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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| hepatocyte | 712 | 0.99 | 0.98 | 0.97 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| macrophage | 326 | 0.88 | 0.88 | 0.90 | 0.90 | 0.00 | 0.90 | 0.92 | 0.94 | 0.95 |\n| endothelial cell | 172 | 0.97 | 0.97 | 0.97 | 0.96 | 0.00 | 0.98 | 0.97 | 0.96 | 0.98 |\n| monocyte | 181 | 0.42 | 0.62 | 0.61 | 0.59 | 0.00 | 0.51 | 0.45 | 0.55 | 0.59 |\n| CD8-positive, alpha-beta T cell | 120 | 0.84 | 0.83 | 0.83 | 0.58 | 0.00 | 0.79 | 0.82 | 0.84 | 0.88 |\n| erythrocyte | 109 | 0.99 | 0.94 | 0.99 | 0.97 | 0.00 | 0.97 | 0.99 | 0.99 | 0.99 |\n| mature NK T cell | 70 | 0.64 | 0.49 | 0.65 | 0.47 | 0.00 | 0.52 | 0.52 | 0.68 | 0.66 |\n| plasma cell | 78 | 0.99 | 0.99 | 0.99 | 0.98 | 0.00 | 1.00 | 0.99 | 0.98 | 1.00 |\n| natural killer cell | 88 | 0.76 | 0.74 | 0.75 | 0.41 | 0.00 | 0.74 | 0.74 | 0.83 | 0.81 |\n| neutrophil | 76 | 0.95 | 0.94 | 0.79 | 0.88 | 0.00 | 0.91 | 0.93 | 0.91 | 0.97 |\n| intrahepatic cholangiocyte | 77 | 0.99 | 0.98 | 0.97 | 0.98 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| intermediate monocyte | 61 | 0.44 | 0.27 | 0.47 | 0.29 | 0.00 | 0.40 | 0.37 | 0.50 | 0.50 |\n| classical monocyte | 29 | 0.21 | 0.00 | 0.11 | 0.12 | 0.00 | 0.25 | 0.23 | 0.36 | 0.04 |\n| CD4-positive, alpha-beta T cell | 29 | 0.66 | 0.37 | 0.57 | 0.27 | 0.00 | 0.53 | 0.59 | 0.73 | 0.72 |\n| hepatic stellate cell | 23 | 0.76 | 0.44 | 0.67 | 0.53 | 0.00 | 0.84 | 0.94 | 0.86 | 0.90 |\n| B cell | 18 | 0.95 | 0.92 | 0.95 | 0.63 | 0.00 | 0.95 | 0.95 | 0.92 | 0.95 |\n| fibroblast | 15 | 0.62 | 0.65 | 0.70 | 0.55 | 0.00 | 0.83 | 0.94 | 0.91 | 0.88 |\n| non-classical monocyte | 12 | 0.63 | 0.00 | 0.61 | 0.22 | 0.00 | 0.69 | 0.81 | 0.88 | 0.83 |\n| myeloid cell | 4 | 0.25 | 0.00 | 0.00 | 0.22 | 0.00 | 0.27 | 0.86 | 0.67 | 0.22 |\n| myeloid dendritic cell | 8 | 0.00 | 0.00 | 0.36 | 0.55 | 0.00 | 0.47 | 0.80 | 0.67 | 0.71 |\n| hematopoietic precursor cell | 6 | 0.00 | 0.50 | 0.50 | 0.50 | 0.00 | 0.73 | 0.50 | 0.55 | 0.67 |\n| T cell | 5 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| mast cell | 3 | 0.75 | 0.86 | 1.00 | 0.50 | 0.00 | 0.67 | 0.86 | 1.00 | 0.86 |\n| plasmacytoid 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| hepatocyte | 6702 | 0.99 | 0.97 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| macrophage | 2906 | 0.88 | 0.88 | 0.94 | 0.91 | 0.00 | 0.91 | 0.93 | 0.95 | 0.96 |\n| endothelial cell | 1602 | 0.98 | 0.96 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| monocyte | 1540 | 0.43 | 0.62 | 0.76 | 0.71 | 0.00 | 0.62 | 0.70 | 0.73 | 0.82 |\n| CD8-positive, alpha-beta T cell | 1170 | 0.81 | 0.81 | 0.86 | 0.72 | 0.00 | 0.84 | 0.89 | 0.92 | 0.90 |\n| erythrocyte | 871 | 0.99 | 0.90 | 0.99 | 0.97 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| mature NK T cell | 738 | 0.63 | 0.48 | 0.76 | 0.62 | 0.00 | 0.72 | 0.85 | 0.89 | 0.84 |\n| plasma cell | 688 | 0.96 | 0.96 | 0.99 | 0.96 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| natural killer cell | 657 | 0.69 | 0.65 | 0.79 | 