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scvi-tools
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human-lung-cell-atlas-scanvi

scvi-tools
biology
genomics
single-cell
model_cls_name:SCANVI
scvi_version:1.2.0
anndata_version:0.11.1
modality:rna
tissue:nose
tissue:respiratory airway
tissue:lung parenchyma
annotated:True
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@@ -68,10 +68,10 @@ preserved by the generated model expression. This value is usually quite high.
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  | Metric | Training Value |
70
  |-------------------------|----------------|
71
- | Mean Absolute Error | 6.59 |
72
- | Pearson Correlation | 0.85 |
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  | Spearman Correlation | 0.98 |
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- | R² (R-Squared) | 0.58 |
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  </details>
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@@ -88,56 +88,56 @@ cell-type.
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  | Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |
90
  | --- | --- | --- | --- | --- | --- | --- | --- |
91
- | respiratory basal cell | 0.98 | 0.29 | 0.91 | 0.99 | 0.28 | 0.98 | 80113.00 |
92
- | alveolar macrophage | 0.98 | 0.24 | 0.95 | 0.99 | 0.27 | 0.98 | 78816.00 |
93
- | type II pneumocyte | 0.96 | 0.27 | 0.91 | 0.98 | 0.20 | 0.99 | 62405.00 |
94
- | club cell | 0.93 | 0.58 | 0.82 | 0.98 | 0.17 | 0.97 | 36023.00 |
95
- | nasal mucosa goblet cell | 0.97 | 0.66 | 0.81 | 0.98 | 0.21 | 0.98 | 35833.00 |
96
- | ciliated columnar cell of tracheobronchial tree | 0.96 | 0.28 | 0.94 | 0.99 | 0.26 | 0.98 | 35225.00 |
97
- | CD8-positive, alpha-beta T cell | 0.95 | 0.33 | 0.90 | 0.98 | 0.30 | 0.97 | 29074.00 |
98
- | elicited macrophage | 0.96 | 0.43 | 0.88 | 0.99 | 0.30 | 0.97 | 28223.00 |
99
- | capillary endothelial cell | 0.98 | 0.67 | 0.83 | 0.96 | 0.28 | 0.99 | 23205.00 |
100
- | CD4-positive, alpha-beta T cell | 0.95 | 0.48 | 0.85 | 0.96 | 0.30 | 0.97 | 21285.00 |
101
- | classical monocyte | 0.94 | 0.46 | 0.82 | 0.97 | 0.28 | 0.96 | 17695.00 |
102
- | natural killer cell | 0.96 | 0.63 | 0.83 | 0.96 | 0.29 | 0.97 | 16978.00 |
103
- | vein endothelial cell | 0.95 | 0.70 | 0.79 | 0.95 | 0.26 | 0.96 | 12975.00 |
104
- | alveolar type 2 fibroblast cell | 0.92 | 0.71 | 0.81 | 0.97 | 0.27 | 0.97 | 10321.00 |
105
- | CD1c-positive myeloid dendritic cell | 0.93 | 0.62 | 0.74 | 0.96 | 0.33 | 0.96 | 9133.00 |
106
- | non-classical monocyte | 0.93 | 0.76 | 0.79 | 0.96 | 0.32 | 0.97 | 8834.00 |
107
