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README.md

@@ -32,77 +32,77 @@ 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 proper of duodenum | 1369 | 0.91 | 0.93 | 0.91 | 0.77 | 0.00 | 0.86 | 0.90 | 0.92 | 0.95 |
-| enterocyte of epithelium proper of ileum | 611 | 0.96 | 0.96 | 0.93 | 0.51 | 0.00 | 0.76 | 0.97 | 0.97 | 0.98 |
-| CD4-positive, alpha-beta T cell | 540 | 0.91 | 0.91 | 0.91 | 0.79 | 0.00 | 0.82 | 0.88 | 0.90 | 0.93 |
-| CD8-positive, alpha-beta T cell | 349 | 0.84 | 0.77 | 0.88 | 0.56 | 0.00 | 0.71 | 0.81 | 0.83 | 0.90 |
-| small intestine goblet cell | 203 | 0.92 | 0.94 | 0.95 | 0.89 | 0.00 | 0.80 | 0.92 | 0.95 | 0.94 |
-| paneth cell of epithelium of small intestine | 180 | 0.66 | 0.73 | 0.79 | 0.63 | 0.00 | 0.68 | 0.68 | 0.72 | 0.78 |
-| enterocyte of epithelium proper of small intestine | 153 | 0.61 | 0.64 | 0.67 | 0.57 | 0.00 | 0.56 | 0.69 | 0.80 | 0.84 |
-| activated CD8-positive, alpha-beta T cell | 114 | 0.74 | 0.46 | 0.88 | 0.55 | 0.00 | 0.55 | 0.73 | 0.73 | 0.84 |
-| plasma cell | 77 | 0.97 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.97 | 0.98 | 0.98 |
-| B cell | 68 | 0.99 | 0.99 | 0.98 | 0.99 | 0.00 | 0.98 | 0.97 | 0.98 | 0.99 |
-| intestinal crypt stem cell of small intestine | 54 | 0.39 | 0.47 | 0.48 | 0.25 | 0.00 | 0.31 | 0.38 | 0.48 | 0.52 |
-| activated CD4-positive, alpha-beta T cell | 64 | 0.49 | 0.30 | 0.60 | 0.08 | 0.00 | 0.42 | 0.48 | 0.52 | 0.57 |
-| fibroblast | 46 | 0.99 | 0.99 | 1.00 | 0.97 | 0.00 | 0.99 | 0.99 | 0.97 | 0.99 |
-| intestinal tuft cell | 49 | 1.00 | 1.00 | 1.00 | 0.98 | 0.00 | 0.95 | 1.00 | 1.00 | 1.00 |
-| enterocyte of epithelium proper of jejunum | 43 | 0.13 | 0.14 | 0.28 | 0.13 | 0.00 | 0.24 | 0.53 | 0.47 | 0.41 |
-| macrophage | 44 | 0.85 | 0.94 | 0.94 | 0.81 | 0.00 | 0.90 | 0.95 | 0.93 | 0.97 |
-| enteroendocrine cell of small intestine | 19 | 0.83 | 0.86 | 0.83 | 0.78 | 0.00 | 0.77 | 0.71 | 0.82 | 0.81 |
-| mast cell | 26 | 0.98 | 1.00 | 1.00 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |
-| natural killer cell | 17 | 0.00 | 0.17 | 0.24 | 0.00 | 0.00 | 0.22 | 0.11 | 0.47 | 0.24 |
-| enteroglial cell | 20 | 0.93 | 0.92 | 0.92 | 0.83 | 0.00 | 0.90 | 0.98 | 0.98 | 0.98 |
-| endothelial cell of arteriole | 16 | 0.82 | 1.00 | 0.85 | 0.79 | 0.00 | 0.88 | 0.94 | 0.82 | 0.91 |
-| gamma-delta T cell | 12 | 0.73 | 0.55 | 0.67 | 0.14 | 0.00 | 0.67 | 0.55 | 0.67 | 0.72 |
-| naive thymus-derived CD4-positive, alpha-beta T cell | 6 | 0.00 | 0.67 | 0.29 | 0.25 | 0.00 | 0.34 | 0.48 | 0.71 | 0.44 |
-| monocyte | 9 | 0.82 | 0.95 | 0.88 | 0.43 | 0.00 | 0.78 | 0.90 | 0.95 | 1.00 |
-| neutrophil | 5 | 0.36 | 0.80 | 0.62 | 0.20 | 0.00 | 0.47 | 0.91 | 0.73 | 0.73 |
