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@@ -33,3 +33,6 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+OnClass.data-00000-of-00001 filter=lfs diff=lfs merge=lfs -text
+faiss_index.faiss filter=lfs diff=lfs merge=lfs -text
+popv_output/predictions.csv filter=lfs diff=lfs merge=lfs -text

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 on bbknn |  knn on harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| B cell | 11277 | 0.99 | 0.99 | 0.98 | 0.98 | 0.00 | 0.99 | 0.97 | 0.98 | 0.99 |\n| CD4-positive, alpha-beta T cell | 9719 | 0.49 | 0.80 | 0.79 | 0.73 | 0.00 | 0.60 | 0.37 | 0.49 | 0.78 |\n| CD8-positive, alpha-beta T cell | 7653 | 0.68 | 0.79 | 0.76 | 0.70 | 0.00 | 0.72 | 0.48 | 0.65 | 0.79 |\n| neutrophil | 7010 | 0.96 | 0.98 | 0.96 | 0.97 | 0.00 | 0.95 | 0.92 | 0.94 | 0.98 |\n| macrophage | 6802 | 0.83 | 0.87 | 0.88 | 0.81 | 0.00 | 0.77 | 0.72 | 0.75 | 0.89 |\n| plasma cell | 2783 | 0.98 | 0.98 | 0.97 | 0.98 | 0.00 | 0.97 | 0.97 | 0.98 | 0.99 |\n| monocyte | 2615 | 0.32 | 0.57 | 0.71 | 0.39 | 0.00 | 0.24 | 0.40 | 0.55 | 0.54 |\n| classical monocyte | 1805 | 0.61 | 0.66 | 0.69 | 0.44 | 0.00 | 0.55 | 0.51 | 0.66 | 0.68 |\n| erythrocyte | 1501 | 0.97 | 0.98 | 0.97 | 0.97 | 0.00 | 0.96 | 0.96 | 0.96 | 0.97 |\n| natural killer cell | 1416 | 0.69 | 0.73 | 0.72 | 0.59 | 0.00 | 0.64 | 0.59 | 0.68 | 0.73 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 997 | 0.20 | 0.04 | 0.25 | 0.05 | 0.00 | 0.19 | 0.19 | 0.25 | 0.20 |\n| T cell | 603 | 0.38 | 0.41 | 0.46 | 0.09 | 0.00 | 0.25 | 0.29 | 0.38 | 0.48 |\n| mast cell | 591 | 0.86 | 0.91 | 0.91 | 0.80 | 0.00 | 0.81 | 0.85 | 0.91 | 0.94 |\n| intermediate monocyte | 546 | 0.31 | 0.26 | 0.45 | 0.10 | 0.00 | 0.20 | 0.29 | 0.42 | 0.47 |\n| mature NK T cell | 546 | 0.51 | 0.51 | 0.55 | 0.21 | 0.00 | 0.40 | 0.33 | 0.46 | 0.58 |\n| mononuclear phagocyte | 554 | 0.66 | 0.01 | 0.56 | 0.11 | 0.00 | 0.01 | 0.59 | 0.56 | 0.50 |\n| CD4-positive, alpha-beta thymocyte | 458 | 0.38 | 0.31 | 0.44 | 0.06 | 0.00 | 0.16 | 0.30 | 0.43 | 0.47 |\n| regulatory T cell | 297 | 0.23 | 0.14 | 0.18 | 0.04 | 0.00 | 0.14 | 0.16 | 0.21 | 0.32 |\n| hematopoietic precursor cell | 204 | 0.49 | 0.73 | 0.76 | 0.58 | 0.00 | 0.42 | 0.46 | 0.54 | 0.66 |\n| gamma-delta T cell | 191 | 0.64 | 0.78 | 0.66 | 0.02 | 