- | type I pneumocyte | 0.95 | 1.27 | 0.67 | 0.88 | 0.18 | 0.95 | 7937.00 |
108
- | pulmonary artery endothelial cell | 0.94 | 1.10 | 0.75 | 0.94 | 0.28 | 0.97 | 7391.00 |
109
- | mast cell | 0.92 | 0.68 | 0.77 | 0.94 | 0.22 | 0.95 | 6623.00 |
110
- | multi-ciliated epithelial cell | 0.90 | 1.38 | 0.75 | 0.94 | 0.30 | 0.97 | 5873.00 |
111
- | alveolar type 1 fibroblast cell | 0.95 | 1.45 | 0.73 | 0.93 | 0.28 | 0.96 | 5182.00 |
112
- | lung macrophage | 0.92 | 1.31 | 0.73 | 0.93 | 0.32 | 0.95 | 4805.00 |
113
- | respiratory hillock cell | 0.93 | 1.47 | 0.73 | 0.95 | 0.28 | 0.96 | 4600.00 |
114
- | endothelial cell of lymphatic vessel | 0.92 | 1.05 | 0.68 | 0.93 | 0.24 | 0.95 | 4595.00 |
115
- | B cell | 0.94 | 1.38 | 0.60 | 0.90 | 0.27 | 0.96 | 4511.00 |
116
- | epithelial cell of lower respiratory tract | 0.94 | 1.08 | 0.61 | 0.89 | 0.16 | 0.95 | 4393.00 |
117
- | lung pericyte | 0.94 | 2.56 | 0.66 | 0.87 | 0.23 | 0.94 | 3032.00 |
118
- | tracheobronchial smooth muscle cell | 0.92 | 1.42 | 0.72 | 0.90 | 0.25 | 0.94 | 2996.00 |
119
- | plasma cell | 0.81 | 1.30 | 0.64 | 0.85 | 0.17 | 0.94 | 1773.00 |
120
- | bronchial goblet cell | 0.93 | 1.78 | 0.66 | 0.91 | 0.21 | 0.93 | 1670.00 |
121
- | bronchus fibroblast of lung | 0.91 | 2.06 | 0.68 | 0.89 | 0.28 | 0.93 | 1573.00 |
122
- | serous secreting cell | 0.91 | 5.05 | 0.59 | 0.71 | 0.14 | 0.98 | 1472.00 |
123
- | epithelial cell of alveolus of lung | 0.93 | 2.37 | 0.56 | 0.84 | 0.22 | 0.91 | 1440.00 |
124
- | tracheobronchial serous cell | 0.83 | 3.61 | 0.55 | 0.68 | 0.11 | 0.96 | 1417.00 |
125
- | acinar cell | 0.88 | 1.97 | 0.70 | 0.91 | 0.23 | 0.93 | 1274.00 |
126
- | tracheobronchial goblet cell | 0.87 | 4.40 | 0.57 | 0.72 | 0.12 | 0.97 | 968.00 |
127
- | myofibroblast cell | 0.77 | 3.53 | 0.65 | 0.83 | 0.32 | 0.92 | 716.00 |
128
- | ionocyte | 0.84 | 3.34 | 0.64 | 0.80 | 0.30 | 0.87 | 561.00 |
129
- | smooth muscle cell | 0.87 | 3.11 | 0.64 | 0.85 | 0.34 | 0.91 | 556.00 |
130
- | plasmacytoid dendritic cell | 0.90 | 4.16 | 0.53 | 0.72 | 0.30 | 0.90 | 552.00 |
131
- | mucus secreting cell | 0.86 | 4.32 | 0.59 | 0.69 | 0.24 | 0.94 | 537.00 |
132
- | T cell | 0.89 | 2.78 | 0.57 | 0.83 | 0.39 | 0.93 | 500.00 |
133
- | stromal cell | 0.79 | 5.41 | 0.58 | 0.70 | 0.24 | 0.91 | 335.00 |
134
- | conventional dendritic cell | 0.73 | 4.27 | 0.53 | 0.73 | 0.37 | 0.90 | 322.00 |
135
- | dendritic cell | 0.73 | 4.49 | 0.49 | 0.74 | 0.34 | 0.85 | 312.00 |
136
- | fibroblast | 0.77 | 3.60 | 0.64 | 0.81 | 0.40 | 0.91 | 276.00 |
137
- | mesothelial cell | 0.76 | 4.31 | 0.54 | 0.71 | 0.38 | 0.87 | 230.00 |
138
