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README.md

@@ -32,73 +32,71 @@ 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 |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| acinar cell of salivary gland | 1199 | 0.96 | 0.93 | 0.98 | 0.96 | 0.00 | 0.92 | 0.95 | 0.96 | 0.97 |
-| B cell | 519 | 0.99 | 1.00 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |
-| fibroblast | 472 | 0.97 | 0.94 | 0.97 | 0.94 | 0.00 | 0.96 | 0.96 | 0.95 | 0.98 |
-| CD8-positive, alpha-beta T cell | 387 | 0.89 | 0.87 | 0.93 | 0.90 | 0.00 | 0.88 | 0.89 | 0.91 | 0.92 |
-| duct epithelial cell | 373 | 0.86 | 0.76 | 0.94 | 0.84 | 0.00 | 0.80 | 0.85 | 0.88 | 0.89 |
-| CD4-positive, alpha-beta T cell | 165 | 0.86 | 0.87 | 0.88 | 0.85 | 0.00 | 0.85 | 0.87 | 0.90 | 0.89 |
-| endothelial cell | 158 | 0.92 | 0.91 | 0.94 | 0.87 | 0.00 | 0.93 | 0.94 | 0.95 | 0.95 |
-| macrophage | 180 | 0.88 | 0.71 | 0.92 | 0.85 | 0.00 | 0.93 | 0.95 | 0.95 | 0.96 |
-| basal cell | 114 | 0.90 | 0.92 | 0.94 | 0.90 | 0.00 | 0.89 | 0.88 | 0.90 | 0.90 |
-| tissue-resident macrophage | 82 | 0.88 | 0.00 | 0.92 | 0.84 | 0.00 | 0.89 | 0.87 | 0.89 | 0.95 |
-| plasma cell | 47 | 0.87 | 0.97 | 0.99 | 0.98 | 0.00 | 0.96 | 0.96 | 0.97 | 0.97 |
-| endothelial cell of lymphatic vessel | 54 | 0.83 | 0.73 | 0.89 | 0.66 | 0.00 | 0.85 | 0.89 | 0.89 | 0.91 |
-| adventitial cell | 56 | 0.85 | 0.25 | 0.75 | 0.58 | 0.00 | 0.77 | 0.76 | 0.71 | 0.84 |
-| vascular associated smooth muscle cell | 47 | 0.98 | 0.98 | 0.98 | 0.96 | 0.00 | 0.90 | 0.98 | 0.99 | 0.98 |
-| neutrophil | 24 | 0.91 | 0.92 | 0.94 | 0.83 | 0.00 | 0.94 | 0.96 | 0.94 | 0.94 |
-| myoepithelial cell | 16 | 0.88 | 0.78 | 0.91 | 1.00 | 0.00 | 0.68 | 0.86 | 0.89 | 0.89 |
-| T cell | 19 | 0.56 | 0.10 | 0.46 | 0.46 | 0.00 | 0.44 | 0.54 | 0.53 | 0.57 |
-| ionocyte | 15 | 0.87 | 0.97 | 0.93 | 0.61 | 0.00 | 0.80 | 0.90 | 0.87 | 0.90 |
-| endothelial cell of artery | 10 | 0.75 | 0.84 | 0.78 | 0.57 | 0.00 | 0.83 | 0.80 | 0.90 | 0.80 |
-| monocyte | 11 | 0.46 | 0.52 | 0.60 | 0.35 | 0.00 | 0.57 | 0.59 | 0.55 | 0.61 |
-| natural killer cell | 10 | 0.49 | 0.57 | 0.74 | 0.00 | 0.00 | 0.43 | 0.71 | 0.57 | 0.69 |
-| mast cell | 5 | 0.00 | 0.77 | 0.60 | 0.67 | 0.00 | 0.77 | 0.67 | 0.80 | 0.67 |
-| classical monocyte | 8 | 0.00 | 0.00 | 0.50 | 0.15 | 0.00 | 0.00 | 0.18 | 0.00 | 0.00 |
-| intermediate monocyte | 7 | 0.00 | 0.00 | 0.67 | 0.00 | 0.00 | 0.13 | 0.20 | 0.36 | 0.25 |
-| mature NK T cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 0.40 | 0.00 | 0.00 |
-| leukocyte | 2 | 0.00 | 0.00 | 0.67 | 0.00 | 0.00 | 1.00 | 0.67 | 0.00 | 0.67 |
+| acinar cell of salivary gland | 1210 | 0.96 | 0.94 | 0.97 | 0.96 | 0.00 | 0.91 | 0.97 | 0.97 | 0.98 |
+| B cell | 532 | 1.00 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
