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README.md

@@ -32,67 +32,67 @@ 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 |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| enterocyte of epithelium of large intestine | 466 | 0.83 | 0.84 | 0.84 | 0.81 | 0.00 | 0.81 | 0.83 | 0.84 | 0.85 |
-| CD4-positive, alpha-beta T cell | 403 | 0.84 | 0.88 | 0.87 | 0.65 | 0.00 | 0.80 | 0.83 | 0.85 | 0.90 |
-| plasma cell | 306 | 0.98 | 0.98 | 0.97 | 0.98 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |
-| CD8-positive, alpha-beta T cell | 285 | 0.80 | 0.84 | 0.84 | 0.55 | 0.00 | 0.76 | 0.82 | 0.82 | 0.87 |
-| fibroblast | 250 | 0.98 | 0.98 | 0.98 | 0.97 | 0.00 | 0.97 | 0.99 | 0.98 | 0.98 |
-| B cell | 229 | 1.00 | 0.99 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
-| gamma-delta T cell | 193 | 0.91 | 0.92 | 0.93 | 0.51 | 0.00 | 0.88 | 0.92 | 0.90 | 0.94 |
-| intestinal crypt stem cell of colon | 170 | 0.83 | 0.87 | 0.84 | 0.81 | 0.00 | 0.74 | 0.85 | 0.84 | 0.90 |
-| large intestine goblet cell | 170 | 0.91 | 0.93 | 0.93 | 0.79 | 0.00 | 0.68 | 0.92 | 0.89 | 0.93 |
-| enteroglial cell | 75 | 0.97 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 0.99 |
-| regulatory T cell | 65 | 0.63 | 0.67 | 0.70 | 0.42 | 0.00 | 0.67 | 0.64 | 0.66 | 0.76 |
-| mast cell | 51 | 0.96 | 0.98 | 0.98 | 0.99 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |
-| myeloid leukocyte | 29 | 0.85 | 0.89 | 0.89 | 0.85 | 0.00 | 0.91 | 0.90 | 0.92 | 0.92 |
-| colon endothelial cell | 38 | 0.94 | 0.96 | 0.95 | 0.89 | 0.00 | 0.90 | 0.97 | 0.96 | 0.97 |
-| colon macrophage | 38 | 0.85 | 0.85 | 0.78 | 0.85 | 0.00 | 0.86 | 0.89 | 0.89 | 0.91 |
-| transit amplifying cell of colon | 22 | 0.71 | 0.57 | 0.63 | 0.46 | 0.00 | 0.55 | 0.64 | 0.63 | 0.72 |
-| naive thymus-derived CD4-positive, alpha-beta T cell | 25 | 0.79 | 0.69 | 0.67 | 0.21 | 0.00 | 0.76 | 0.75 | 0.74 | 0.81 |
-| paneth cell of colon | 23 | 0.55 | 0.53 | 0.65 | 0.72 | 0.00 | 0.47 | 0.68 | 0.60 | 0.73 |
-| tuft cell of colon | 18 | 0.95 | 0.97 | 1.00 | 0.91 | 0.00 | 0.92 | 0.97 | 1.00 | 1.00 |
-| myofibroblast cell | 12 | 0.86 | 0.88 | 0.96 | 0.88 | 0.00 | 0.89 | 1.00 | 0.85 | 0.96 |
-| monocyte | 3 | 0.80 | 0.80 | 0.44 | 0.40 | 0.00 | 0.80 | 0.80 | 0.67 | 0.80 |
-| mature NK T cell | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.50 | 0.67 | 0.00 |
-| type L enteroendocrine cell | 4 | 0.57 | 1.00 | 0.89 | 0.73 | 0.00 | 0.80 | 1.00 | 0.73 | 1.00 |
-| myeloid dendritic cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.36 | 0.00 | 0.50 | 0.00 |
-| enterochromaffin-like cell | 5 | 0.00 | 0.91 | 0.75 | 0.25 | 0.00 | 0.67 | 1.00 | 0.89 | 0.89 |
-| natural killer cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
-| innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.29 | 0.67 | 0.67 | 0.00 |
+| enterocyte of epithelium of large intestine | 471 | 0.82 | 0.84 | 0.84 | 0.82 | 0.00 | 0.79 | 0.82 | 0.86 | 0.84 |
+| CD4-positive, alpha-beta T cell | 413 | 0.85 | 0.88 | 0.86 | 0.72 | 0.00 | 0.73 | 0.86 | 0.86 | 0.89 |
+| plasma cell | 315 | 0.98 | 0.98 | 0.97 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
+| CD8-positive, alpha-beta T cell | 289 | 0.80 | 0.85 | 0.83 | 0.55 | 0.00 | 0.70 | 0.80 | 0.83 | 0.87 |
+| fibroblast | 250 | 0.96 | 0.98 | 0.98 | 0.97 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |
+| B cell | 228 | 0.99 | 0.99 | 0.99 | 0.98 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
+| gamma-delta T cell | 190 | 0.88 | 0.91 | 0.94 | 0.64 | 0.00 | 0.81 | 0.90 | 0.90 | 0.93 |
+| intestinal crypt stem cell of colon | 151 | 0.81 | 0.84 | 0.86 | 0.81 | 0.00 | 0.80 | 0.83 | 0.84 | 0.89 |
+| large intestine goblet cell | 169 | 0.90 | 0.94 | 0.93 | 0.79 | 0.00 | 0.79 | 0.91 | 0.90 | 0.93 |
+| enteroglial cell | 77 | 0.99 | 0.99 | 0.97 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.98 |
+| regulatory T cell | 64 | 0.66 | 0.64 | 0.63 | 0.30 | 0.00 | 0.60 | 0.72 | 0.68 | 0.78 |
+| mast cell | 48 | 0.99 | 0.97 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
+| myeloid leukocyte | 31 | 0.89 | 0.91 | 0.92 | 0.85 | 0.00 | 0.98 | 0.92 | 0.95 | 1.00 |
+| colon endothelial cell | 37 | 0.93 | 0.90 | 0.91 | 0.92 | 0.00 | 0.90 | 0.97 | 0.95 | 0.97 |
+| colon macrophage | 33 | 0.83 | 0.85 | 0.84 | 0.83 | 0.00 | 0.91 | 0.88 | 0.88 | 0.94 |
+| transit amplifying cell of colon | 25 | 0.75 | 0.59 | 0.67 | 0.60 | 0.00 | 0.55 | 0.60 | 0.64 | 0.77 |
+| naive thymus-derived CD4-positive, alpha-beta T cell | 23 | 0.75 | 0.75 | 0.69 | 0.12 | 0.00 | 0.77 | 0.69 | 0.72 | 0.83 |
+| paneth cell of colon | 21 | 0.63 | 0.37 | 0.68 | 0.76 | 0.00 | 0.64 | 0.73 | 0.52 | 0.85 |
+| tuft cell of colon | 17 | 1.00 | 1.00 | 0.97 | 0.94 | 0.00 | 0.89 | 1.00 | 0.97 | 1.00 |
+| myofibroblast cell | 11 | 0.79 | 0.88 | 0.87 | 0.95 | 0.00 | 0.79 | 0.96 | 0.83 | 0.88 |
+| monocyte | 4 | 0.86 | 0.86 | 0.55 | 0.67 | 0.00 | 0.86 | 0.86 | 0.75 | 0.86 |
+| mature NK T cell | 6 | 0.00 | 0.29 | 0.29 | 0.00 | 0.00 | 0.32 | 0.50 | 0.60 | 0.44 |
+| type L enteroendocrine cell | 5 | 0.59 | 0.83 | 0.77 | 0.75 | 0.00 | 0.48 | 1.00 | 0.91 | 1.00 |
+| myeloid dendritic cell | 2 | 0.00 | 0.00 | 0.67 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
+| enterochromaffin-like cell | 6 | 0.00 | 0.80 | 0.67 | 0.67 | 0.00 | 0.67 | 0.91 | 1.00 | 1.00 |
+| natural killer cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 0.67 | 0.67 | 0.00 |
+| innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 0.67 | 0.50 | 0.00 |
