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README.md

@@ -32,73 +32,75 @@ computed on a 10% random subset of the data that was not used for training.
 
 | Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| mesenchymal stem cell | 2349 | 0.98 | 0.98 | 0.99 | 0.98 | 0.00 | 0.93 | 0.97 | 0.97 | 0.99 |
-| skeletal muscle satellite stem cell | 595 | 0.96 | 0.97 | 0.97 | 0.97 | 0.00 | 0.97 | 0.97 | 0.97 | 0.97 |
-| endothelial cell | 358 | 0.95 | 0.95 | 0.93 | 0.95 | 0.00 | 0.95 | 0.95 | 0.95 | 0.96 |
-| capillary endothelial cell | 336 | 0.92 | 0.92 | 0.91 | 0.89 | 0.00 | 0.89 | 0.88 | 0.89 | 0.92 |
-| macrophage | 275 | 0.96 | 0.96 | 0.96 | 0.97 | 0.00 | 0.88 | 0.94 | 0.94 | 0.96 |
-| pericyte | 249 | 0.88 | 0.91 | 0.90 | 0.86 | 0.00 | 0.83 | 0.88 | 0.90 | 0.91 |
-| CD8-positive, alpha-beta T cell | 148 | 0.66 | 0.77 | 0.78 | 0.76 | 0.00 | 0.71 | 0.70 | 0.75 | 0.79 |
-| endothelial cell of vascular tree | 70 | 0.90 | 0.89 | 0.74 | 0.82 | 0.00 | 0.86 | 0.83 | 0.82 | 0.89 |
-| CD4-positive, alpha-beta T cell | 44 | 0.44 | 0.45 | 0.36 | 0.31 | 0.00 | 0.52 | 0.43 | 0.50 | 0.50 |
-| fast muscle cell | 53 | 0.86 | 0.90 | 0.90 | 0.80 | 0.00 | 0.87 | 0.86 | 0.93 | 0.90 |
-| tendon cell | 36 | 0.69 | 0.82 | 0.79 | 0.33 | 0.00 | 0.28 | 0.54 | 0.54 | 0.80 |
-| smooth muscle cell | 20 | 0.27 | 0.48 | 0.34 | 0.19 | 0.00 | 0.36 | 0.56 | 0.57 | 0.61 |
-| endothelial cell of artery | 18 | 0.86 | 0.94 | 0.88 | 0.89 | 0.00 | 0.74 | 0.82 | 0.83 | 0.97 |
-| neutrophil | 24 | 0.76 | 0.82 | 0.82 | 0.71 | 0.00 | 0.75 | 0.78 | 0.80 | 0.79 |
-| slow muscle cell | 17 | 0.76 | 0.80 | 0.78 | 0.55 | 0.00 | 0.64 | 0.78 | 0.82 | 0.78 |
-| endothelial cell of lymphatic vessel | 10 | 0.76 | 0.84 | 0.80 | 0.67 | 0.00 | 0.67 | 0.80 | 0.73 | 0.80 |
-| erythrocyte | 15 | 0.38 | 0.40 | 0.93 | 0.74 | 0.00 | 0.84 | 0.59 | 0.60 | 0.81 |
-| T cell | 15 | 0.00 | 0.12 | 0.24 | 0.00 | 0.00 | 0.23 | 0.36 | 0.41 | 0.12 |
-| mature NK T cell | 7 | 0.31 | 0.00 | 0.18 | 0.00 | 0.00 | 0.25 | 0.29 | 0.29 | 0.36 |
-| granulocyte | 6 | 0.60 | 0.00 | 0.56 | 0.36 | 0.00 | 0.20 | 0.60 | 0.62 | 0.67 |
-| natural killer cell | 5 | 0.50 | 0.40 | 0.33 | 0.57 | 0.00 | 0.62 | 0.50 | 0.73 | 0.50 |
-| mast cell | 4 | 0.42 | 0.62 | 0.62 | 0.57 | 0.00 | 0.57 | 0.53 | 0.62 | 0.53 |
-| epithelial cell | 7 | 0.55 | 0.36 | 0.44 | 0.73 | 0.00 | 0.33 | 0.55 | 0.55 | 0.55 |
-| B cell | 7 | 0.53 | 0.73 | 0.73 | 0.62 | 0.00 | 0.44 | 0.92 | 0.83 | 0.73 |
-| monocyte | 4 | 0.00 | 0.00 | 0.00 | 0.40 | 0.00 | 0.19 | 0.18 | 0.36 | 0.00 |
-| basophil | 3 | 0.00 | 0.00 | 0.40 | 0.00 | 0.00 | 1.00 | 0.00 | 0.80 | 0.50 |
-| myeloid dendritic cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 0.40 | 0.00 |
+| mesenchymal stem cell | 2346 | 0.98 | 0.98 | 0.99 | 0.98 | 0.00 | 0.91 | 0.97 | 0.97 | 0.99 |