0.55 | 0.00 | 0.79 | 0.89 | 0.90 | 0.88 |\n| neutrophil | 663 | 0.93 | 0.79 | 0.94 | 0.89 | 0.00 | 0.95 | 0.97 | 0.98 | 0.97 |\n| intrahepatic cholangiocyte | 588 | 0.97 | 0.97 | 0.98 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| intermediate monocyte | 496 | 0.42 | 0.28 | 0.65 | 0.45 | 0.00 | 0.56 | 0.72 | 0.75 | 0.79 |\n| classical monocyte | 297 | 0.28 | 0.06 | 0.49 | 0.33 | 0.00 | 0.50 | 0.73 | 0.75 | 0.79 |\n| CD4-positive, alpha-beta T cell | 262 | 0.57 | 0.44 | 0.63 | 0.39 | 0.00 | 0.69 | 0.84 | 0.89 | 0.82 |\n| hepatic stellate cell | 200 | 0.77 | 0.33 | 0.85 | 0.72 | 0.00 | 0.89 | 0.96 | 0.96 | 0.96 |\n| B cell | 145 | 0.94 | 0.93 | 0.96 | 0.80 | 0.00 | 0.97 | 1.00 | 0.99 | 0.98 |\n| fibroblast | 146 | 0.70 | 0.63 | 0.82 | 0.75 | 0.00 | 0.93 | 0.98 | 0.99 | 0.98 |\n| non-classical monocyte | 101 | 0.47 | 0.13 | 0.85 | 0.39 | 0.00 | 0.89 | 0.84 | 0.86 | 0.88 |\n| myeloid cell | 77 | 0.62 | 0.00 | 0.45 | 0.62 | 0.00 | 0.75 | 0.92 | 0.90 | 0.93 |\n| myeloid dendritic cell | 48 | 0.00 | 0.00 | 0.41 | 0.26 | 0.00 | 0.64 | 0.87 | 0.83 | 0.83 |\n| hematopoietic precursor cell | 35 | 0.00 | 0.33 | 0.68 | 0.52 | 0.00 | 0.81 | 0.97 | 0.97 | 0.92 |\n| T cell | 27 | 0.00 | 0.00 | 0.07 | 0.06 | 0.00 | 0.63 | 1.00 | 0.98 | 0.92 |\n| mast cell | 25 | 0.88 | 0.57 | 0.96 | 0.67 | 0.00 | 0.54 | 1.00 | 0.96 | 1.00 |\n| plasmacytoid dendritic cell | 8 | 0.00 | 0.00 | 0.88 | 0.71 | 0.00 | 0.78 | 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| hepatocyte | 714 | 0.99 | 0.98 | 0.97 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| macrophage | 330 | 0.90 | 0.88 | 0.92 | 0.83 | 0.00 | 0.90 | 0.91 | 0.95 | 0.94 |\n| endothelial cell | 178 | 0.98 | 0.98 | 0.98 | 0.96 | 0.00 | 0.97 | 0.97 | 0.97 | 0.97 |\n| monocyte | 181 | 0.26 | 0.63 | 0.64 | 0.51 | 0.00 | 0.48 | 0.42 | 0.52 | 0.59 |\n| CD8-positive, alpha-beta T cell | 120 | 0.86 | 0.83 | 0.83 | 0.61 | 0.00 | 0.76 | 0.77 | 0.85 | 0.89 |\n| erythrocyte | 110 | 0.97 | 0.94 | 0.99 | 0.97 | 0.00 | 0.97 | 0.99 | 0.94 | 0.99 |\n| mature NK T cell | 68 | 0.63 | 0.56 | 0.62 | 0.48 | 0.00 | 0.58 | 0.58 | 0.66 | 0.68 |\n| plasma cell | 73 | 1.00 | 0.99 | 0.98 | 0.99 | 0.00 | 1.00 | 0.99 | 0.98 | 0.99 |\n| natural killer cell | 88 | 0.72 | 0.74 | 0.73 | 0.53 | 0.00 | 0.66 | 0.74 | 0.81 | 0.80 |\n| neutrophil | 76 | 0.94 | 0.94 | 0.80 | 0.87 | 0.00 | 0.93 | 0.92 | 0.94 | 0.96 |\n| intrahepatic cholangiocyte | 73 | 0.99 | 0.99 | 0.98 | 0.99 | 0.00 | 0.99 | 0.99 | 0.97 | 1.00 |\n| intermediate monocyte | 62 | 0.49 | 0.27 | 0.49 | 0.20 | 0.00 | 0.40 | 0.44 | 0.48 | 0.51 |\n| classical monocyte | 30 | 0.26 | 0.00 | 0.07 | 0.11 | 0.00 | 0.25 | 0.25 | 0.32 | 0.17 |\n| CD4-positive, alpha-beta T cell | 28 | 0.65 | 0.41 | 0.65 | 0.05 | 0.00 | 0.55 | 0.52 | 0.74 | 0.72 |\n| hepatic stellate cell | 22 | 0.69 | 0.47 | 0.67 | 0.67 | 0.00 | 0.88 | 0.93 | 0.89 | 0.90 |\n| B cell | 18 | 0.86 | 0.92 | 0.95 | 0.81 | 0.00 | 0.92 | 0.95 | 0.92 | 0.95 |\n| fibroblast | 14 | 0.70 | 0.63 | 0.72 | 0.60 | 0.00 | 0.88 | 0.93 | 0.93 | 0.90 |\n| non-classical monocyte | 11 | 0.77 | 0.15 | 