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README.md

@@ -31,45 +31,45 @@ computed on a 10% random subset of the data that was not used for training.
 
 | Cell Type | N cells |  celltypist |  knn on bbknn |  knn on harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| luminal epithelial cell of mammary gland | 1529 | 0.99 | 0.94 | 1.00 | 1.00 | 0.00 | 0.88 | 0.99 | 0.99 | 1.00 |
-| fibroblast of breast | 544 | 0.99 | 0.96 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
-| CD8-positive, alpha-beta T cell | 260 | 0.89 | 0.89 | 0.90 | 0.81 | 0.00 | 0.79 | 0.86 | 0.90 | 0.91 |
-| basal cell | 194 | 0.94 | 0.95 | 0.97 | 0.98 | 0.00 | 0.96 | 0.97 | 0.96 | 0.97 |
-| progenitor cell of mammary luminal epithelium | 174 | 0.99 | 0.22 | 1.00 | 1.00 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |
-| endothelial cell | 148 | 0.97 | 0.96 | 0.98 | 0.99 | 0.00 | 0.95 | 0.97 | 0.97 | 0.98 |
-| macrophage | 70 | 0.95 | 0.96 | 0.98 | 0.98 | 0.00 | 0.96 | 0.97 | 0.97 | 0.97 |
-| CD4-positive, alpha-beta T cell | 70 | 0.66 | 0.66 | 0.63 | 0.20 | 0.00 | 0.54 | 0.59 | 0.76 | 0.71 |
-| vascular associated smooth muscle cell | 46 | 0.96 | 0.96 | 0.97 | 0.95 | 0.00 | 0.95 | 0.89 | 0.90 | 0.97 |
-| plasma cell | 32 | 1.00 | 0.92 | 1.00 | 0.97 | 0.00 | 0.83 | 0.98 | 1.00 | 1.00 |
-| T cell | 21 | 0.50 | 0.06 | 0.41 | 0.00 | 0.00 | 0.44 | 0.51 | 0.54 | 0.51 |
-| mast cell | 2 | 0.29 | 0.00 | 0.67 | 1.00 | 0.00 | 0.80 | 0.80 | 1.00 | 0.80 |
-| B cell | 2 | 0.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.33 | 0.67 | 0.67 | 1.00 |
-| mature NK T cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
-| basophil | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
-| natural killer cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 | 1.00 | 0.00 |
-| regulatory T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
+| luminal epithelial cell of mammary gland | 1565 | 0.99 | 0.95 | 1.00 | 0.99 | 0.00 | 0.96 | 0.99 | 0.99 | 1.00 |
+| fibroblast of breast | 541 | 0.98 | 0.95 | 0.99 | 0.98 | 0.00 | 0.97 | 0.97 | 0.98 | 0.99 |
+| CD8-positive, alpha-beta T cell | 246 | 0.87 | 0.90 | 0.90 | 0.82 | 0.00 | 0.78 | 0.87 | 0.89 | 0.92 |
+| basal cell | 172 | 0.95 | 0.92 | 0.98 | 0.95 | 0.00 | 0.92 | 0.94 | 0.93 | 0.96 |
+| progenitor cell of mammary luminal epithelium | 156 | 0.98 | 0.28 | 0.98 | 0.99 | 0.00 | 0.97 | 0.97 | 0.97 | 1.00 |
+| endothelial cell | 166 | 0.98 | 0.99 | 1.00 | 0.97 | 0.00 | 0.99 | 0.97 | 0.97 | 0.99 |
+| macrophage | 68 | 0.96 | 0.95 | 0.98 | 0.98 | 0.00 | 0.96 | 0.96 | 0.94 | 0.98 |
+| CD4-positive, alpha-beta T cell | 72 | 0.66 | 0.68 | 0.70 | 0.33 | 0.00 | 0.56 | 0.67 | 0.75 | 0.77 |
+| vascular associated smooth muscle cell | 52 | 0.96 | 0.95 | 0.97 | 0.98 | 0.00 | 0.84 | 0.94 | 0.90 | 0.95 |
+| plasma cell | 26 | 1.00 | 0.96 | 1.00 | 0.96 | 0.00 | 0.68 | 1.00 | 0.98 | 1.00 |
+| T cell | 19 | 0.50 | 0.26 | 0.32 | 0.29 | 0.00 | 0.45 | 0.51 | 0.46 | 0.51 |
+| mast cell | 4 | 0.31 | 0.00 | 0.89 | 0.89 | 0.00 | 0.50 | 0.80 | 0.89 | 0.80 |
+| B cell | 3 | 1.00 | 0.80 | 1.00 | 1.00 | 0.00 | 0.50 | 0.80 | 0.50 | 1.00 |
+| mature NK T cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
+| basophil | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |
+| natural killer cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