+| skeletal muscle satellite stem cell | 619 | 0.97 | 0.98 | 0.97 | 0.98 | 0.00 | 0.97 | 0.98 | 0.97 | 0.98 |
+| endothelial cell | 353 | 0.94 | 0.95 | 0.92 | 0.94 | 0.00 | 0.93 | 0.94 | 0.95 | 0.96 |
+| capillary endothelial cell | 327 | 0.91 | 0.92 | 0.91 | 0.89 | 0.00 | 0.89 | 0.88 | 0.90 | 0.93 |
+| macrophage | 277 | 0.96 | 0.97 | 0.97 | 0.94 | 0.00 | 0.89 | 0.94 | 0.94 | 0.96 |
+| pericyte | 240 | 0.88 | 0.89 | 0.90 | 0.87 | 0.00 | 0.82 | 0.89 | 0.89 | 0.91 |
+| CD8-positive, alpha-beta T cell | 147 | 0.74 | 0.77 | 0.74 | 0.73 | 0.00 | 0.66 | 0.72 | 0.82 | 0.80 |
+| endothelial cell of vascular tree | 70 | 0.91 | 0.90 | 0.76 | 0.88 | 0.00 | 0.82 | 0.82 | 0.84 | 0.90 |
+| CD4-positive, alpha-beta T cell | 50 | 0.52 | 0.50 | 0.35 | 0.28 | 0.00 | 0.42 | 0.36 | 0.57 | 0.54 |
+| fast muscle cell | 50 | 0.85 | 0.86 | 0.87 | 0.88 | 0.00 | 0.82 | 0.89 | 0.91 | 0.89 |
+| tendon cell | 38 | 0.68 | 0.77 | 0.79 | 0.59 | 0.00 | 0.26 | 0.50 | 0.48 | 0.82 |
+| smooth muscle cell | 20 | 0.38 | 0.46 | 0.23 | 0.29 | 0.00 | 0.40 | 0.58 | 0.64 | 0.65 |
+| endothelial cell of artery | 20 | 0.90 | 0.95 | 0.95 | 0.76 | 0.00 | 0.57 | 0.84 | 0.93 | 0.95 |
+| slow muscle cell | 20 | 0.76 | 0.78 | 0.77 | 0.67 | 0.00 | 0.74 | 0.85 | 0.89 | 0.80 |
+| neutrophil | 21 | 0.72 | 0.84 | 0.81 | 0.76 | 0.00 | 0.72 | 0.78 | 0.78 | 0.79 |
+| endothelial cell of lymphatic vessel | 8 | 0.75 | 0.80 | 0.71 | 0.38 | 0.00 | 0.40 | 0.75 | 0.67 | 0.80 |
+| erythrocyte | 12 | 0.43 | 0.32 | 0.92 | 0.67 | 0.00 | 0.65 | 0.74 | 0.59 | 0.81 |
+| T cell | 15 | 0.00 | 0.12 | 0.12 | 0.00 | 0.00 | 0.05 | 0.22 | 0.46 | 0.11 |
+| mature NK T cell | 6 | 0.29 | 0.00 | 0.00 | 0.25 | 0.00 | 0.19 | 0.29 | 0.29 | 0.36 |
+| granulocyte | 6 | 0.63 | 0.00 | 0.59 | 0.67 | 0.00 | 0.44 | 0.56 | 0.59 | 0.71 |
+| natural killer cell | 4 | 0.22 | 0.00 | 0.00 | 0.33 | 0.00 | 0.57 | 0.50 | 0.89 | 0.50 |
+| mast cell | 4 | 0.44 | 0.53 | 0.57 | 0.50 | 0.00 | 0.53 | 0.57 | 0.62 | 0.53 |
+| epithelial cell | 8 | 0.57 | 0.55 | 0.71 | 0.53 | 0.00 | 0.15 | 0.50 | 0.47 | 0.62 |
+| B cell | 8 | 0.71 | 0.77 | 0.77 | 0.57 | 0.00 | 0.70 | 0.93 | 0.86 | 0.86 |
+| monocyte | 4 | 0.00 | 0.00 | 0.40 | 0.00 | 0.00 | 0.24 | 0.40 | 0.50 | 0.00 |
+| basophil | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 0.00 | 0.50 | 0.00 |
+| myeloid dendritic cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 0.00 | 0.50 | 0.00 |
 | plasma cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | non-classical monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | intermediate monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | mesenchymal cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
+| mesothelial cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 
 The train accuracies are computed on the training data.
