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Browse files- OnClass.data-00000-of-00001 +1 -1
- OnClass.index +0 -0
- OnClass.meta +0 -0
- OnClass.npz +2 -2
- accuracies.json +2 -2
- celltypist.pkl +1 -1
- harmony_knn_classifier.joblib +2 -2
- popv_output/predictions.csv +0 -0
- preprocessing.json +17 -17
- pynndescent_index.joblib +2 -2
- scanvi/model.pt +1 -1
- scvi/model.pt +1 -1
- scvi_knn_classifier.joblib +2 -2
- svm_classifier.joblib +1 -1
- svm_classifier_cuml.joblib +1 -1
- xgboost_classifier.model +2 -2
OnClass.data-00000-of-00001
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OnClass.index
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OnClass.meta
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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| macrophage |
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"ref_accuracy": "| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| macrophage |
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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| macrophage | 1632 | 0.96 | 0.97 | 0.98 | 0.98 | 0.00 | 0.94 | 0.96 | 0.96 | 0.98 |\n| pulmonary alveolar type 2 cell | 1146 | 0.97 | 0.97 | 0.98 | 0.98 | 0.00 | 0.97 | 0.97 | 0.97 | 0.98 |\n| capillary endothelial cell | 698 | 0.97 | 0.95 | 0.98 | 0.97 | 0.00 | 0.97 | 0.96 | 0.96 | 0.97 |\n| basal cell | 411 | 0.92 | 0.93 | 0.94 | 0.93 | 0.00 | 0.94 | 0.93 | 0.93 | 0.95 |\n| pulmonary alveolar type 1 cell | 302 | 0.98 | 0.99 | 0.98 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| intermediate monocyte | 278 | 0.64 | 0.62 | 0.67 | 0.69 | 0.00 | 0.54 | 0.77 | 0.84 | 0.77 |\n| CD4-positive, alpha-beta T cell | 206 | 0.87 | 0.89 | 0.85 | 0.85 | 0.00 | 0.89 | 0.88 | 0.90 | 0.91 |\n| CD8-positive, alpha-beta T cell | 201 | 0.85 | 0.86 | 0.78 | 0.80 | 0.00 | 0.88 | 0.83 | 0.87 | 0.87 |\n| endothelial cell of artery | 158 | 0.79 | 0.78 | 0.84 | 0.75 | 0.00 | 0.81 | 0.77 | 0.79 | 0.82 |\n| club cell | 181 | 0.82 | 0.82 | 0.85 | 0.83 | 0.00 | 0.83 | 0.85 | 0.83 | 0.87 |\n| classical monocyte | 154 | 0.58 | 0.57 | 0.61 | 0.61 | 0.00 | 0.57 | 0.73 | 0.89 | 0.74 |\n| vein endothelial cell | 142 | 0.81 | 0.80 | 0.87 | 0.79 | 0.00 | 0.84 | 0.81 | 0.84 | 0.85 |\n| basophil | 145 | 0.97 | 0.99 | 0.99 | 1.00 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| lung ciliated cell | 134 | 0.97 | 0.99 | 0.99 | 0.99 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |\n| alveolar adventitial fibroblast | 117 | 0.85 | 0.86 | 0.86 | 0.90 | 0.00 | 0.90 | 0.91 | 0.91 | 0.94 |\n| respiratory goblet cell | 107 | 0.76 | 0.82 | 0.83 | 0.80 | 0.00 | 0.84 | 0.83 | 0.83 | 0.84 |\n| natural killer cell | 104 | 0.87 | 0.88 | 0.87 | 0.85 | 0.00 | 0.90 | 0.87 | 0.89 | 0.90 |\n| pericyte | 76 | 0.79 | 0.86 | 0.88 | 0.89 | 0.00 | 0.90 | 0.90 | 0.92 | 0.92 |\n| B cell | 67 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |\n| adventitial cell | 61 | 0.68 | 0.83 | 0.81 | 0.85 | 0.00 | 0.85 | 0.87 | 0.88 | 0.90 |\n| non-classical monocyte | 55 | 0.32 | 0.11 | 0.34 | 0.06 | 0.00 | 0.36 | 0.56 | 0.77 | 0.55 |\n| monocyte | 51 | 0.42 | 0.33 | 0.38 | 0.46 | 0.00 | 0.32 | 0.48 | 0.72 | 0.58 |\n| neutrophil | 35 | 0.92 | 0.97 | 0.94 | 0.94 | 0.00 | 0.96 | 0.97 | 0.89 | 0.96 |\n| endothelial cell of lymphatic vessel | 32 | 0.96 | 0.97 | 0.92 | 0.96 | 0.00 | 0.94 | 0.97 | 0.97 | 0.98 |\n| bronchial smooth muscle cell | 24 | 0.49 | 0.48 | 0.69 | 0.51 | 0.00 | 0.54 | 0.64 | 0.78 | 0.73 |\n| mature NK T cell | 27 | 0.00 | 0.25 | 0.31 | 0.21 | 0.00 | 0.56 | 0.48 | 0.51 | 0.45 |\n| plasma cell | 12 | 0.87 | 0.85 | 0.92 | 0.96 | 0.00 | 0.92 | 0.89 | 0.92 | 0.96 |\n| vascular associated smooth muscle cell | 18 | 0.53 | 0.52 | 0.47 | 0.64 | 0.00 | 0.79 | 0.76 | 0.75 | 0.73 |\n| myeloid dendritic cell | 6 | 0.00 | 0.00 | 0.83 | 0.80 | 0.00 | 0.77 | 0.67 | 0.92 | 0.91 |\n| pulmonary ionocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 1.00 | 1.00 | 0.00 |\n| plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 1.00 | 0.67 | 0.00 | 0.40 | 1.00 | 1.00 | 1.00 |\n| mesothelial cell | 1 | 0.00 | 0.50 | 0.50 | 0.50 | 0.00 | 0.40 | 0.40 | 0.50 | 0.50 |\n| serous cell of epithelium of bronchus | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.40 | 0.80 | 1.00 | 0.00 |\n| mast cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
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"ref_accuracy": "| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| macrophage | 14854 | 0.96 | 0.98 | 0.98 | 0.98 | 0.00 | 0.94 | 0.96 | 0.96 | 0.98 |\n| pulmonary alveolar type 2 cell | 10448 | 0.97 | 0.97 | 0.99 | 0.98 | 0.00 | 0.97 | 0.97 | 0.97 | 0.98 |\n| capillary endothelial cell | 6545 | 0.97 | 0.96 | 0.98 | 0.98 | 0.00 | 0.97 | 0.96 | 0.96 | 0.98 |\n| basal cell | 3604 | 0.92 | 0.94 | 0.96 | 0.96 | 0.00 | 0.94 | 0.95 | 0.95 | 0.97 |\n| pulmonary alveolar type 1 cell | 2814 | 0.98 | 0.97 | 0.98 | 0.98 | 0.00 | 0.97 | 0.98 | 0.97 | 0.98 |\n| intermediate monocyte | 2507 | 0.62 | 0.62 | 0.78 | 0.78 | 0.00 | 0.63 | 0.81 | 0.87 | 0.83 |\n| CD4-positive, alpha-beta T cell | 1918 | 0.87 | 0.87 | 0.90 | 0.90 | 0.00 | 0.91 | 0.90 | 0.92 | 0.93 |\n| CD8-positive, alpha-beta T cell | 1697 | 0.85 | 0.83 | 0.87 | 0.87 | 0.00 | 0.89 | 0.87 | 0.90 | 0.91 |\n| endothelial cell of artery | 1596 | 0.78 | 0.79 | 0.86 | 0.85 | 0.00 | 0.82 | 0.82 | 0.83 | 0.86 |\n| club cell | 1566 | 0.82 | 0.82 | 0.91 | 0.90 | 0.00 | 0.86 | 0.88 | 0.86 | 0.91 |\n| classical monocyte | 1415 | 0.60 | 0.56 | 0.72 | 0.71 | 0.00 | 0.71 | 0.81 | 0.93 | 0.84 |\n| vein endothelial cell | 1194 | 0.81 | 0.81 | 0.88 | 0.86 | 0.00 | 0.85 | 0.86 | 0.89 | 0.88 |\n| basophil | 1177 | 0.97 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |\n| lung ciliated cell | 1075 | 0.96 | 0.97 | 0.99 | 0.99 | 0.00 | 0.95 | 