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OnClass.data-00000-of-00001

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OnClass.npz

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accuracies.json

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 {
-    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| basal cell | 1041 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.96 | 0.98 | 0.97 | 0.99 |\n| neutrophil | 451 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.97 | 0.98 | 0.99 | 0.99 |\n| fibroblast | 171 | 0.97 | 0.96 | 0.97 | 0.96 | 0.00 | 0.96 | 0.97 | 0.97 | 0.98 |\n| CD8-positive, alpha-beta T cell | 131 | 0.91 | 0.92 | 0.92 | 0.71 | 0.00 | 0.93 | 0.94 | 0.95 | 0.93 |\n| ciliated columnar cell of tracheobronchial tree | 73 | 0.96 | 0.97 | 0.94 | 0.99 | 0.00 | 0.92 | 0.95 | 0.96 | 0.96 |\n| macrophage | 63 | 0.97 | 0.97 | 0.93 | 0.95 | 0.00 | 0.94 | 0.96 | 0.95 | 0.97 |\n| B cell | 66 | 0.98 | 0.98 | 0.99 | 0.66 | 0.00 | 0.99 | 0.98 | 0.99 | 0.99 |\n| endothelial cell | 46 | 0.97 | 0.96 | 0.94 | 0.95 | 0.00 | 0.98 | 1.00 | 0.97 | 0.98 |\n| serous cell of epithelium of trachea | 34 | 0.58 | 0.06 | 0.77 | 0.85 | 0.00 | 0.53 | 0.64 | 0.64 | 0.77 |\n| plasma cell | 23 | 0.96 | 0.93 | 0.93 | 0.87 | 0.00 | 0.93 | 0.96 | 0.91 | 0.96 |\n| CD4-positive, alpha-beta T cell | 31 | 0.81 | 0.79 | 0.79 | 0.05 | 0.00 | 0.82 | 0.85 | 0.88 | 0.86 |\n| mucus secreting cell | 31 | 0.77 | 0.81 | 0.86 | 0.86 | 0.00 | 0.76 | 0.78 | 0.79 | 0.86 |\n| tracheal goblet cell | 33 | 0.78 | 0.67 | 0.86 | 0.88 | 0.00 | 0.82 | 0.89 | 0.89 | 0.94 |\n| connective tissue cell | 9 | 0.84 | 0.00 | 0.95 | 0.75 | 0.00 | 0.86 | 0.86 | 0.90 | 1.00 |\n| smooth muscle cell | 15 | 0.82 | 0.90 | 0.82 | 0.79 | 0.00 | 0.80 | 0.82 | 0.85 | 0.82 |\n| mast cell | 16 | 0.97 | 0.97 | 1.00 | 1.00 | 0.00 | 1.00 | 0.97 | 0.97 | 1.00 |\n| monocyte | 5 | 0.80 | 0.67 | 0.67 | 0.00 | 0.00 | 0.73 | 1.00 | 0.80 | 0.89 |\n| natural killer cell | 9 | 0.64 | 0.75 | 0.75 | 0.18 | 0.00 | 0.64 | 0.76 | 0.73 | 0.80 |\n| granulocyte | 6 | 0.00 | 0.00 | 0.29 | 0.00 | 0.00 | 0.26 | 0.50 | 0.44 | 0.00 |\n| mature NK T cell | 5 | 0.25 | 0.00 | 0.50 | 0.33 | 0.00 | 0.57 | 0.73 | 0.80 | 0.25 |\n| T cell | 2 | 0.00 | 0.67 | 0.67 | 0.00 | 0.00 | 0.33 | 0.00 | 0.00 | 0.00 |\n| ionocyte | 2 | 0.50 | 0.00 | 0.50 | 0.67 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| regulatory T cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| intermediate monocyte | 1 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| non-classical monocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| innate lymphoid cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| plasmacytoid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| myeloid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