+| regulatory T cell | 1 | 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 on bbknn |  knn on harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| luminal epithelial cell of mammary gland | 13903 | 0.99 | 0.94 | 1.00 | 1.00 | 0.00 | 0.89 | 0.99 | 0.99 | 0.99 |
-| fibroblast of breast | 4726 | 0.99 | 0.93 | 0.99 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |
-| CD8-positive, alpha-beta T cell | 2393 | 0.90 | 0.90 | 0.94 | 0.87 | 0.00 | 0.84 | 0.92 | 0.94 | 0.96 |
-| basal cell | 1625 | 0.93 | 0.90 | 0.98 | 0.97 | 0.00 | 0.95 | 0.96 | 0.96 | 0.97 |
-| progenitor cell of mammary luminal epithelium | 1520 | 0.99 | 0.02 | 0.99 | 0.99 | 0.00 | 0.97 | 0.98 | 0.98 | 0.99 |
-| endothelial cell | 1386 | 0.96 | 0.96 | 0.98 | 0.99 | 0.00 | 0.94 | 0.98 | 0.97 | 0.98 |
-| macrophage | 615 | 0.96 | 0.96 | 0.98 | 0.98 | 0.00 | 0.97 | 0.98 | 0.98 | 0.98 |
-| CD4-positive, alpha-beta T cell | 611 | 0.66 | 0.62 | 0.77 | 0.45 | 0.00 | 0.65 | 0.80 | 0.86 | 0.88 |
-| vascular associated smooth muscle cell | 520 | 0.95 | 0.93 | 0.97 | 0.95 | 0.00 | 0.94 | 0.94 | 0.93 | 0.96 |
-| plasma cell | 261 | 0.98 | 0.85 | 0.98 | 0.95 | 0.00 | 0.81 | 0.99 | 0.97 | 0.99 |
-| T cell | 202 | 0.58 | 0.18 | 0.66 | 0.35 | 0.00 | 0.68 | 0.84 | 0.84 | 0.89 |
-| mast cell | 35 | 0.61 | 0.00 | 0.89 | 0.81 | 0.00 | 0.84 | 1.00 | 0.93 | 1.00 |
-| B cell | 13 | 0.00 | 0.82 | 0.92 | 0.64 | 0.00 | 0.30 | 1.00 | 1.00 | 1.00 |
-| mature NK T cell | 13 | 0.00 | 0.00 | 0.00 | 0.14 | 0.00 | 0.63 | 1.00 | 1.00 | 0.76 |
-| basophil | 12 | 0.00 | 0.11 | 0.38 | 0.14 | 0.00 | 0.01 | 1.00 | 1.00 | 0.96 |
-| natural killer cell | 5 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.31 | 1.00 | 1.00 | 0.33 |
-| regulatory T cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 0.67 |
+| luminal epithelial cell of mammary gland | 13867 | 0.99 | 0.95 | 1.00 | 1.00 | 0.00 | 0.96 | 0.99 | 0.99 | 0.99 |
+| fibroblast of breast | 4729 | 0.99 | 0.91 | 0.99 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |
+| CD8-positive, alpha-beta T cell | 2407 | 0.88 | 0.90 | 0.94 | 0.89 | 0.00 | 0.84 | 0.93 | 0.93 | 0.95 |
+| basal cell | 1647 | 0.97 | 0.90 | 0.98 | 0.97 | 0.00 | 0.91 | 0.96 | 0.96 | 0.97 |
+| progenitor cell of mammary luminal epithelium | 1538 | 0.99 | 0.04 | 0.99 | 0.99 | 0.00 | 0.98 | 0.97 | 0.98 | 0.99 |
+| endothelial cell | 1368 | 0.97 | 0.96 | 0.99 | 0.98 | 0.00 | 0.97 | 0.97 | 0.97 | 0.98 |
+| macrophage | 617 | 0.96 | 0.96 | 0.99 | 0.98 | 0.00 | 0.97 | 0.97 | 0.97 | 0.98 |
+| CD4-positive, alpha-beta T cell | 609 | 0.65 | 0.61 | 0.77 | 0.52 | 0.00 | 0.62 | 0.83 | 0.84 | 0.86 |
+| vascular associated smooth muscle cell | 514 | 0.95 | 0.94 | 0.97 | 0.96 | 0.00 | 0.89 | 0.96 | 0.92 | 0.96 |
+| plasma cell | 267 | 0.98 | 0.88 | 0.98 | 0.95 | 0.00 | 0.71 | 0.99 | 0.98 | 0.99 |
+| T cell | 204 | 0.61 | 0.27 | 0.69 | 0.48 | 0.00 | 0.74 | 0.82 | 0.82 | 0.86 |
+| mast cell | 33 | 0.49 | 0.04 | 0.91 | 0.85 | 0.00 | 0.58 | 0.99 | 0.93 | 0.99 |
+| B cell | 12 | 0.76 | 0.40 | 0.91 | 0.74 | 0.00 | 0.41 | 1.00 | 1.00 | 1.00 |
+| mature NK T cell | 12 | 0.00 | 0.00 | 0.14 | 0.29 | 0.00 | 0.60 | 1.00 | 1.00 | 0.80 |
+| basophil | 11 | 0.00 | 0.00 | 0.31 | 0.00 | 0.00 | 0.04 | 1.00 | 0.88 | 0.90 |
+| natural killer cell | 6 | 0.00 | 0.00 | 0.29 | 0.00 | 0.00 | 0.62 | 1.00 | 1.00 | 0.67 |
+| regulatory T cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 0.00 |
 
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