-| endothelial cell of lymphatic vessel | 8 | 1.00 | 1.00 | 0.93 | 0.94 | 0.00 | 0.94 | 1.00 | 1.00 | 1.00 |
-| endothelial cell of venule | 6 | 0.00 | 0.92 | 0.67 | 0.40 | 0.00 | 0.77 | 0.83 | 0.60 | 0.60 |
-| myofibroblast cell | 6 | 0.71 | 0.91 | 1.00 | 0.44 | 0.00 | 0.80 | 1.00 | 1.00 | 1.00 |
-| transit amplifying cell of small intestine | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
-| innate lymphoid cell | 3 | 0.00 | 1.00 | 1.00 | 0.80 | 0.00 | 0.67 | 0.00 | 1.00 | 1.00 |
-| pericyte | 3 | 0.00 | 1.00 | 1.00 | 0.40 | 0.00 | 0.86 | 1.00 | 0.86 | 1.00 |
-| regulatory T cell | 3 | 0.00 | 0.50 | 0.00 | 0.50 | 0.00 | 0.00 | 0.00 | 0.50 | 0.00 |
+| enterocyte of epithelium proper of duodenum | 1336 | 0.92 | 0.93 | 0.92 | 0.79 | 0.00 | 0.87 | 0.91 | 0.93 | 0.94 |
+| enterocyte of epithelium proper of ileum | 627 | 0.96 | 0.96 | 0.92 | 0.56 | 0.00 | 0.75 | 0.97 | 0.97 | 0.98 |
+| CD4-positive, alpha-beta T cell | 532 | 0.89 | 0.89 | 0.92 | 0.68 | 0.00 | 0.78 | 0.89 | 0.89 | 0.91 |
+| CD8-positive, alpha-beta T cell | 349 | 0.86 | 0.78 | 0.91 | 0.54 | 0.00 | 0.74 | 0.82 | 0.82 | 0.89 |
+| small intestine goblet cell | 214 | 0.94 | 0.94 | 0.95 | 0.90 | 0.00 | 0.89 | 0.93 | 0.92 | 0.94 |
+| paneth cell of epithelium of small intestine | 194 | 0.71 | 0.74 | 0.80 | 0.74 | 0.00 | 0.65 | 0.71 | 0.79 | 0.83 |
+| enterocyte of epithelium proper of small intestine | 149 | 0.59 | 0.59 | 0.66 | 0.56 | 0.00 | 0.52 | 0.75 | 0.77 | 0.81 |
+| activated CD8-positive, alpha-beta T cell | 103 | 0.79 | 0.43 | 0.87 | 0.42 | 0.00 | 0.57 | 0.67 | 0.73 | 0.80 |
+| plasma cell | 80 | 0.99 | 0.99 | 0.98 | 0.97 | 0.00 | 0.96 | 0.98 | 0.98 | 0.99 |
+| B cell | 70 | 0.99 | 0.99 | 0.99 | 0.98 | 0.00 | 0.99 | 0.99 | 0.96 | 0.99 |
+| intestinal crypt stem cell of small intestine | 56 | 0.40 | 0.53 | 0.54 | 0.33 | 0.00 | 0.29 | 0.40 | 0.47 | 0.55 |
+| activated CD4-positive, alpha-beta T cell | 64 | 0.43 | 0.25 | 0.57 | 0.16 | 0.00 | 0.37 | 0.46 | 0.52 | 0.55 |
+| fibroblast | 45 | 0.99 | 0.99 | 0.99 | 0.95 | 0.00 | 1.00 | 1.00 | 0.99 | 0.99 |
+| intestinal tuft cell | 54 | 1.00 | 1.00 | 0.99 | 0.96 | 0.00 | 0.97 | 1.00 | 1.00 | 1.00 |
+| enterocyte of epithelium proper of jejunum | 46 | 0.11 | 0.12 | 0.23 | 0.18 | 0.00 | 0.08 | 0.51 | 0.51 | 0.31 |
+| macrophage | 49 | 0.82 | 0.92 | 0.92 | 0.85 | 0.00 | 0.97 | 0.94 | 0.91 | 0.92 |
+| enteroendocrine cell of small intestine | 19 | 0.86 | 0.84 | 0.86 | 0.79 | 0.00 | 0.63 | 0.84 | 0.80 | 0.84 |
+| mast cell | 24 | 0.98 | 1.00 | 0.98 | 0.94 | 0.00 | 0.98 | 1.00 | 1.00 | 1.00 |
+| natural killer cell | 19 | 0.00 | 0.26 | 0.30 | 0.00 | 0.00 | 0.21 | 0.14 | 0.36 | 0.24 |
+| enteroglial cell | 20 | 0.95 | 0.95 | 0.97 | 0.81 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |
+| endothelial cell of arteriole | 15 | 0.77 | 0.94 | 0.77 | 0.63 | 0.00 | 0.82 | 1.00 | 0.90 | 0.91 |
+| gamma-delta T cell | 9 | 0.62 | 0.67 | 0.71 | 0.12 | 0.00 | 0.48 | 0.56 | 0.56 | 0.76 |
+| naive thymus-derived CD4-positive, alpha-beta T cell | 8 | 0.00 | 0.20 | 0.40 | 0.15 | 0.00 | 0.70 | 0.70 | 0.50 | 0.55 |
+| monocyte | 8 | 0.64 | 0.78 | 0.80 | 0.59 | 0.00 | 0.88 | 0.82 | 0.74 | 0.82 |
+| neutrophil | 6 | 0.57 | 0.91 | 0.75 | 0.20 | 0.00 | 0.75 | 0.92 | 0.67 | 0.83 |
+| endothelial cell of lymphatic vessel | 5 | 1.00 | 1.00 | 1.00 | 0.60 | 0.00 | 0.83 | 1.00 | 1.00 | 1.00 |
+| endothelial cell of venule | 6 | 0.00 | 0.83 | 0.67 | 0.22 | 0.00 | 0.83 | 0.92 | 0.91 | 0.91 |
+| myofibroblast cell | 5 | 0.50 | 1.00 | 1.00 | 0.33 | 0.00 | 0.67 | 1.00 | 1.00 | 1.00 |
+| transit amplifying cell of small intestine | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
+| innate lymphoid cell | 3 | 0.80 | 0.80 | 0.40 | 0.67 | 0.00 | 0.50 | 0.00 | 0.80 | 1.00 |
+| pericyte | 4 | 0.00 | 1.00 | 1.00 | 0.00 | 0.00 | 0.80 | 1.00 | 1.00 | 1.00 |
+| regulatory T cell | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 0.40 | 0.40 | 0.00 |
 | myeloid dendritic 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 |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| enterocyte of epithelium proper of duodenum | 12126 | 0.91 | 0.90 | 0.95 | 0.86 | 0.00 | 0.94 | 0.92 | 0.93 | 0.96 |
-| enterocyte of epithelium proper of ileum | 5866 | 0.97 | 0.95 | 0.95 | 0.72 | 0.00 | 0.95 | 0.98 | 0.98 | 0.98 |
-| CD4-positive, alpha-beta T cell | 4615 | 0.91 | 0.90 | 0.94 | 0.85 | 0.00 | 0.91 | 0.90 | 0.92 | 0.96 |
-| CD8-positive, alpha-beta T cell | 3123 | 0.83 | 0.75 | 0.93 | 0.72 | 0.00 | 0.85 | 0.84 | 0.87 | 0.93 |
-| small intestine goblet cell | 1841 | 0.92 | 0.94 | 0.96 | 0.89 | 0.00 | 0.82 | 0.93 | 0.94 | 0.94 |
-| paneth cell of epithelium of small intestine | 1673 | 0.69 | 0.71 | 0.82 | 0.79 | 0.00 | 0.74 | 0.74 | 0.78 | 0.83 |
-| enterocyte of epithelium proper of small intestine | 1262 | 0.59 | 0.44 | 0.80 | 0.76 | 0.00 | 0.77 | 0.80 | 0.84 | 0.87 |
-| activated CD8-positive, alpha-beta T cell | 1033 | 0.69 | 0.40 | 0.91 | 0.74 | 0.00 | 0.82 | 0.80 | 0.83 | 0.90 |
-| plasma cell | 745 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 0.98 | 0.99 | 0.99 |
-| B cell | 705 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |
-| intestinal crypt stem cell of small intestine | 533 | 0.37 | 0.45 | 0.55 | 0.50 | 0.00 | 0.43 | 0.60 | 0.67 | 0.67 |
-| activated CD4-positive, alpha-beta T cell | 506 | 0.47 | 0.30 | 0.72 | 0.39 | 0.00 | 0.65 | 0.64 | 0.66 | 0.78 |
-| fibroblast | 447 | 0.97 | 0.98 | 0.98 | 0.96 | 0.00 | 0.97 | 0.99 | 0.98 | 0.98 |