-    "ref_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| basal cell | 9206 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.97 | 0.98 | 0.98 | 0.99 |\n| neutrophil | 4233 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.97 | 0.99 | 0.99 | 1.00 |\n| fibroblast | 1629 | 0.96 | 0.92 | 0.98 | 0.98 | 0.00 | 0.96 | 0.99 | 0.99 | 0.98 |\n| CD8-positive, alpha-beta T cell | 1071 | 0.91 | 0.90 | 0.94 | 0.83 | 0.00 | 0.96 | 0.98 | 0.98 | 0.96 |\n| ciliated columnar cell of tracheobronchial tree | 640 | 0.97 | 0.96 | 0.96 | 0.99 | 0.00 | 0.93 | 0.98 | 0.97 | 0.99 |\n| macrophage | 649 | 0.92 | 0.92 | 0.95 | 0.93 | 0.00 | 0.95 | 0.98 | 0.99 | 0.97 |\n| B cell | 561 | 0.97 | 0.95 | 0.98 | 0.81 | 0.00 | 0.99 | 1.00 | 1.00 | 0.99 |\n| endothelial cell | 540 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.97 | 0.99 | 0.99 | 0.99 |\n| serous cell of epithelium of trachea | 292 | 0.63 | 0.03 | 0.89 | 0.89 | 0.00 | 0.67 | 0.76 | 0.79 | 0.88 |\n| plasma cell | 269 | 0.97 | 0.97 | 0.99 | 0.95 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| CD4-positive, alpha-beta T cell | 247 | 0.73 | 0.61 | 0.78 | 0.34 | 0.00 | 0.86 | 0.94 | 0.95 | 0.86 |\n| mucus secreting cell | 239 | 0.75 | 0.73 | 0.89 | 0.89 | 0.00 | 0.84 | 0.87 | 0.86 | 0.92 |\n| tracheal goblet cell | 199 | 0.69 | 0.51 | 0.89 | 0.88 | 0.00 | 0.83 | 0.88 | 0.86 | 0.93 |\n| connective tissue cell | 143 | 0.78 | 0.00 | 0.93 | 0.92 | 0.00 | 0.92 | 0.96 | 0.92 | 0.96 |\n| smooth muscle cell | 116 | 0.80 | 0.73 | 0.87 | 0.89 | 0.00 | 0.80 | 0.91 | 0.91 | 0.87 |\n| mast cell | 103 | 0.96 | 0.96 | 0.96 | 0.97 | 0.00 | 0.98 | 1.00 | 1.00 | 1.00 |\n| monocyte | 76 | 0.52 | 0.52 | 0.71 | 0.63 | 0.00 | 0.88 | 0.96 | 0.97 | 0.85 |\n| natural killer cell | 55 | 0.63 | 0.61 | 0.77 | 0.42 | 0.00 | 0.85 | 0.92 | 0.92 | 0.94 |\n| granulocyte | 33 | 0.00 | 0.00 | 0.10 | 0.11 | 0.00 | 0.22 | 0.56 | 0.62 | 0.21 |\n| mature NK T cell | 32 | 0.28 | 0.00 | 0.69 | 0.33 | 0.00 | 0.87 | 0.97 | 0.97 | 0.87 |\n| T cell | 17 | 0.00 | 0.00 | 0.64 | 0.00 | 0.00 | 0.74 | 1.00 | 0.97 | 0.90 |\n| ionocyte | 16 | 0.47 | 0.00 | 0.81 | 0.64 | 0.00 | 0.85 | 0.97 | 1.00 | 0.97 |\n| regulatory T cell | 14 | 0.00 | 0.12 | 0.32 | 0.24 | 0.00 | 0.79 | 1.00 | 1.00 | 0.78 |\n| intermediate monocyte | 15 | 0.00 | 0.00 | 0.50 | 0.29 | 0.00 | 0.79 | 1.00 | 1.00 | 0.80 |\n| non-classical monocyte | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.47 | 1.00 | 1.00 | 0.67 |\n| innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.36 | 0.80 | 0.80 | 1.00 |\n| plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| myeloid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.25 | 1.00 | 1.00 | 1.00 |"