0.00 | 0.24 | 0.43 | 0.48 | 0.77 |\n| basophil | 170 | 0.60 | 0.72 | 0.66 | 0.26 | 0.00 | 0.50 | 0.67 | 0.80 | 0.85 |\n| tissue-resident macrophage | 136 | 0.62 | 0.00 | 0.70 | 0.25 | 0.00 | 0.30 | 0.43 | 0.49 | 0.65 |\n| non-classical monocyte | 113 | 0.21 | 0.34 | 0.36 | 0.02 | 0.00 | 0.29 | 0.22 | 0.31 | 0.46 |\n| activated CD8-positive, alpha-beta T cell | 123 | 0.29 | 0.24 | 0.29 | 0.05 | 0.00 | 0.09 | 0.23 | 0.32 | 0.45 |\n| naive thymus-derived CD8-positive, alpha-beta T cell | 112 | 0.12 | 0.02 | 0.30 | 0.02 | 0.00 | 0.12 | 0.12 | 0.17 | 0.27 |\n| myeloid leukocyte | 90 | 0.17 | 0.53 | 0.59 | 0.04 | 0.00 | 0.12 | 0.20 | 0.23 | 0.53 |\n| erythroid progenitor cell | 104 | 0.66 | 0.75 | 0.63 | 0.57 | 0.00 | 0.58 | 0.62 | 0.66 | 0.73 |\n| innate lymphoid cell | 85 | 0.20 | 0.29 | 0.30 | 0.23 | 0.00 | 0.30 | 0.16 | 0.24 | 0.33 |\n| hematopoietic stem cell | 72 | 0.71 | 0.74 | 0.75 | 0.59 | 0.00 | 0.46 | 0.68 | 0.73 | 0.77 |\n| granulocyte | 74 | 0.39 | 0.30 | 0.50 | 0.21 | 0.00 | 0.19 | 0.20 | 0.24 | 0.60 |\n| CD8-positive, alpha-beta thymocyte | 66 | 0.42 | 0.28 | 0.23 | 0.12 | 0.00 | 0.23 | 0.14 | 0.26 | 0.46 |\n| activated CD4-positive, alpha-beta T cell | 65 | 0.08 | 0.06 | 0.09 | 0.00 | 0.00 | 0.12 | 0.10 | 0.18 | 0.22 |\n| myeloid dendritic cell | 47 | 0.16 | 0.32 | 0.34 | 0.04 | 0.00 | 0.15 | 0.10 | 0.15 | 0.21 |\n| platelet | 49 | 0.62 | 0.95 | 0.98 | 0.92 | 0.00 | 0.33 | 0.77 | 0.69 | 0.87 |\n| common myeloid progenitor | 42 | 0.58 | 0.73 | 0.67 | 0.27 | 0.00 | 0.59 | 0.60 | 0.71 | 0.76 |\n| thymocyte | 48 | 0.00 | 0.17 | 0.28 | 0.15 | 0.00 | 0.37 | 0.15 | 0.43 | 0.57 |\n| microglial cell | 39 | 0.13 | 0.05 | 0.32 | 0.09 | 0.00 | 0.08 | 0.17 | 0.17 | 0.26 |\n| colon macrophage | 41 | 0.35 | 0.42 | 0.69 | 0.00 | 0.00 | 0.07 | 0.25 | 0.40 | 0.64 |\n| leukocyte | 16 | 0.09 | 0.29 | 0.11 | 0.00 | 0.00 | 0.05 | 0.03 | 0.14 | 0.14 |\n| plasmacytoid dendritic cell | 8 | 0.50 | 0.36 | 0.53 | 0.15 | 0.00 | 0.06 | 0.18 | 0.31 | 0.50 |\n| hematopoietic cell | 8 | 0.88 | 0.80 | 0.67 | 0.40 | 0.00 | 0.18 | 1.00 | 0.44 | 0.84 |\n| myeloid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.13 | 0.67 |\n| Langerhans cell | 6 | 0.00 | 0.22 | 0.67 | 0.00 | 0.00 | 0.21 | 0.30 | 0.32 | 0.80 |\n| T follicular helper cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| erythroid lineage 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 on bbknn |  knn on harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| B cell | 103204 | 0.99 | 0.99 | 0.98 | 0.98 | 0.00 | 0.98 | 0.97 | 0.98 | 0.99 |\n| CD4-positive, alpha-beta T cell | 87396 | 0.48 | 0.79 | 0.84 | 0.79 | 0.00 | 0.59 | 0.38 | 0.50 | 0.80 |\n| CD8-positive, alpha-beta T cell | 68604 | 0.68 | 0.78 | 0.83 | 0.77 | 0.00 | 0.70 | 0.49 | 0.65 | 0.81 |\n| neutrophil | 62514 | 0.96 | 0.97 | 0.97 | 0.95 | 0.00 | 0.95 | 0.93 | 0.94 | 0.98 |\n| macrophage | 62221 | 0.83 | 0.86 | 0.92 | 0.84 | 0.00 | 0.81 | 0.71 | 0.76 | 0.91 |\n| plasma cell | 24561 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.97 | 0.97 | 0.98 | 0.99 |\n| monocyte | 23134 | 0.32 | 0.51 | 0.81 | 0.59 | 0.00 | 0.54 | 0.42 | 0.55 | 0.68 |\n| classical monocyte | 16394 | 0.62 | 0.64 | 0.81 | 0.65 | 0.00 | 0.70 | 0.52 | 0.67 | 0.75 |\n| erythrocyte | 13107 | 0.96 | 0.97 | 0.98 | 0.98 | 0.00 | 0.95 | 0.96 | 0.96 | 0.97 |\n| natural killer cell | 12814 | 0.70 | 0.73 | 0.81 | 0.71 | 0.00 | 0.70 | 0.61 | 0.69 | 0.76 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 8830 | 0.20 | 0.06 | 0.40 | 0.18 | 0.00 | 0.32 | 0.21 | 0.26 | 0.33 |\n| T cell | 5685 | 0.40 | 0.40 | 0.62 | 0.29 | 0.00 | 0.44 | 0.32 | 0.40 | 0.58 |\n| mast cell | 5626 | 0.85 | 0.89 | 0.94 | 0.89 | 0.00 | 0.91 | 0.88 | 0.92 | 0.95 |\n| intermediate monocyte | 4931 | 0.32 | 0.20 | 0.63 | 0.35 | 0.00 | 0.30 | 0.32 | 0.43 | 0.53 |\n| mature NK T cell | 4845 | 0.52 | 0.47 | 0.66 | 0.39 | 0.00 | 0.49 | 0.35 | 0.48 | 0.62 |\n| mononuclear phagocyte | 4782 | 0.64 | 0.00 | 0.83 | 0.35 | 0.00 | 0.88 | 0.58 | 0.56 | 0.89 |\n| CD4-positive, alpha-beta thymocyte | 4227 | 0.39 | 0.27 | 0.60 | 0.18 | 0.00 | 0.63 | 0.35 | 0.45 | 0.64 |\n| regulatory T cell | 2352 | 0.20 | 0.09 | 0.36 | 0.11 | 0.00 | 0.15 | 0.18 | 0.22 | 0.38 |\n| hematopoietic precursor cell | 1936 | 0.52 | 0.71 | 0.82 | 0.68 | 0.00 | 0.48 | 0.50 | 0.57 | 0.72 |\n| gamma-delta T cell | 1784 | 0.63 | 0.74 | 0.77 | 0.13 | 0.00 | 0.47 | 0.46 | 0.48 | 0.78 |\n| basophil | 1499 | 0.51 | 0.63 | 0.82 | 0.70 | 0.00 | 0.85 | 0.70 | 0.81 | 0.89 |\n| tissue-resident macrophage | 1219 | 0.62 | 0.01 | 0.83 | 0.48 | 0.00 | 0.53 | 0.45 | 0.50 | 0.74 |\n| non-classical