- | brush cell of trachebronchial tree | 0.62 | 4.85 | 0.60 | 0.74 | 0.36 | 0.83 | 165.00 |
139
- | lung neuroendocrine cell | 0.77 | 4.35 | 0.57 | 0.70 | 0.40 | 0.86 | 159.00 |
140
- | hematopoietic stem cell | 0.40 | 6.97 | 0.50 | 0.58 | 0.37 | 0.74 | 60.00 |
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  </details>
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  | Metric | Training Value |
70
  |-------------------------|----------------|
71
+ | Mean Absolute Error | 6.25 |
72
+ | Pearson Correlation | 0.88 |
73
  | Spearman Correlation | 0.98 |
74
+ | R² (R-Squared) | 0.66 |
75
 
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  </details>
77
 
 
88
 
89
  | Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |
90
  | --- | --- | --- | --- | --- | --- | --- | --- |
91
+ | respiratory basal cell | 0.98 | 0.25 | 0.94 | 0.99 | 0.34 | 0.04 | 80113.00 |
92
+ | alveolar macrophage | 0.98 | 0.23 | 0.95 | 0.99 | 0.34 | 0.04 | 78816.00 |
93
+ | type II pneumocyte | 0.96 | 0.29 | 0.89 | 0.98 | 0.34 | 0.05 | 62405.00 |
94
+ | club cell | 0.94 | 0.55 | 0.83 | 0.97 | 0.34 | 0.05 | 36023.00 |
95
+ | nasal mucosa goblet cell | 0.97 | 0.65 | 0.81 | 0.97 | 0.34 | 0.05 | 35833.00 |
96
+ | ciliated columnar cell of tracheobronchial tree | 0.97 | 0.23 | 0.97 | 0.99 | 0.34 | 0.05 | 35225.00 |
97
+ | CD8-positive, alpha-beta T cell | 0.95 | 0.35 | 0.89 | 0.98 | 0.34 | 0.05 | 29074.00 |
98
+ | elicited macrophage | 0.96 | 0.46 | 0.85 | 0.98 | 0.34 | 0.05 | 28223.00 |
99
+ | capillary endothelial cell | 0.98 | 0.73 | 0.82 | 0.96 | 0.34 | 0.05 | 23205.00 |
100
+ | CD4-positive, alpha-beta T cell | 0.96 | 0.43 | 0.89 | 0.97 | 0.34 | 0.05 | 21285.00 |
101
+ | classical monocyte | 0.94 | 0.46 | 0.82 | 0.97 | 0.31 | 0.04 | 17695.00 |
102
+ | natural killer cell | 0.96 | 0.61 | 0.83 | 0.96 | 0.34 | 0.05 | 16978.00 |
103
+ | vein endothelial cell | 0.95 | 0.73 | 0.77 | 0.95 | 0.31 | 0.05 | 12975.00 |
104
+ | alveolar type 2 fibroblast cell | 0.93 | 0.60 | 0.85 | 0.97 | 0.28 | 0.04 | 10321.00 |
105
+ | CD1c-positive myeloid dendritic cell | 0.93 | 0.62 | 0.71 | 0.95 | 0.21 | 0.04 | 9133.00 |
106
+ | non-classical monocyte | 0.93 | 0.76 | 0.78 | 0.96 | 0.26 | 0.04 | 8834.00 |
107
+ | type I pneumocyte | 0.95 | 1.27 | 0.66 | 0.88 | 0.34 | 0.04 | 7937.00 |
108
+ | pulmonary artery endothelial cell | 0.96 | 1.24 | 0.71 | 0.93 | 0.29 | 0.04 | 7391.00 |
109
+ | mast cell | 0.93 | 0.72 | 0.75 | 0.94 | 0.25 | 0.04 | 6623.00 |
110
+ | multi-ciliated epithelial cell | 0.88 | 1.48 | 0.72 | 0.94 | 0.28 | 0.04 | 5873.00 |
111