+    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| basal cell | 1033 | 0.99 | 0.98 | 0.98 | 0.99 | 0.00 | 0.95 | 0.98 | 0.98 | 0.99 |\n| neutrophil | 452 | 0.99 | 0.99 | 0.98 | 0.99 | 0.00 | 0.98 | 0.98 | 0.99 | 0.99 |\n| fibroblast | 178 | 0.97 | 0.95 | 0.97 | 0.97 | 0.00 | 0.96 | 0.98 | 0.97 | 0.98 |\n| CD8-positive, alpha-beta T cell | 128 | 0.89 | 0.92 | 0.93 | 0.88 | 0.00 | 0.94 | 0.93 | 0.94 | 0.93 |\n| ciliated columnar cell of tracheobronchial tree | 78 | 0.97 | 0.96 | 0.95 | 0.98 | 0.00 | 0.95 | 0.97 | 0.96 | 0.97 |\n| macrophage | 69 | 0.97 | 0.98 | 0.95 | 0.95 | 0.00 | 0.97 | 0.98 | 0.98 | 0.99 |\n| B cell | 65 | 0.98 | 0.98 | 0.97 | 0.94 | 0.00 | 0.98 | 0.98 | 1.00 | 0.99 |\n| endothelial cell | 48 | 0.97 | 0.96 | 0.94 | 0.97 | 0.00 | 0.92 | 0.97 | 0.98 | 0.97 |\n| serous cell of epithelium of trachea | 27 | 0.63 | 0.00 | 0.68 | 0.67 | 0.00 | 0.51 | 0.54 | 0.66 | 0.73 |\n| plasma cell | 22 | 0.95 | 0.93 | 0.93 | 0.90 | 0.00 | 0.93 | 0.93 | 0.96 | 0.93 |\n| CD4-positive, alpha-beta T cell | 31 | 0.82 | 0.72 | 0.81 | 0.57 | 0.00 | 0.83 | 0.78 | 0.85 | 0.83 |\n| mucus secreting cell | 32 | 0.75 | 0.78 | 0.81 | 0.85 | 0.00 | 0.76 | 0.78 | 0.82 | 0.83 |\n| tracheal goblet cell | 33 | 0.71 | 0.70 | 0.91 | 0.87 | 0.00 | 0.73 | 0.89 | 0.90 | 0.97 |\n| connective tissue cell | 11 | 0.91 | 0.00 | 0.92 | 0.53 | 0.00 | 0.96 | 0.96 | 0.92 | 1.00 |\n| smooth muscle cell | 13 | 0.77 | 0.86 | 0.80 | 0.92 | 0.00 | 0.77 | 0.80 | 0.80 | 0.80 |\n| mast cell | 16 | 0.97 | 0.97 | 0.97 | 0.94 | 0.00 | 0.97 | 0.97 | 1.00 | 0.97 |\n| monocyte | 5 | 0.73 | 0.75 | 0.73 | 0.33 | 0.00 | 0.73 | 1.00 | 0.80 | 0.89 |\n| natural killer cell | 9 | 0.67 | 0.71 | 0.75 | 0.46 | 0.00 | 0.67 | 0.73 | 0.69 | 0.73 |\n| granulocyte | 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.37 | 0.33 | 0.27 | 0.00 |\n| mature NK T cell | 5 | 0.29 | 0.00 | 0.57 | 0.25 | 0.00 | 0.75 | 0.80 | 0.80 | 0.57 |\n| T cell | 2 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.00 | 0.00 |\n| ionocyte | 1 | 0.50 | 0.00 | 0.67 | 1.00 | 0.00 | 0.29 | 1.00 | 1.00 | 1.00 |\n| regulatory T cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| intermediate monocyte | 1 | 0.00 | 0.00 | 0.00 | 0.67 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| non-classical monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| innate lymphoid cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| plasmacytoid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| myeloid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