 
 | Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| mesenchymal stem cell | 21131 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.94 | 0.97 | 0.97 | 0.99 |
-| skeletal muscle satellite stem cell | 5555 | 0.97 | 0.98 | 0.98 | 0.98 | 0.00 | 0.97 | 0.98 | 0.98 | 0.98 |
-| endothelial cell | 3168 | 0.92 | 0.93 | 0.95 | 0.95 | 0.00 | 0.94 | 0.94 | 0.94 | 0.95 |
-| capillary endothelial cell | 2954 | 0.89 | 0.90 | 0.93 | 0.92 | 0.00 | 0.90 | 0.90 | 0.91 | 0.92 |
-| macrophage | 2454 | 0.96 | 0.96 | 0.97 | 0.96 | 0.00 | 0.89 | 0.96 | 0.96 | 0.97 |
-| pericyte | 2137 | 0.90 | 0.90 | 0.93 | 0.93 | 0.00 | 0.89 | 0.92 | 0.93 | 0.94 |
-| CD8-positive, alpha-beta T cell | 1269 | 0.66 | 0.76 | 0.85 | 0.81 | 0.00 | 0.79 | 0.84 | 0.89 | 0.89 |
-| endothelial cell of vascular tree | 653 | 0.89 | 0.89 | 0.89 | 0.90 | 0.00 | 0.91 | 0.88 | 0.89 | 0.92 |
-| CD4-positive, alpha-beta T cell | 470 | 0.51 | 0.50 | 0.63 | 0.53 | 0.00 | 0.63 | 0.78 | 0.81 | 0.78 |
-| fast muscle cell | 421 | 0.94 | 0.96 | 0.95 | 0.92 | 0.00 | 0.94 | 0.93 | 0.95 | 0.96 |
-| tendon cell | 384 | 0.73 | 0.76 | 0.84 | 0.50 | 0.00 | 0.34 | 0.59 | 0.61 | 0.81 |
-| smooth muscle cell | 198 | 0.46 | 0.46 | 0.54 | 0.68 | 0.00 | 0.62 | 0.80 | 0.81 | 0.88 |
-| endothelial cell of artery | 162 | 0.78 | 0.83 | 0.90 | 0.80 | 0.00 | 0.76 | 0.84 | 0.84 | 0.90 |
-| neutrophil | 150 | 0.77 | 0.81 | 0.87 | 0.82 | 0.00 | 0.87 | 0.93 | 0.96 | 0.96 |
-| slow muscle cell | 157 | 0.92 | 0.93 | 0.91 | 0.80 | 0.00 | 0.73 | 0.98 | 0.99 | 0.97 |
-| endothelial cell of lymphatic vessel | 145 | 0.89 | 0.88 | 0.92 | 0.84 | 0.00 | 0.78 | 0.93 | 0.91 | 0.93 |
-| erythrocyte | 109 | 0.45 | 0.27 | 0.93 | 0.88 | 0.00 | 0.77 | 0.74 | 0.69 | 0.91 |
-| T cell | 93 | 0.00 | 0.06 | 0.33 | 0.22 | 0.00 | 0.63 | 0.89 | 0.86 | 0.84 |
-| mature NK T cell | 91 | 0.49 | 0.06 | 0.49 | 0.28 | 0.00 | 0.43 | 0.82 | 0.87 | 0.84 |
-| granulocyte | 88 | 0.71 | 0.00 | 0.79 | 0.67 | 0.00 | 0.44 | 0.73 | 0.93 | 0.96 |
-| natural killer cell | 86 | 0.62 | 0.41 | 0.50 | 0.39 | 0.00 | 0.68 | 0.86 | 0.84 | 0.84 |
-| mast cell | 62 | 0.70 | 0.70 | 0.81 | 0.79 | 0.00 | 0.81 | 0.95 | 0.94 | 0.85 |
-| epithelial cell | 50 | 0.67 | 0.12 | 0.73 | 0.73 | 0.00 | 0.45 | 0.87 | 0.85 | 0.79 |
-| B cell | 42 | 0.63 | 0.81 | 0.93 | 0.78 | 0.00 | 0.78 | 0.99 | 0.99 | 0.96 |
-| monocyte | 28 | 0.00 | 0.07 | 0.12 | 0.32 | 0.00 | 0.16 | 0.72 | 0.74 | 0.44 |
-| basophil | 8 | 0.00 | 0.00 | 0.17 | 0.36 | 0.00 | 0.76 | 1.00 | 0.94 | 0.77 |
-| myeloid dendritic cell | 7 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.56 | 1.00 | 0.67 | 0.00 |
-| plasma cell | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.33 | 1.00 | 0.89 | 1.00 |
-| non-classical monocyte | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.29 | 0.86 | 0.86 | 0.50 |
+| mesenchymal stem cell | 21134 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.92 | 0.97 | 0.97 | 0.99 |
+| skeletal muscle satellite stem cell | 5531 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.97 | 0.98 | 0.98 | 0.98 |