 | neutrophil | 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 |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| enterocyte of epithelium of large intestine | 4101 | 0.85 | 0.85 | 0.87 | 0.89 | 0.00 | 0.83 | 0.85 | 0.88 | 0.87 |
-| CD4-positive, alpha-beta T cell | 3837 | 0.85 | 0.88 | 0.91 | 0.76 | 0.00 | 0.84 | 0.89 | 0.89 | 0.92 |
-| plasma cell | 3002 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
-| CD8-positive, alpha-beta T cell | 2677 | 0.80 | 0.84 | 0.88 | 0.65 | 0.00 | 0.80 | 0.86 | 0.86 | 0.89 |
-| fibroblast | 2347 | 0.98 | 0.98 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
-| B cell | 1840 | 0.99 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |
-| gamma-delta T cell | 1663 | 0.91 | 0.92 | 0.95 | 0.64 | 0.00 | 0.89 | 0.92 | 0.91 | 0.95 |
-| intestinal crypt stem cell of colon | 1562 | 0.85 | 0.85 | 0.91 | 0.87 | 0.00 | 0.78 | 0.89 | 0.89 | 0.93 |
-| large intestine goblet cell | 1387 | 0.93 | 0.94 | 0.94 | 0.79 | 0.00 | 0.71 | 0.94 | 0.94 | 0.95 |
-| enteroglial cell | 773 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 0.99 |
-| regulatory T cell | 568 | 0.73 | 0.71 | 0.82 | 0.50 | 0.00 | 0.77 | 0.79 | 0.79 | 0.89 |
-| mast cell | 342 | 0.97 | 0.97 | 0.98 | 0.95 | 0.00 | 0.98 | 1.00 | 0.99 | 0.99 |
-| myeloid leukocyte | 325 | 0.86 | 0.91 | 0.93 | 0.88 | 0.00 | 0.96 | 1.00 | 0.99 | 0.97 |
-| colon endothelial cell | 310 | 0.89 | 0.87 | 0.93 | 0.94 | 0.00 | 0.91 | 0.96 | 0.95 | 0.95 |
-| colon macrophage | 290 | 0.80 | 0.86 | 0.87 | 0.85 | 0.00 | 0.93 | 0.99 | 1.00 | 0.94 |
-| transit amplifying cell of colon | 215 | 0.77 | 0.71 | 0.80 | 0.60 | 0.00 | 0.60 | 0.78 | 0.77 | 0.87 |
-| naive thymus-derived CD4-positive, alpha-beta T cell | 203 | 0.70 | 0.68 | 0.76 | 0.47 | 0.00 | 0.71 | 0.83 | 0.79 | 0.81 |
-| paneth cell of colon | 194 | 0.60 | 0.36 | 0.82 | 0.76 | 0.00 | 0.58 | 0.83 | 0.62 | 0.88 |
-| tuft cell of colon | 160 | 0.92 | 0.96 | 0.95 | 0.94 | 0.00 | 0.90 | 0.97 | 0.97 | 0.98 |
-| myofibroblast cell | 70 | 0.81 | 0.81 | 0.88 | 0.87 | 0.00 | 0.88 | 1.00 | 0.99 | 0.95 |
-| monocyte | 63 | 0.76 | 0.81 | 0.77 | 0.72 | 0.00 | 0.90 | 0.99 | 0.98 | 0.94 |
-| mature NK T cell | 43 | 0.00 | 0.47 | 0.66 | 0.45 | 0.00 | 0.56 | 0.95 | 0.93 | 0.90 |
-| type L enteroendocrine cell | 40 | 0.76 | 0.88 | 0.92 | 0.74 | 0.00 | 0.88 | 0.98 | 0.98 | 1.00 |
-| myeloid dendritic cell | 38 | 0.00 | 0.18 | 0.37 | 0.23 | 0.00 | 0.77 | 0.99 | 1.00 | 0.69 |
-| enterochromaffin-like cell | 22 | 0.00 | 0.80 | 0.87 | 0.78 | 0.00 | 0.76 | 1.00 | 0.98 | 0.98 |
-| natural killer cell | 12 | 0.00 | 0.00 | 0.00 | 0.29 | 0.00 | 0.75 | 0.96 | 1.00 | 0.86 |
-| innate lymphoid cell | 11 | 0.00 | 0.00 | 0.43 | 0.00 | 0.00 | 0.45 | 0.96 | 1.00 | 0.59 |
-| neutrophil | 9 | 0.00 | 0.00 | 0.36 | 0.62 | 0.00 | 0.82 | 1.00 | 0.95 | 1.00 |