+    "ref_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| basal cell | 9214 | 0.99 | 0.98 | 0.99 | 0.99 | 0.00 | 0.95 | 0.98 | 0.98 | 0.99 |\n| neutrophil | 4232 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| fibroblast | 1622 | 0.96 | 0.93 | 0.98 | 0.98 | 0.00 | 0.96 | 0.99 | 0.98 | 0.99 |\n| CD8-positive, alpha-beta T cell | 1074 | 0.88 | 0.90 | 0.94 | 0.90 | 0.00 | 0.96 | 0.98 | 0.98 | 0.96 |\n| ciliated columnar cell of tracheobronchial tree | 635 | 0.97 | 0.97 | 0.96 | 0.98 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |\n| macrophage | 643 | 0.93 | 0.91 | 0.95 | 0.93 | 0.00 | 0.96 | 0.99 | 0.99 | 0.97 |\n| B cell | 562 | 0.97 | 0.96 | 0.97 | 0.96 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| endothelial cell | 538 | 0.99 | 0.98 | 0.98 | 0.99 | 0.00 | 0.96 | 0.99 | 0.99 | 1.00 |\n| serous cell of epithelium of trachea | 299 | 0.69 | 0.03 | 0.91 | 0.86 | 0.00 | 0.64 | 0.73 | 0.76 | 0.88 |\n| plasma cell | 270 | 0.97 | 0.98 | 0.98 | 0.94 | 0.00 | 0.98 | 1.00 | 0.99 | 1.00 |\n| CD4-positive, alpha-beta T cell | 247 | 0.73 | 0.65 | 0.78 | 0.60 | 0.00 | 0.90 | 0.94 | 0.97 | 0.86 |\n| mucus secreting cell | 238 | 0.77 | 0.74 | 0.89 | 0.87 | 0.00 | 0.73 | 0.87 | 0.85 | 0.90 |\n| tracheal goblet cell | 199 | 0.71 | 0.51 | 0.90 | 0.87 | 0.00 | 0.68 | 0.87 | 0.81 | 0.95 |\n| connective tissue cell | 141 | 0.76 | 0.00 | 0.94 | 0.96 | 0.00 | 0.94 | 0.95 | 0.94 | 0.98 |\n| smooth muscle cell | 118 | 0.81 | 0.72 | 0.87 | 0.90 | 0.00 | 0.85 | 0.93 | 0.91 | 0.89 |\n| mast cell | 103 | 0.96 | 0.96 | 0.96 | 0.98 | 0.00 | 0.94 | 1.00 | 1.00 | 0.99 |\n| monocyte | 76 | 0.62 | 0.36 | 0.71 | 0.58 | 0.00 | 0.83 | 0.97 | 0.99 | 0.85 |\n| natural killer cell | 55 | 0.70 | 0.57 | 0.75 | 0.43 | 0.00 | 0.83 | 0.90 | 0.89 | 0.91 |\n| granulocyte | 33 | 0.00 | 0.00 | 0.15 | 0.06 | 0.00 | 0.42 | 0.70 | 0.62 | 0.17 |\n| mature NK T cell | 32 | 0.28 | 0.17 | 0.65 | 0.31 | 0.00 | 0.93 | 0.93 | 0.94 | 0.82 |\n| T cell | 17 | 0.00 | 0.00 | 0.54 | 0.00 | 0.00 | 0.22 | 1.00 | 1.00 | 0.87 |\n| ionocyte | 17 | 0.64 | 0.00 | 0.82 | 0.67 | 0.00 | 0.43 | 1.00 | 1.00 | 0.97 |\n| regulatory T cell | 14 | 0.00 | 0.00 | 0.32 | 0.00 | 0.00 | 0.80 | 1.00 | 1.00 | 0.67 |\n| intermediate monocyte | 15 | 0.00 | 0.00 | 0.52 | 0.22 | 0.00 | 0.79 | 1.00 | 1.00 | 0.80 |\n| non-classical monocyte | 5 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.47 | 1.00 | 1.00 | 0.57 |\n| innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.57 | 0.80 | 1.00 | 0.67 |\n| plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 0.00 |\n| myeloid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 1.00 | 1.00 | 1.00 |"
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celltypist.pkl

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harmony_knn_classifier.joblib

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preprocessing.json

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