+| fibroblast | 455 | 0.97 | 0.94 | 0.97 | 0.94 | 0.00 | 0.96 | 0.96 | 0.96 | 0.97 |
+| CD8-positive, alpha-beta T cell | 385 | 0.92 | 0.89 | 0.94 | 0.91 | 0.00 | 0.90 | 0.90 | 0.91 | 0.94 |
+| duct epithelial cell | 385 | 0.87 | 0.78 | 0.94 | 0.84 | 0.00 | 0.77 | 0.88 | 0.89 | 0.91 |
+| CD4-positive, alpha-beta T cell | 175 | 0.89 | 0.87 | 0.87 | 0.87 | 0.00 | 0.86 | 0.88 | 0.90 | 0.91 |
+| endothelial cell | 160 | 0.95 | 0.90 | 0.95 | 0.90 | 0.00 | 0.94 | 0.94 | 0.93 | 0.96 |
+| macrophage | 169 | 0.91 | 0.72 | 0.92 | 0.82 | 0.00 | 0.90 | 0.94 | 0.95 | 0.95 |
+| basal cell | 101 | 0.89 | 0.91 | 0.93 | 0.88 | 0.00 | 0.86 | 0.87 | 0.90 | 0.91 |
+| tissue-resident macrophage | 76 | 0.88 | 0.00 | 0.89 | 0.67 | 0.00 | 0.82 | 0.89 | 0.90 | 0.95 |
+| plasma cell | 49 | 0.92 | 0.96 | 0.94 | 0.98 | 0.00 | 0.96 | 0.98 | 0.96 | 0.98 |
+| endothelial cell of lymphatic vessel | 48 | 0.89 | 0.72 | 0.92 | 0.74 | 0.00 | 0.84 | 0.87 | 0.84 | 0.93 |
+| adventitial cell | 56 | 0.86 | 0.24 | 0.76 | 0.62 | 0.00 | 0.75 | 0.79 | 0.80 | 0.83 |
+| vascular associated smooth muscle cell | 48 | 0.99 | 0.99 | 0.97 | 0.95 | 0.00 | 0.97 | 0.98 | 0.98 | 0.99 |
+| neutrophil | 23 | 0.94 | 0.90 | 1.00 | 0.94 | 0.00 | 0.94 | 0.98 | 0.98 | 0.96 |
+| myoepithelial cell | 22 | 0.91 | 0.84 | 0.91 | 0.91 | 0.00 | 0.81 | 0.88 | 0.86 | 0.92 |
+| T cell | 24 | 0.60 | 0.15 | 0.51 | 0.56 | 0.00 | 0.47 | 0.53 | 0.59 | 0.62 |
+| ionocyte | 14 | 0.75 | 0.75 | 0.88 | 0.60 | 0.00 | 0.63 | 0.86 | 0.81 | 0.85 |
+| endothelial cell of artery | 9 | 0.67 | 0.56 | 0.62 | 0.46 | 0.00 | 0.59 | 0.90 | 0.67 | 0.78 |
+| monocyte | 12 | 0.55 | 0.57 | 0.52 | 0.48 | 0.00 | 0.57 | 0.65 | 0.58 | 0.59 |
+| natural killer cell | 7 | 0.50 | 0.62 | 0.77 | 0.40 | 0.00 | 0.50 | 0.61 | 0.52 | 0.71 |
+| mast cell | 4 | 0.00 | 0.73 | 0.60 | 0.67 | 0.00 | 0.67 | 0.57 | 0.80 | 0.67 |
+| classical monocyte | 8 | 0.00 | 0.00 | 0.17 | 0.31 | 0.00 | 0.12 | 0.22 | 0.17 | 0.00 |
+| intermediate monocyte | 8 | 0.00 | 0.00 | 0.17 | 0.31 | 0.00 | 0.00 | 0.17 | 0.18 | 0.00 |
+| mature NK T cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.57 | 0.00 | 0.00 | 0.00 |
+| leukocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | pericyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | salivary gland cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | myeloid dendritic 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 |
-| hematopoietic precursor 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 |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| acinar cell of salivary gland | 11038 | 0.96 | 0.92 | 0.98 | 0.98 | 0.00 | 0.93 | 0.95 | 0.96 | 0.97 |
-| B cell | 4429 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |
-| fibroblast | 3995 | 0.97 | 0.93 | 0.98 | 0.98 | 0.00 | 0.97 | 0.96 | 0.97 | 0.99 |
-| CD8-positive, alpha-beta T cell | 3678 | 0.89 | 0.86 | 0.94 | 0.92 | 0.00 | 0.89 | 0.91 | 0.92 | 0.94 |
-| duct epithelial cell | 3516 | 0.85 | 0.74 | 0.95 | 0.91 | 0.00 | 0.83 | 0.86 | 0.88 | 0.92 |
-| CD4-positive, alpha-beta T cell | 1721 | 0.86 | 0.86 | 0.91 | 0.88 | 0.00 | 0.88 | 0.90 | 0.91 | 0.91 |
-| endothelial cell | 1471 | 0.92 | 0.88 | 0.96 | 0.95 | 0.00 | 0.96 | 0.97 | 0.97 | 0.98 |
-| macrophage | 1443 | 0.88 | 0.71 | 0.96 | 0.92 | 0.00 | 0.95 | 0.97 | 0.97 | 0.98 |
-| basal cell | 1068 | 0.91 | 0.92 | 0.96 | 0.94 | 0.00 | 0.92 | 0.94 | 0.94 | 0.95 |
-| tissue-resident macrophage | 572 | 0.83 | 0.00 | 0.94 | 0.91 | 0.00 | 0.90 | 0.88 | 0.88 | 0.95 |
-| plasma cell | 536 | 0.91 | 0.96 | 0.99 | 0.98 | 0.00 | 0.95 | 0.99 | 0.98 | 0.99 |
-| endothelial cell of lymphatic vessel | 492 | 0.84 | 0.64 | 0.95 | 0.87 | 0.00 | 0.94 | 0.94 | 0.95 | 0.97 |
-| adventitial cell | 404 | 0.84 | 0.18 | 0.88 | 0.81 | 0.00 | 0.79 | 0.80 | 0.81 | 0.93 |
-| vascular associated smooth muscle cell | 356 | 0.96 | 0.97 | 0.96 | 0.98 | 0.00 | 0.93 | 0.97 | 0.98 | 0.97 |
-| neutrophil | 219 | 0.93 | 0.93 | 0.97 | 0.90 | 0.00 | 0.91 | 0.98 | 0.97 | 0.97 |
-| myoepithelial cell | 200 | 0.92 | 0.88 | 0.95 | 0.93 | 0.00 | 0.80 | 0.92 | 0.90 | 0.94 |
-| T cell | 174 | 0.66 | 0.27 | 0.75 | 0.73 | 0.00 | 0.65 | 0.81 | 0.83 | 0.83 |
-| ionocyte | 127 | 0.86 | 0.87 | 0.94 | 0.72 | 0.00 | 0.75 | 0.94 | 0.91 | 0.94 |
-| endothelial cell of artery | 106 | 0.74 | 0.60 | 0.93 | 0.80 | 0.00 | 0.84 | 0.93 | 0.90 | 0.90 |
-| monocyte | 88 | 0.46 | 0.48 | 0.64 | 0.40 | 0.00 | 0.79 | 0.84 | 0.91 | 0.87 |
-| natural killer cell | 63 | 0.38 | 0.43 | 0.52 | 0.51 | 0.00 | 0.40 | 0.59 | 0.60 | 0.68 |
-| mast cell | 40 | 0.00 | 0.73 | 0.78 | 0.73 | 0.00 | 0.85 | 1.00 | 0.99 | 0.96 |
-| classical monocyte | 35 | 0.00 | 0.00 | 0.45 | 0.44 | 0.00 | 0.96 | 1.00 | 0.96 | 0.92 |
-| intermediate monocyte | 35 | 0.00 | 0.00 | 0.56 | 0.30 | 0.00 | 0.66 | 0.88 | 0.90 | 0.92 |
-| mature NK T cell | 20 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.42 | 0.83 | 0.78 | 0.75 |
-| leukocyte | 4 | 0.00 | 0.00 | 0.86 | 0.67 | 0.00 | 0.62 | 0.80 | 1.00 | 1.00 |
-| pericyte | 3 | 0.00 | 0.00 | 0.40 | 0.00 | 0.00 | 0.67 | 1.00 | 1.00 | 0.50 |
-| salivary gland cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 1.00 | 0.80 | 1.00 |
-| myeloid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.33 | 0.22 | 1.00 | 0.00 |
-| non-classical monocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.40 | 1.00 | 1.00 | 1.00 |
-| hematopoietic precursor cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 1.00 | 1.00 | 1.00 |
+| acinar cell of salivary gland | 11027 | 0.96 | 0.93 | 0.98 | 0.97 | 0.00 | 0.94 | 0.96 | 0.96 | 0.98 |