+| enterocyte of epithelium of large intestine | 4096 | 0.84 | 0.85 | 0.87 | 0.88 | 0.00 | 0.82 | 0.85 | 0.89 | 0.87 |
+| CD4-positive, alpha-beta T cell | 3827 | 0.86 | 0.88 | 0.91 | 0.80 | 0.00 | 0.80 | 0.89 | 0.90 | 0.92 |
+| plasma cell | 2993 | 0.98 | 0.98 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
+| CD8-positive, alpha-beta T cell | 2673 | 0.80 | 0.84 | 0.88 | 0.70 | 0.00 | 0.75 | 0.86 | 0.87 | 0.89 |
+| fibroblast | 2347 | 0.97 | 0.98 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
+| B cell | 1841 | 0.99 | 0.99 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
+| gamma-delta T cell | 1666 | 0.91 | 0.92 | 0.95 | 0.79 | 0.00 | 0.85 | 0.93 | 0.93 | 0.95 |
+| intestinal crypt stem cell of colon | 1581 | 0.85 | 0.86 | 0.91 | 0.88 | 0.00 | 0.85 | 0.89 | 0.91 | 0.93 |
+| large intestine goblet cell | 1388 | 0.93 | 0.94 | 0.95 | 0.83 | 0.00 | 0.84 | 0.95 | 0.96 | 0.97 |
+| enteroglial cell | 771 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 0.99 |
+| regulatory T cell | 569 | 0.70 | 0.71 | 0.80 | 0.38 | 0.00 | 0.67 | 0.78 | 0.81 | 0.88 |
+| mast cell | 345 | 0.97 | 0.97 | 0.98 | 0.97 | 0.00 | 0.98 | 0.99 | 0.99 | 0.98 |
+| myeloid leukocyte | 323 | 0.88 | 0.90 | 0.92 | 0.90 | 0.00 | 0.94 | 0.99 | 1.00 | 0.97 |
+| colon endothelial cell | 311 | 0.90 | 0.88 | 0.93 | 0.93 | 0.00 | 0.90 | 0.98 | 0.98 | 0.96 |
+| colon macrophage | 295 | 0.82 | 0.85 | 0.86 | 0.85 | 0.00 | 0.93 | 0.99 | 1.00 | 0.94 |
+| transit amplifying cell of colon | 212 | 0.74 | 0.70 | 0.79 | 0.60 | 0.00 | 0.61 | 0.81 | 0.80 | 0.87 |
+| naive thymus-derived CD4-positive, alpha-beta T cell | 205 | 0.69 | 0.68 | 0.74 | 0.37 | 0.00 | 0.74 | 0.80 | 0.81 | 0.83 |
+| paneth cell of colon | 196 | 0.61 | 0.36 | 0.82 | 0.76 | 0.00 | 0.76 | 0.84 | 0.57 | 0.91 |
+| tuft cell of colon | 161 | 0.92 | 0.96 | 0.95 | 0.96 | 0.00 | 0.88 | 0.98 | 0.97 | 0.98 |
+| myofibroblast cell | 71 | 0.82 | 0.80 | 0.87 | 0.85 | 0.00 | 0.87 | 1.00 | 0.98 | 0.95 |
+| monocyte | 62 | 0.74 | 0.79 | 0.77 | 0.75 | 0.00 | 0.96 | 0.99 | 0.98 | 0.91 |
+| mature NK T cell | 41 | 0.00 | 0.37 | 0.65 | 0.38 | 0.00 | 0.46 | 0.98 | 0.96 | 0.86 |
+| type L enteroendocrine cell | 39 | 0.77 | 0.83 | 0.92 | 0.62 | 0.00 | 0.59 | 0.97 | 0.99 | 0.99 |
+| myeloid dendritic cell | 38 | 0.41 | 0.18 | 0.47 | 0.38 | 0.00 | 0.85 | 0.99 | 1.00 | 0.62 |
+| enterochromaffin-like cell | 21 | 0.00 | 0.68 | 0.86 | 0.76 | 0.00 | 0.54 | 1.00 | 0.95 | 0.93 |
+| natural killer cell | 13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.79 | 1.00 | 0.96 | 0.76 |
+| innate lymphoid cell | 11 | 0.00 | 0.00 | 0.17 | 0.00 | 0.00 | 0.54 | 0.96 | 0.96 | 0.53 |
+| neutrophil | 9 | 0.00 | 0.00 | 0.20 | 0.46 | 0.00 | 0.78 | 1.00 | 0.95 | 0.94 |
 
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