-| intestinal tuft cell | 399 | 0.97 | 0.97 | 0.97 | 0.96 | 0.00 | 0.97 | 0.99 | 0.99 | 0.98 |
-| enterocyte of epithelium proper of jejunum | 362 | 0.21 | 0.01 | 0.79 | 0.46 | 0.00 | 0.85 | 0.60 | 0.56 | 0.80 |
-| macrophage | 322 | 0.83 | 0.91 | 0.93 | 0.88 | 0.00 | 0.97 | 0.99 | 0.98 | 0.98 |
-| enteroendocrine cell of small intestine | 245 | 0.91 | 0.92 | 0.93 | 0.87 | 0.00 | 0.84 | 0.92 | 0.93 | 0.94 |
-| mast cell | 224 | 0.95 | 0.97 | 0.98 | 0.97 | 0.00 | 0.97 | 0.98 | 0.98 | 0.98 |
-| natural killer cell | 144 | 0.00 | 0.20 | 0.45 | 0.37 | 0.00 | 0.48 | 0.74 | 0.89 | 0.85 |
-| enteroglial cell | 122 | 0.93 | 0.93 | 0.95 | 0.89 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |
-| endothelial cell of arteriole | 116 | 0.80 | 0.94 | 0.93 | 0.84 | 0.00 | 0.99 | 0.97 | 0.99 | 0.95 |
-| gamma-delta T cell | 109 | 0.72 | 0.69 | 0.78 | 0.57 | 0.00 | 0.92 | 0.91 | 0.95 | 0.97 |
-| naive thymus-derived CD4-positive, alpha-beta T cell | 109 | 0.00 | 0.45 | 0.50 | 0.31 | 0.00 | 0.77 | 0.85 | 0.90 | 0.78 |
-| monocyte | 69 | 0.75 | 0.81 | 0.81 | 0.68 | 0.00 | 0.93 | 1.00 | 1.00 | 0.99 |
-| neutrophil | 72 | 0.54 | 0.75 | 0.82 | 0.61 | 0.00 | 0.85 | 0.99 | 0.99 | 0.94 |
-| endothelial cell of lymphatic vessel | 65 | 0.98 | 0.98 | 0.97 | 0.93 | 0.00 | 0.99 | 0.98 | 0.98 | 0.98 |
-| endothelial cell of venule | 46 | 0.00 | 0.89 | 0.86 | 0.53 | 0.00 | 0.92 | 0.95 | 0.97 | 0.92 |
-| myofibroblast cell | 45 | 0.73 | 0.95 | 0.95 | 0.84 | 0.00 | 0.90 | 0.99 | 0.96 | 0.95 |
-| transit amplifying cell of small intestine | 33 | 0.00 | 0.00 | 0.52 | 0.06 | 0.00 | 0.42 | 0.86 | 0.92 | 0.86 |
-| innate lymphoid cell | 31 | 0.00 | 0.63 | 0.66 | 0.59 | 0.00 | 0.86 | 0.98 | 0.98 | 0.94 |
-| pericyte | 21 | 0.00 | 0.98 | 0.95 | 0.63 | 0.00 | 0.98 | 1.00 | 0.98 | 0.98 |
-| regulatory T cell | 12 | 0.00 | 0.40 | 0.29 | 0.29 | 0.00 | 0.86 | 1.00 | 1.00 | 0.86 |
-| myeloid dendritic cell | 11 | 0.00 | 0.63 | 0.50 | 0.50 | 0.00 | 0.63 | 0.96 | 0.96 | 0.87 |
+| enterocyte of epithelium proper of duodenum | 12159 | 0.92 | 0.90 | 0.95 | 0.86 | 0.00 | 0.94 | 0.92 | 0.93 | 0.96 |
+| enterocyte of epithelium proper of ileum | 5850 | 0.97 | 0.95 | 0.95 | 0.75 | 0.00 | 0.95 | 0.98 | 0.98 | 0.99 |
+| CD4-positive, alpha-beta T cell | 4623 | 0.91 | 0.89 | 0.95 | 0.83 | 0.00 | 0.89 | 0.91 | 0.91 | 0.95 |
+| CD8-positive, alpha-beta T cell | 3123 | 0.85 | 0.75 | 0.93 | 0.69 | 0.00 | 0.84 | 0.83 | 0.87 | 0.93 |
+| small intestine goblet cell | 1830 | 0.93 | 0.94 | 0.96 | 0.90 | 0.00 | 0.88 | 0.94 | 0.94 | 0.95 |
+| paneth cell of epithelium of small intestine | 1659 | 0.70 | 0.72 | 0.81 | 0.79 | 0.00 | 0.72 | 0.77 | 0.81 | 0.86 |