0.98 | 0.98 | 0.98 |\n| alveolar adventitial fibroblast | 996 | 0.87 | 0.85 | 0.89 | 0.94 | 0.00 | 0.93 | 0.96 | 0.97 | 0.96 |\n| respiratory goblet cell | 933 | 0.80 | 0.86 | 0.89 | 0.89 | 0.00 | 0.87 | 0.88 | 0.88 | 0.91 |\n| natural killer cell | 915 | 0.90 | 0.91 | 0.93 | 0.93 | 0.00 | 0.94 | 0.95 | 0.96 | 0.96 |\n| pericyte | 663 | 0.78 | 0.89 | 0.94 | 0.92 | 0.00 | 0.95 | 0.98 | 0.98 | 0.97 |\n| B cell | 596 | 0.98 | 0.97 | 0.98 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| adventitial cell | 520 | 0.75 | 0.80 | 0.83 | 0.91 | 0.00 | 0.91 | 0.95 | 0.96 | 0.95 |\n| non-classical monocyte | 472 | 0.26 | 0.08 | 0.34 | 0.30 | 0.00 | 0.45 | 0.71 | 0.80 | 0.68 |\n| monocyte | 455 | 0.43 | 0.27 | 0.53 | 0.53 | 0.00 | 0.49 | 0.76 | 0.83 | 0.77 |\n| neutrophil | 336 | 0.93 | 0.97 | 0.98 | 0.96 | 0.00 | 0.97 | 0.99 | 0.95 | 0.99 |\n| endothelial cell of lymphatic vessel | 283 | 0.96 | 0.98 | 0.98 | 0.98 | 0.00 | 0.97 | 0.99 | 0.99 | 0.98 |\n| bronchial smooth muscle cell | 196 | 0.50 | 0.55 | 0.77 | 0.60 | 0.00 | 0.80 | 0.91 | 0.95 | 0.91 |\n| mature NK T cell | 136 | 0.00 | 0.15 | 0.53 | 0.40 | 0.00 | 0.70 | 0.83 | 0.91 | 0.91 |\n| plasma cell | 136 | 0.81 | 0.83 | 0.95 | 0.94 | 0.00 | 0.94 | 0.97 | 0.94 | 0.98 |\n| vascular associated smooth muscle cell | 113 | 0.48 | 0.50 | 0.75 | 0.61 | 0.00 | 0.83 | 0.95 | 0.95 | 0.94 |\n| myeloid dendritic cell | 27 | 0.00 | 0.12 | 0.84 | 0.73 | 0.00 | 0.77 | 0.93 | 0.90 | 0.96 |\n| pulmonary ionocyte | 24 | 0.00 | 0.89 | 0.98 | 0.88 | 0.00 | 0.79 | 0.96 | 0.94 | 0.96 |\n| plasmacytoid dendritic cell | 18 | 0.00 | 0.00 | 0.95 | 0.95 | 0.00 | 0.86 | 0.97 | 0.97 | 0.97 |\n| mesothelial cell | 17 | 0.00 | 0.79 | 0.81 | 0.77 | 0.00 | 0.60 | 0.92 | 0.87 | 0.83 |\n| serous cell of epithelium of bronchus | 13 | 0.00 | 0.00 | 0.64 | 0.27 | 0.00 | 0.68 | 0.90 | 0.93 | 0.70 |\n| mast cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.29 | 1.00 | 0.86 | 0.50 |"
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celltypist.pkl
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harmony_knn_classifier.joblib
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preprocessing.json
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3233 |
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|
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3234 |
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3235 |
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3236 |
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@@ -3290,7 +3292,6 @@
|
|
3290 |
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3291 |
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3292 |
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3293 |
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3294 |
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3295 |
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3296 |
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@@ -3421,7 +3422,6 @@
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|
3421 |
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3422 |
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3423 |
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3424 |
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3425 |
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3426 |
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3427 |
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@@ -3583,6 +3583,7 @@
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3583 |
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3586 |
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@@ -3655,7 +3656,6 @@
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|
3655 |
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3656 |
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|
3657 |
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|
3658 |
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3659 |
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3660 |
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3661 |
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@@ -3704,6 +3704,7 @@
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|
3704 |
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3706 |
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|
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3707 |
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|
3708 |
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3709 |
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@@ -3750,7 +3751,6 @@
|
|
3750 |
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|
3751 |
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|
3752 |
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|
3753 |
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3754 |
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3755 |
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3756 |
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|
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|
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"ENSG00000004848",
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|
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|
|
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239 |
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240 |
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248 |
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251 |
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1004 |
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1010 |
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1479 |
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1480 |