+ | alveolar type 1 fibroblast cell | 0.96 | 1.48 | 0.70 | 0.92 | 0.24 | 0.04 | 5182.00 |
112
+ | lung macrophage | 0.93 | 1.40 | 0.71 | 0.93 | 0.21 | 0.03 | 4805.00 |
113
+ | respiratory hillock cell | 0.91 | 1.48 | 0.73 | 0.95 | 0.26 | 0.04 | 4600.00 |
114
+ | endothelial cell of lymphatic vessel | 0.93 | 1.15 | 0.64 | 0.92 | 0.21 | 0.04 | 4595.00 |
115
+ | B cell | 0.92 | 1.33 | 0.63 | 0.89 | 0.22 | 0.04 | 4511.00 |
116
+ | epithelial cell of lower respiratory tract | 0.94 | 1.14 | 0.57 | 0.88 | 0.31 | 0.04 | 4393.00 |
117
+ | lung pericyte | 0.94 | 2.59 | 0.65 | 0.87 | 0.26 | 0.04 | 3032.00 |
118
+ | tracheobronchial smooth muscle cell | 0.93 | 1.55 | 0.68 | 0.90 | 0.17 | 0.03 | 2996.00 |
119
+ | plasma cell | 0.80 | 1.32 | 0.63 | 0.85 | 0.16 | 0.03 | 1773.00 |
120
+ | bronchial goblet cell | 0.93 | 1.53 | 0.73 | 0.93 | 0.19 | 0.03 | 1670.00 |
121
+ | bronchus fibroblast of lung | 0.89 | 2.13 | 0.68 | 0.87 | 0.15 | 0.04 | 1573.00 |
122
+ | serous secreting cell | 0.91 | 5.12 | 0.58 | 0.70 | 0.37 | 0.04 | 1472.00 |
123
+ | epithelial cell of alveolus of lung | 0.93 | 2.34 | 0.57 | 0.84 | 0.19 | 0.04 | 1440.00 |
124
+ | tracheobronchial serous cell | 0.81 | 3.34 | 0.59 | 0.70 | 0.38 | 0.04 | 1417.00 |
125
+ | acinar cell | 0.88 | 1.98 | 0.69 | 0.91 | 0.20 | 0.04 | 1274.00 |
126
+ | tracheobronchial goblet cell | 0.87 | 4.29 | 0.58 | 0.73 | 0.36 | 0.04 | 968.00 |
127
+ | myofibroblast cell | 0.79 | 3.65 | 0.64 | 0.83 | 0.23 | 0.04 | 716.00 |
128
+ | ionocyte | 0.85 | 3.36 | 0.64 | 0.79 | 0.25 | 0.03 | 561.00 |
129
+ | smooth muscle cell | 0.84 | 3.10 | 0.64 | 0.85 | 0.22 | 0.03 | 556.00 |
130
+ | plasmacytoid dendritic cell | 0.89 | 4.15 | 0.52 | 0.73 | 0.33 | 0.04 | 552.00 |
131
+ | mucus secreting cell | 0.84 | 4.46 | 0.58 | 0.69 | 0.29 | 0.03 | 537.00 |
132
+ | T cell | 0.91 | 2.85 | 0.57 | 0.83 | 0.25 | 0.03 | 500.00 |
133
+ | stromal cell | 0.80 | 5.26 | 0.59 | 0.71 | 0.33 | 0.04 | 335.00 |
134
+ | conventional dendritic cell | 0.73 | 4.25 | 0.52 | 0.73 | 0.32 | 0.04 | 322.00 |
135
+ | dendritic cell | 0.69 | 4.74 | 0.48 | 0.73 | 0.37 | 0.04 | 312.00 |
136
+ | fibroblast | 0.76 | 3.46 | 0.66 | 0.82 | 0.31 | 0.03 | 276.00 |
137
+ | mesothelial cell | 0.77 | 4.37 | 0.52 | 0.70 | 0.34 | 0.04 | 230.00 |
138
+ | brush cell of trachebronchial tree | 0.61 | 5.05 | 0.58 | 0.73 | 0.33 | 0.03 | 165.00 |
139
+ | lung neuroendocrine cell | 0.73 | 4.32 | 0.58 | 0.70 | 0.31 | 0.03 | 159.00 |
140
+ | hematopoietic stem cell | 0.42 | 7.59 | 0.45 | 0.55 | 0.40 | 0.04 | 60.00 |
141
 
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  </details>
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