+| enterocyte of epithelium proper of small intestine | 1266 | 0.58 | 0.43 | 0.80 | 0.80 | 0.00 | 0.80 | 0.79 | 0.85 | 0.89 |
+| activated CD8-positive, alpha-beta T cell | 1044 | 0.76 | 0.40 | 0.91 | 0.72 | 0.00 | 0.80 | 0.79 | 0.84 | 0.91 |
+| plasma cell | 742 | 0.99 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
+| B cell | 703 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |
+| intestinal crypt stem cell of small intestine | 531 | 0.34 | 0.43 | 0.53 | 0.44 | 0.00 | 0.36 | 0.60 | 0.65 | 0.66 |
+| activated CD4-positive, alpha-beta T cell | 506 | 0.43 | 0.32 | 0.74 | 0.42 | 0.00 | 0.58 | 0.64 | 0.66 | 0.77 |
+| fibroblast | 448 | 0.97 | 0.97 | 0.98 | 0.93 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
+| intestinal tuft cell | 394 | 0.97 | 0.97 | 0.97 | 0.96 | 0.00 | 0.95 | 0.99 | 0.99 | 0.98 |
+| enterocyte of epithelium proper of jejunum | 359 | 0.21 | 0.01 | 0.82 | 0.36 | 0.00 | 0.95 | 0.60 | 0.55 | 0.88 |
+| macrophage | 317 | 0.82 | 0.92 | 0.93 | 0.91 | 0.00 | 0.98 | 0.99 | 0.99 | 0.98 |
+| enteroendocrine cell of small intestine | 245 | 0.92 | 0.91 | 0.94 | 0.87 | 0.00 | 0.69 | 0.92 | 0.93 | 0.95 |
+| mast cell | 226 | 0.95 | 0.96 | 0.98 | 0.96 | 0.00 | 0.94 | 0.99 | 0.99 | 0.98 |
+| natural killer cell | 142 | 0.00 | 0.15 | 0.47 | 0.33 | 0.00 | 0.46 | 0.75 | 0.80 | 0.85 |
+| enteroglial cell | 122 | 0.93 | 0.93 | 0.95 | 0.89 | 0.00 | 0.95 | 0.99 | 0.99 | 0.98 |
+| endothelial cell of arteriole | 117 | 0.80 | 0.95 | 0.91 | 0.79 | 0.00 | 0.95 | 0.99 | 1.00 | 0.97 |
+| gamma-delta T cell | 112 | 0.73 | 0.70 | 0.78 | 0.52 | 0.00 | 0.89 | 0.94 | 0.96 | 0.96 |
+| naive thymus-derived CD4-positive, alpha-beta T cell | 107 | 0.00 | 0.27 | 0.42 | 0.35 | 0.00 | 0.88 | 0.91 | 0.90 | 0.77 |
+| monocyte | 70 | 0.75 | 0.87 | 0.81 | 0.76 | 0.00 | 0.90 | 1.00 | 1.00 | 1.00 |
+| neutrophil | 71 | 0.71 | 0.73 | 0.81 | 0.74 | 0.00 | 0.91 | 1.00 | 0.99 | 0.95 |
+| endothelial cell of lymphatic vessel | 68 | 0.98 | 0.98 | 0.99 | 0.87 | 0.00 | 0.94 | 0.99 | 0.99 | 0.99 |
+| endothelial cell of venule | 46 | 0.00 | 0.87 | 0.83 | 0.45 | 0.00 | 0.99 | 0.95 | 0.95 | 0.92 |
+| myofibroblast cell | 46 | 0.64 | 0.94 | 0.95 | 0.75 | 0.00 | 0.70 | 0.97 | 0.95 | 0.95 |
+| transit amplifying cell of small intestine | 32 | 0.00 | 0.00 | 0.54 | 0.17 | 0.00 | 0.28 | 0.85 | 0.90 | 0.92 |
+| innate lymphoid cell | 31 | 0.64 | 0.67 | 0.68 | 0.59 | 0.00 | 0.66 | 1.00 | 1.00 | 0.95 |
+| pericyte | 20 | 0.00 | 0.98 | 0.98 | 0.60 | 0.00 | 0.93 | 1.00 | 1.00 | 1.00 |
+| regulatory T cell | 11 | 0.00 | 0.29 | 0.43 | 0.00 | 0.00 | 0.91 | 1.00 | 1.00 | 0.84 |
+| myeloid dendritic cell | 11 | 0.00 | 0.43 | 0.50 | 0.50 | 0.00 | 0.88 | 1.00 | 1.00 | 0.91 |
 
 </details>