+| B cell | 4416 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
+| fibroblast | 4012 | 0.97 | 0.94 | 0.98 | 0.97 | 0.00 | 0.97 | 0.97 | 0.97 | 0.99 |
+| CD8-positive, alpha-beta T cell | 3680 | 0.91 | 0.86 | 0.95 | 0.93 | 0.00 | 0.90 | 0.91 | 0.92 | 0.94 |
+| duct epithelial cell | 3504 | 0.86 | 0.75 | 0.95 | 0.90 | 0.00 | 0.82 | 0.87 | 0.88 | 0.92 |
+| CD4-positive, alpha-beta T cell | 1711 | 0.89 | 0.85 | 0.92 | 0.89 | 0.00 | 0.89 | 0.90 | 0.91 | 0.92 |
+| endothelial cell | 1469 | 0.94 | 0.88 | 0.96 | 0.94 | 0.00 | 0.96 | 0.97 | 0.97 | 0.98 |
+| macrophage | 1454 | 0.89 | 0.71 | 0.95 | 0.95 | 0.00 | 0.96 | 0.97 | 0.98 | 0.98 |
+| basal cell | 1081 | 0.92 | 0.92 | 0.96 | 0.93 | 0.00 | 0.91 | 0.95 | 0.94 | 0.96 |
+| tissue-resident macrophage | 578 | 0.81 | 0.00 | 0.93 | 0.92 | 0.00 | 0.88 | 0.89 | 0.90 | 0.94 |
+| plasma cell | 534 | 0.94 | 0.96 | 0.98 | 0.98 | 0.00 | 0.97 | 0.99 | 0.98 | 0.99 |
+| endothelial cell of lymphatic vessel | 498 | 0.91 | 0.66 | 0.94 | 0.88 | 0.00 | 0.93 | 0.94 | 0.95 | 0.97 |
+| adventitial cell | 404 | 0.84 | 0.21 | 0.87 | 0.74 | 0.00 | 0.80 | 0.81 | 0.82 | 0.94 |
+| vascular associated smooth muscle cell | 355 | 0.96 | 0.96 | 0.96 | 0.98 | 0.00 | 0.97 | 0.96 | 0.97 | 0.97 |
+| neutrophil | 220 | 0.93 | 0.91 | 0.97 | 0.93 | 0.00 | 0.93 | 0.98 | 0.96 | 0.97 |
+| myoepithelial cell | 194 | 0.91 | 0.90 | 0.94 | 0.93 | 0.00 | 0.80 | 0.90 | 0.90 | 0.94 |
+| T cell | 169 | 0.65 | 0.23 | 0.76 | 0.71 | 0.00 | 0.64 | 0.82 | 0.85 | 0.87 |
+| ionocyte | 128 | 0.88 | 0.86 | 0.93 | 0.70 | 0.00 | 0.73 | 0.93 | 0.88 | 0.94 |
+| endothelial cell of artery | 107 | 0.76 | 0.60 | 0.92 | 0.58 | 0.00 | 0.82 | 0.93 | 0.92 | 0.92 |
+| monocyte | 87 | 0.50 | 0.51 | 0.66 | 0.58 | 0.00 | 0.81 | 0.88 | 0.93 | 0.88 |
+| natural killer cell | 66 | 0.44 | 0.42 | 0.61 | 0.48 | 0.00 | 0.47 | 0.55 | 0.63 | 0.69 |
+| mast cell | 41 | 0.00 | 0.73 | 0.73 | 0.64 | 0.00 | 0.86 | 1.00 | 0.99 | 0.99 |
+| classical monocyte | 35 | 0.00 | 0.00 | 0.44 | 0.37 | 0.00 | 0.80 | 0.99 | 0.99 | 0.87 |
+| intermediate monocyte | 34 | 0.00 | 0.00 | 0.55 | 0.48 | 0.00 | 0.77 | 0.92 | 0.94 | 0.94 |
+| mature NK T cell | 21 | 0.00 | 0.00 | 0.09 | 0.31 | 0.00 | 0.54 | 0.84 | 0.79 | 0.69 |
+| leukocyte | 6 | 0.00 | 0.00 | 0.92 | 0.57 | 0.00 | 0.55 | 1.00 | 1.00 | 1.00 |
+| pericyte | 3 | 0.00 | 0.00 | 0.33 | 0.57 | 0.00 | 0.00 | 1.00 | 1.00 | 0.50 |
+| salivary gland cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 1.00 | 0.80 | 0.67 |
+| myeloid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 0.50 | 1.00 | 0.00 |
+| non-classical monocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 1.00 | 1.00 | 1.00 |
 
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