1.14 | 0.81 | 0.94 | 0.24 | 0.92 | 12160.00 |
87
+ | type II pneumocyte | 0.95 | 0.84 | 0.81 | 0.95 | 0.32 | 0.87 | 9146.00 |
88
+ | basal cell | 0.91 | 1.42 | 0.71 | 0.86 | 0.42 | 0.81 | 2188.00 |
89
+ | capillary endothelial cell | 0.95 | 2.81 | 0.63 | 0.79 | 0.28 | 0.79 | 1534.00 |
90
+ | classical monocyte | 0.90 | 3.12 | 0.63 | 0.75 | 0.21 | 0.81 | 1487.00 |
91
+ | club cell | 0.91 | 2.96 | 0.63 | 0.72 | 0.30 | 0.78 | 1038.00 |
92
+ | non-classical monocyte | 0.92 | 2.92 | 0.68 | 0.75 | 0.28 | 0.83 | 1005.00 |
93
+ | respiratory goblet cell | 0.90 | 2.28 | 0.70 | 0.79 | 0.32 | 0.81 | 762.00 |
94
+ | basophil | 0.94 | 3.41 | 0.66 | 0.71 | 0.24 | 0.84 | 686.00 |
95
+ | lung ciliated cell | 0.63 | 2.32 | 0.76 | 0.84 | 0.41 | 0.84 | 602.00 |
96
+ | CD8-positive, alpha-beta T cell | 0.89 | 3.66 | 0.64 | 0.70 | 0.28 | 0.82 | 552.00 |
97
+ | CD4-positive, alpha-beta T cell | 0.89 | 4.03 | 0.60 | 0.63 | 0.26 | 0.82 | 543.00 |
98
+ | vein endothelial cell | 0.90 | 3.83 | 0.58 | 0.69 | 0.33 | 0.77 | 508.00 |
99
+ | lung microvascular endothelial cell | 0.89 | 3.72 | 0.65 | 0.69 | 0.31 | 0.85 | 485.00 |
100
+ | adventitial cell | 0.75 | 2.84 | 0.76 | 0.91 | 0.34 | 0.80 | 373.00 |
101
+ | fibroblast | 0.85 | 4.35 | 0.56 | 0.69 | 0.33 | 0.76 | 336.00 |
102
+ | dendritic cell | 0.85 | 4.21 | 0.63 | 0.73 | 0.29 | 0.81 | 316.00 |
103
+ | intermediate monocyte | 0.91 | 4.10 | 0.62 | 0.62 | 0.30 | 0.83 | 252.00 |
104
+ | pericyte | 0.85 | 4.75 | 0.57 | 0.57 | 0.34 | 0.78 | 213.00 |
105
+ | type I pneumocyte | 0.87 | 3.81 | 0.64 | 0.66 | 0.32 | 0.77 | 211.00 |
106
+ | endothelial cell of artery | 0.86 | 5.21 | 0.55 | 0.62 | 0.34 | 0.77 | 187.00 |
107
+ | neutrophil | 0.87 | 4.68 | 0.58 | 0.55 | 0.28 | 0.88 | 174.00 |
108
+ | plasma cell | 0.77 | 4.42 | 0.60 | 0.57 | 0.26 | 0.85 | 134.00 |
109
+ | effector CD4-positive, alpha-beta T cell | 0.86 | 4.21 | 0.62 | 0.60 | 0.34 | 0.81 | 132.00 |
110
+ | mature NK T cell | 0.84 | 4.97 | 0.56 | 0.55 | 0.37 | 0.79 | 132.00 |
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+ | B cell | 0.75 | 5.11 | 0.54 | 0.49 | 0.35 | 0.76 | 87.00 |
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+ | bronchial smooth muscle cell | 0.72 | 5.16 | 0.59 | 0.59 | 0.31 | 0.76 | 81.00 |
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+ | effector CD8-positive, alpha-beta T cell | 0.82 | 4.10 | 0.63 | 0.60 | 0.36 | 0.82 | 80.00 |
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+ | vascular associated smooth muscle cell | 0.76 | 4.66 | 0.61 | 0.60 | 0.35 | 0.78 | 80.00 |
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+ | endothelial cell of lymphatic vessel | 0.48 | 5.91 | 0.53 | 0.49 | 0.32 | 0.74 | 47.00 |
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+ | blood vessel endothelial cell | 0.70 | 4.10 | 0.66 | 0.65 | 0.37 | 0.81 | 47.00 |
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+ | smooth muscle cell | 0.68 | 4.07 | 0.64 | 0.62 | 0.35 | 0.80 | 25.00 |
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+ | pulmonary ionocyte | 0.41 | 6.50 | 0.45 | 0.31 | 0.34 | 0.72 | 19.00 |
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+ | plasmacytoid dendritic cell | 0.54 | 5.05 | 0.51 | 0.51 | 0.35 | 0.83 | 18.00 |
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+ | mesothelial cell | 0.51 | 5.78 | 0.53 | 0.46 | 0.37 | 0.73 | 17.00 |
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+ | serous cell of epithelium of bronchus | 0.58 | 5.22 | 0.53 | 0.46 | 0.38 | 0.79 | 15.00 |
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  </details>
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