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popV
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tabula_sapiens_Prostate

Joblib
popV
biology
genomics
single-cell
AnnData:0.12.2
scikit_learn:1.7.2
organism:Homo sapiens
Python:3.12.8
popV:0.6.0
tissue: Prostate
Model card Files
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 Community
canergen commited on
Commit
8645c0f
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1 Parent(s): 40c4d73

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Files changed (16) hide show
  1. OnClass.data-00000-of-00001 +1 -1
  2. OnClass.index +0 -0
  3. OnClass.meta +0 -0
  4. OnClass.npz +1 -1
  5. accuracies.json +2 -2
  6. celltypist.pkl +1 -1
  7. harmony_knn_classifier.joblib +2 -2
  8. popv_output/predictions.csv +0 -0
  9. preprocessing.json +11 -11
  10. pynndescent_index.joblib +2 -2
  11. scanvi/model.pt +1 -1
  12. scvi/model.pt +1 -1
  13. scvi_knn_classifier.joblib +2 -2
  14. svm_classifier.joblib +2 -2
  15. svm_classifier_cuml.joblib +1 -1
  16. xgboost_classifier.model +2 -2
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accuracies.json CHANGED
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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| luminal cell of prostate epithelium | 1052 | 0.94 | 0.97 | 0.97 | 0.94 | 0.00 | 0.94 | 0.95 | 0.93 | 0.96 |\n| basal cell of prostate epithelium | 352 | 0.85 | 0.89 | 0.90 | 0.84 | 0.00 | 0.87 | 0.87 | 0.84 | 0.90 |\n| CD8-positive, alpha-beta T cell | 256 | 0.94 | 0.88 | 0.95 | 0.88 | 0.00 | 0.93 | 0.92 | 0.93 | 0.96 |\n| endothelial cell | 121 | 0.98 | 0.97 | 0.97 | 0.94 | 0.00 | 0.97 | 0.97 | 0.97 | 0.98 |\n| macrophage | 94 | 0.96 | 0.98 | 0.98 | 0.96 | 0.00 | 0.99 | 0.97 | 0.97 | 0.98 |\n| fibroblast | 59 | 0.96 | 0.95 | 0.97 | 0.84 | 0.00 | 0.94 | 0.95 | 0.94 | 0.97 |\n| mature NK T cell | 51 | 0.93 | 0.15 | 0.91 | 0.32 | 0.00 | 0.93 | 0.94 | 0.91 | 0.96 |\n| smooth muscle cell | 48 | 0.92 | 0.95 | 0.91 | 0.80 | 0.00 | 0.92 | 0.92 | 0.91 | 0.96 |\n| neutrophil | 23 | 0.98 | 0.98 | 0.98 | 0.89 | 0.00 | 0.96 | 0.96 | 1.00 | 0.98 |\n| erythrocyte | 21 | 0.85 | 0.91 | 0.95 | 0.95 | 0.00 | 0.83 | 0.98 | 0.93 | 0.98 |\n| CD4-positive, alpha-beta T cell | 13 | 0.11 | 0.00 | 0.25 | 0.00 | 0.00 | 0.44 | 0.39 | 0.53 | 0.24 |\n| B cell | 8 | 0.75 | 0.86 | 0.80 | 0.75 | 0.00 | 0.89 | 0.93 | 0.86 | 0.80 |\n| mast cell | 4 | 1.00 | 0.75 | 1.00 | 0.67 | 0.00 | 0.35 | 0.89 | 1.00 | 1.00 |\n| T cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
3
- "ref_accuracy": "| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| luminal cell of prostate epithelium | 9600 | 0.94 | 0.96 | 0.98 | 0.97 | 0.00 | 0.94 | 0.95 | 0.94 | 0.96 |\n| basal cell of prostate epithelium | 3143 | 0.85 | 0.87 | 0.94 | 0.91 | 0.00 | 0.87 | 0.89 | 0.86 | 0.90 |\n| CD8-positive, alpha-beta T cell | 2260 | 0.95 | 0.88 | 0.96 | 0.91 | 0.00 | 0.92 | 0.95 | 0.95 | 0.97 |\n| endothelial cell | 1084 | 0.98 | 0.92 | 0.98 | 0.96 | 0.00 | 0.97 | 0.98 | 0.97 | 0.99 |\n| macrophage | 928 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| fibroblast | 460 | 0.96 | 0.95 | 0.98 | 0.86 | 0.00 | 0.96 | 0.98 | 0.98 | 0.99 |\n| mature NK T cell | 436 | 0.91 | 0.18 | 0.92 | 0.54 | 0.00 | 0.92 | 0.92 | 0.93 | 0.95 |\n| smooth muscle cell | 429 | 0.93 | 0.91 | 0.97 | 0.83 | 0.00 | 0.94 | 0.97 | 0.97 | 0.99 |\n| neutrophil | 238 | 0.99 | 0.98 | 0.99 | 0.95 | 0.00 | 0.99 | 1.00 | 1.00 | 1.00 |\n| erythrocyte | 118 | 0.87 | 0.86 | 0.97 | 0.93 | 0.00 | 0.83 | 0.99 | 0.99 | 0.98 |\n| CD4-positive, alpha-beta T cell | 103 | 0.26 | 0.00 | 0.23 | 0.09 | 0.00 | 0.47 | 0.67 | 0.69 | 0.43 |\n| B cell | 93 | 0.82 | 0.82 | 0.84 | 0.90 | 0.00 | 0.92 | 0.99 | 0.98 | 0.97 |\n| mast cell | 22 | 1.00 | 0.64 | 0.98 | 0.68 | 0.00 | 0.38 | 0.98 | 0.98 | 1.00 |\n| T cell | 13 | 0.00 | 0.00 | 0.25 | 0.00 | 0.00 | 0.75 | 0.96 | 0.67 | 0.83 |"
4
  }
 