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1570 |
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1649 |
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1650 |
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1651 |
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1652 |
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1707 |
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1708 |
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1711 |
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1725 |
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1726 |
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1727 |
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1728 |
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1729 |
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1730 |
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1731 |
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2196 |
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2198 |
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2199 |
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2200 |
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2201 |
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2202 |
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2203 |
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2204 |
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2205 |
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2206 |
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2409 |
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2410 |
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2411 |
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2412 |
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2414 |
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2415 |
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2583 |
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2639 |
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2640 |
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2641 |
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2875 |
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2876 |
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2877 |
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2878 |
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2880 |
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2881 |
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3053 |
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3054 |
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3055 |
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3056 |
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3057 |
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3059 |
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3145 |
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3148 |
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3150 |
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3161 |
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3187 |
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3188 |
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3190 |
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3191 |
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3192 |
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|
3232 |
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3233 |
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3234 |
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3235 |
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3236 |
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3237 |
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3238 |
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3292 |
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3293 |
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3294 |
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3295 |
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3296 |
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3297 |
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3422 |
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3423 |
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3424 |
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3425 |
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3426 |
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3427 |
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3583 |
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3584 |
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3585 |
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3586 |
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3588 |
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3589 |
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3656 |
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3657 |
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3658 |
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3659 |
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3660 |
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3661 |
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3704 |
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3705 |
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3706 |
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3707 |
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3709 |
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3710 |
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3751 |
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pynndescent_index.joblib
CHANGED
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