0.47 | 0.14 | 0.00 | 0.62 | 0.79 | 0.82 | 0.87 |\n| myeloid cell | 4 | 0.29 | 0.00 | 0.00 | 0.36 | 0.00 | 0.40 | 0.60 | 0.67 | 0.50 |\n| myeloid dendritic cell | 8 | 0.53 | 0.00 | 0.33 | 0.33 | 0.00 | 0.60 | 0.71 | 0.59 | 0.71 |\n| hematopoietic precursor cell | 6 | 0.00 | 0.67 | 0.67 | 0.44 | 0.00 | 0.80 | 0.80 | 0.36 | 0.67 |\n| T cell | 5 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.29 | 0.00 | 0.00 |\n| mast cell | 3 | 0.00 | 0.86 | 0.80 | 0.57 | 0.00 | 0.60 | 0.86 | 1.00 | 1.00 |\n| plasmacytoid 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| hepatocyte | 6700 | 0.99 | 0.97 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| macrophage | 2902 | 0.91 | 0.88 | 0.95 | 0.90 | 0.00 | 0.92 | 0.94 | 0.94 | 0.96 |\n| endothelial cell | 1596 | 0.97 | 0.96 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| monocyte | 1540 | 0.29 | 0.63 | 0.76 | 0.70 | 0.00 | 0.59 | 0.70 | 0.72 | 0.80 |\n| CD8-positive, alpha-beta T cell | 1170 | 0.81 | 0.81 | 0.87 | 0.74 | 0.00 | 0.79 | 0.87 | 0.91 | 0.90 |\n| erythrocyte | 870 | 0.98 | 0.89 | 0.99 | 0.97 | 0.00 | 0.98 | 0.99 | 0.97 | 0.99 |\n| mature NK T cell | 740 | 0.66 | 0.53 | 0.75 | 0.67 | 0.00 | 0.74 | 0.84 | 0.87 | 0.84 |\n| plasma cell | 693 | 0.98 | 0.97 | 0.98 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 0.99 |\n| natural killer cell | 657 | 0.69 | 0.66 | 0.79 | 0.61 | 0.00 | 0.77 | 0.88 | 0.89 | 0.88 |\n| neutrophil | 663 | 0.93 | 0.80 | 0.95 | 0.89 | 0.00 | 0.95 | 0.97 | 0.97 | 0.98 |\n| intrahepatic cholangiocyte | 592 | 0.96 | 0.97 | 0.98 | 0.98 | 0.00 | 0.97 | 0.99 | 0.98 | 0.99 |\n| intermediate monocyte | 495 | 0.42 | 0.29 | 0.63 | 0.47 | 0.00 | 0.55 | 0.75 | 0.74 | 0.79 |\n| classical monocyte | 296 | 0.30 | 0.07 | 0.46 | 0.41 | 0.00 | 0.54 | 0.73 | 0.76 | 0.80 |\n| CD4-positive, alpha-beta T cell | 263 | 0.54 | 0.41 | 0.66 | 0.48 | 0.00 | 0.64 | 0.81 | 0.87 | 0.79 |\n| hepatic stellate cell | 201 | 0.74 | 0.35 | 0.84 | 0.80 | 0.00 | 0.94 | 0.97 | 0.95 | 0.97 |\n| B cell | 145 | 0.86 | 0.95 | 0.97 | 0.86 | 0.00 | 0.93 | 0.99 | 0.98 | 0.98 |\n| fibroblast | 147 | 0.77 | 0.66 | 0.80 | 0.84 | 0.00 | 0.96 | 0.99 | 0.98 | 0.96 |\n| non-classical monocyte | 102 | 0.66 | 0.11 | 0.83 | 0.47 | 0.00 | 0.80 | 0.83 | 0.84 | 0.88 |\n| myeloid cell | 77 | 0.54 | 0.00 | 0.51 | 0.63 | 0.00 | 0.73 | 0.88 | 0.84 | 0.84 |\n| myeloid dendritic cell | 48 | 0.41 | 0.00 | 0.47 | 0.28 | 0.00 | 0.65 | 0.76 | 0.71 | 0.84 |\n| hematopoietic precursor cell | 35 | 0.00 | 0.27 | 0.56 | 0.59 | 0.00 | 0.92 | 0.97 | 0.99 | 0.92 |\n| T cell | 27 | 0.00 | 0.00 | 0.07 | 0.18 | 0.00 | 0.79 | 0.98 | 1.00 | 0.90 |\n| mast cell | 25 | 0.00 | 0.60 | 0.96 | 0.91 | 0.00 | 0.98 | 1.00 | 0.94 | 1.00 |\n| plasmacytoid dendritic cell | 8 | 0.00 | 0.00 | 0.75 | 0.67 | 0.00 | 0.78 | 0.94 | 0.94 | 0.93 |"
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celltypist.pkl

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harmony_knn_classifier.joblib

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preprocessing.json

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