+| endothelial cell | 3173 | 0.92 | 0.93 | 0.95 | 0.94 | 0.00 | 0.92 | 0.94 | 0.94 | 0.95 |
+| capillary endothelial cell | 2963 | 0.90 | 0.90 | 0.93 | 0.91 | 0.00 | 0.87 | 0.90 | 0.91 | 0.92 |
+| macrophage | 2452 | 0.96 | 0.96 | 0.97 | 0.96 | 0.00 | 0.92 | 0.96 | 0.97 | 0.97 |
+| pericyte | 2146 | 0.89 | 0.90 | 0.93 | 0.93 | 0.00 | 0.86 | 0.92 | 0.92 | 0.94 |
+| CD8-positive, alpha-beta T cell | 1270 | 0.70 | 0.76 | 0.85 | 0.79 | 0.00 | 0.77 | 0.86 | 0.90 | 0.89 |
+| endothelial cell of vascular tree | 653 | 0.89 | 0.89 | 0.88 | 0.88 | 0.00 | 0.88 | 0.89 | 0.90 | 0.92 |
+| CD4-positive, alpha-beta T cell | 464 | 0.49 | 0.52 | 0.62 | 0.52 | 0.00 | 0.58 | 0.80 | 0.84 | 0.78 |
+| fast muscle cell | 424 | 0.95 | 0.95 | 0.95 | 0.92 | 0.00 | 0.92 | 0.96 | 0.94 | 0.96 |
+| tendon cell | 382 | 0.72 | 0.79 | 0.85 | 0.72 | 0.00 | 0.33 | 0.53 | 0.51 | 0.80 |
+| smooth muscle cell | 198 | 0.44 | 0.44 | 0.48 | 0.66 | 0.00 | 0.51 | 0.80 | 0.81 | 0.85 |
+| endothelial cell of artery | 160 | 0.76 | 0.83 | 0.90 | 0.71 | 0.00 | 0.61 | 0.84 | 0.84 | 0.89 |
+| slow muscle cell | 154 | 0.92 | 0.91 | 0.92 | 0.84 | 0.00 | 0.94 | 0.98 | 0.97 | 0.96 |
+| neutrophil | 153 | 0.78 | 0.82 | 0.87 | 0.79 | 0.00 | 0.89 | 0.97 | 0.96 | 0.97 |
+| endothelial cell of lymphatic vessel | 147 | 0.88 | 0.91 | 0.91 | 0.71 | 0.00 | 0.85 | 0.91 | 0.90 | 0.93 |
+| erythrocyte | 112 | 0.45 | 0.28 | 0.93 | 0.88 | 0.00 | 0.66 | 0.80 | 0.65 | 0.83 |
+| T cell | 93 | 0.04 | 0.10 | 0.34 | 0.15 | 0.00 | 0.47 | 0.86 | 0.87 | 0.81 |
+| mature NK T cell | 92 | 0.41 | 0.06 | 0.44 | 0.37 | 0.00 | 0.43 | 0.77 | 0.83 | 0.82 |
+| granulocyte | 88 | 0.72 | 0.07 | 0.81 | 0.73 | 0.00 | 0.51 | 0.81 | 0.95 | 0.96 |
+| natural killer cell | 87 | 0.57 | 0.34 | 0.63 | 0.38 | 0.00 | 0.73 | 0.86 | 0.84 | 0.86 |
+| mast cell | 62 | 0.70 | 0.72 | 0.82 | 0.78 | 0.00 | 0.88 | 0.96 | 0.91 | 0.85 |
+| epithelial cell | 49 | 0.67 | 0.41 | 0.76 | 0.59 | 0.00 | 0.26 | 0.74 | 0.92 | 0.79 |
+| B cell | 41 | 0.81 | 0.91 | 0.91 | 0.84 | 0.00 | 0.77 | 1.00 | 0.99 | 0.96 |
+| monocyte | 28 | 0.00 | 0.00 | 0.18 | 0.07 | 0.00 | 0.41 | 0.74 | 0.80 | 0.25 |
+| basophil | 8 | 0.00 | 0.00 | 0.17 | 0.22 | 0.00 | 0.70 | 1.00 | 1.00 | 0.55 |
+| myeloid dendritic cell | 7 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.26 | 1.00 | 0.88 | 0.00 |
+| plasma cell | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 1.00 | 1.00 | 1.00 |
+| non-classical monocyte | 3 | 0.00 | 0.00 | 0.50 | 0.00 | 0.00 | 0.19 | 0.86 | 0.75 | 0.50 |
 | intermediate monocyte | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 1.00 | 1.00 | 0.00 |
-| mesenchymal cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.80 | 0.80 | 0.00 |
+| mesenchymal cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.80 | 0.57 | 0.00 |
+| mesothelial cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.29 | 0.67 | 1.00 |
 
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