monocyte | 1171 | 0.23 | 0.32 | 0.47 | 0.19 | 0.00 | 0.33 | 0.27 | 0.37 | 0.53 |\n| activated CD8-positive, alpha-beta T cell | 1024 | 0.28 | 0.12 | 0.30 | 0.13 | 0.00 | 0.60 | 0.25 | 0.33 | 0.66 |\n| naive thymus-derived CD8-positive, alpha-beta T cell | 944 | 0.13 | 0.01 | 0.53 | 0.04 | 0.00 | 0.28 | 0.14 | 0.18 | 0.51 |\n| myeloid leukocyte | 904 | 0.17 | 0.33 | 0.68 | 0.24 | 0.00 | 0.56 | 0.29 | 0.30 | 0.64 |\n| erythroid progenitor cell | 867 | 0.63 | 0.62 | 0.78 | 0.75 | 0.00 | 0.66 | 0.72 | 0.73 | 0.77 |\n| innate lymphoid cell | 886 | 0.22 | 0.25 | 0.50 | 0.36 | 0.00 | 0.64 | 0.24 | 0.30 | 0.50 |\n| hematopoietic stem cell | 786 | 0.72 | 0.76 | 0.84 | 0.73 | 0.00 | 0.65 | 0.81 | 0.87 | 0.85 |\n| granulocyte | 695 | 0.37 | 0.21 | 0.64 | 0.52 | 0.00 | 0.39 | 0.25 | 0.27 | 0.72 |\n| CD8-positive, alpha-beta thymocyte | 665 | 0.37 | 0.28 | 0.33 | 0.14 | 0.00 | 0.44 | 0.23 | 0.37 | 0.68 |\n| activated CD4-positive, alpha-beta T cell | 507 | 0.06 | 0.02 | 0.29 | 0.20 | 0.00 | 0.19 | 0.13 | 0.18 | 0.28 |\n| myeloid dendritic cell | 523 | 0.16 | 0.23 | 0.53 | 0.23 | 0.00 | 0.27 | 0.16 | 0.23 | 0.34 |\n| platelet | 445 | 0.68 | 0.89 | 0.95 | 0.94 | 0.00 | 0.33 | 0.83 | 0.80 | 0.91 |\n| common myeloid progenitor | 414 | 0.56 | 0.57 | 0.76 | 0.69 | 0.00 | 0.74 | 0.76 | 0.90 | 0.87 |\n| thymocyte | 407 | 0.00 | 0.20 | 0.35 | 0.16 | 0.00 | 0.61 | 0.21 | 0.59 | 0.85 |\n| microglial cell | 353 | 0.13 | 0.04 | 0.51 | 0.10 | 0.00 | 0.56 | 0.23 | 0.23 | 0.49 |\n| colon macrophage | 286 | 0.28 | 0.23 | 0.78 | 0.21 | 0.00 | 0.49 | 0.28 | 0.37 | 0.72 |\n| leukocyte | 170 | 0.05 | 0.04 | 0.36 | 0.18 | 0.00 | 0.37 | 0.10 | 0.19 | 0.37 |\n| plasmacytoid dendritic cell | 90 | 0.56 | 0.50 | 0.75 | 0.53 | 0.00 | 0.13 | 0.30 | 0.48 | 0.67 |\n| hematopoietic cell | 90 | 0.79 | 0.73 | 0.92 | 0.63 | 0.00 | 0.30 | 0.96 | 0.58 | 0.85 |\n| myeloid cell | 79 | 0.00 | 0.00 | 0.31 | 0.05 | 0.00 | 0.45 | 0.28 | 0.37 | 0.83 |\n| Langerhans cell | 70 | 0.00 | 0.43 | 0.74 | 0.38 | 0.00 | 0.18 | 0.33 | 0.35 | 0.73 |\n| T follicular helper cell | 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.46 | 0.35 | 0.91 |\n| erythroid lineage cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 1.00 | 1.00 | 0.00 |"
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