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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| luminal cell of prostate epithelium | 1055 | 0.94 | 0.96 | 0.97 | 0.94 | 0.00 | 0.92 | 0.95 | 0.94 | 0.96 |\n| basal cell of prostate epithelium | 348 | 0.85 | 0.88 | 0.90 | 0.83 | 0.00 | 0.82 | 0.87 | 0.86 | 0.89 |\n| CD8-positive, alpha-beta T cell | 255 | 0.91 | 0.88 | 0.95 | 0.87 | 0.00 | 0.92 | 0.92 | 0.93 | 0.95 |\n| endothelial cell | 127 | 0.98 | 0.98 | 0.99 | 0.96 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |\n| macrophage | 94 | 0.96 | 0.98 | 0.98 | 0.97 | 0.00 | 0.99 | 0.99 | 0.96 | 0.98 |\n| fibroblast | 58 | 0.96 | 0.95 | 0.97 | 0.83 | 0.00 | 0.96 | 0.97 | 0.95 | 0.98 |\n| mature NK T cell | 50 | 0.91 | 0.18 | 0.92 | 0.12 | 0.00 | 0.90 | 0.91 | 0.92 | 0.93 |\n| smooth muscle cell | 46 | 0.94 | 0.94 | 0.93 | 0.80 | 0.00 | 0.86 | 0.93 | 0.88 | 0.94 |\n| neutrophil | 23 | 0.98 | 1.00 | 1.00 | 0.96 | 0.00 | 0.96 | 1.00 | 1.00 | 1.00 |\n| erythrocyte | 20 | 0.90 | 0.86 | 0.95 | 0.95 | 0.00 | 0.88 | 0.97 | 0.97 | 0.97 |\n| CD4-positive, alpha-beta T cell | 14 | 0.17 | 0.00 | 0.00 | 0.00 | 0.00 | 0.49 | 0.50 | 0.34 | 0.19 |\n| B cell | 8 | 0.75 | 0.77 | 0.80 | 0.71 | 0.00 | 0.89 | 0.88 | 0.80 | 0.80 |\n| mast cell | 4 | 1.00 | 0.73 | 1.00 | 0.29 | 0.00 | 0.50 | 1.00 | 1.00 | 1.00 |\n| T cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
3
+ "ref_accuracy": "| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| luminal cell of prostate epithelium | 9597 | 0.95 | 0.96 | 0.98 | 0.96 | 0.00 | 0.93 | 0.96 | 0.95 | 0.97 |\n| basal cell of prostate epithelium | 3147 | 0.87 | 0.88 | 0.94 | 0.90 | 0.00 | 0.84 | 0.89 | 0.88 | 0.91 |\n| CD8-positive, alpha-beta T cell | 2261 | 0.93 | 0.89 | 0.96 | 0.91 | 0.00 | 0.94 | 0.94 | 0.95 | 0.96 |\n| endothelial cell | 1078 | 0.98 | 0.96 | 0.98 | 0.94 | 0.00 | 0.97 | 0.97 | 0.97 | 0.99 |\n| macrophage | 928 | 0.98 | 0.98 | 0.98 | 0.97 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| fibroblast | 461 | 0.96 | 0.95 | 0.98 | 0.86 | 0.00 | 0.95 | 0.98 | 0.97 | 0.99 |\n| mature NK T cell | 437 | 0.91 | 0.17 | 0.91 | 0.54 | 0.00 | 0.89 | 0.92 | 0.93 | 0.94 |\n| smooth muscle cell | 431 | 0.95 | 0.92 | 0.97 | 0.81 | 0.00 | 0.93 | 0.97 | 0.96 | 0.99 |\n| neutrophil | 238 | 0.99 | 0.98 | 0.99 | 0.96 | 0.00 | 0.99 | 1.00 | 1.00 | 0.99 |\n| erythrocyte | 119 | 0.93 | 0.85 | 0.97 | 0.92 | 0.00 | 0.90 | 0.99 | 0.98 | 0.98 |\n| CD4-positive, alpha-beta T cell | 102 | 0.31 | 0.00 | 0.19 | 0.13 | 0.00 | 0.65 | 0.64 | 0.65 | 0.47 |\n| B cell | 93 | 0.82 | 0.81 | 0.84 | 0.82 | 0.00 | 0.92 | 0.96 | 0.96 | 0.96 |\n| mast cell | 22 | 1.00 | 0.65 | 1.00 | 0.69 | 0.00 | 0.70 | 0.98 | 0.98 | 0.98 |\n| T cell | 13 | 0.00 | 0.00 | 0.24 | 0.00 | 0.00 | 0.51 | 0.93 | 0.70 | 0.92 |"
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3290
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