Hugging Face's logo

popV
/
tabula_sapiens_Liver

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: Liver
Model card Files
xet
 Community
canergen commited on
Commit
80100d8
·
verified ·
1 Parent(s): ae79ee7

Upload README.md with huggingface_hub

Browse files
Files changed (1) hide show
  1. README.md +50 -49
README.md CHANGED
@@ -5,7 +5,8 @@ tags:
5
  - biology
6
  - genomics
7
  - single-cell
8
- - anndata_version:0.11.1
 
9
  - popV
10
  - 'tissue: Liver'
11
  ---
@@ -31,59 +32,59 @@ computed on a 10% random subset of the data that was not used for training.
31
 
32
  | Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
33
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
34
- | hepatocyte | 709 | 0.99 | 0.98 | 0.97 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
35
- | macrophage | 329 | 0.89 | 0.88 | 0.92 | 0.90 | 0.00 | 0.89 | 0.92 | 0.94 | 0.94 |
36
- | endothelial cell | 175 | 0.97 | 0.98 | 0.97 | 0.97 | 0.00 | 0.98 | 0.98 | 0.97 | 0.97 |
37
- | monocyte | 187 | 0.42 | 0.65 | 0.64 | 0.57 | 0.00 | 0.23 | 0.43 | 0.47 | 0.54 |
38
- | CD8-positive, alpha-beta T cell | 121 | 0.83 | 0.84 | 0.84 | 0.61 | 0.00 | 0.82 | 0.76 | 0.86 | 0.86 |
39
- | erythrocyte | 112 | 0.96 | 0.94 | 0.96 | 0.97 | 0.00 | 0.94 | 0.99 | 0.96 | 0.99 |
40
- | mature NK T cell | 74 | 0.60 | 0.56 | 0.60 | 0.54 | 0.00 | 0.57 | 0.54 | 0.66 | 0.63 |
41
- | plasma cell | 79 | 0.97 | 0.99 | 0.98 | 0.99 | 0.00 | 0.97 | 0.99 | 0.99 | 0.99 |
42
- | natural killer cell | 90 | 0.70 | 0.74 | 0.70 | 0.49 | 0.00 | 0.73 | 0.71 | 0.82 | 0.77 |
43
- | neutrophil | 79 | 0.92 | 0.93 | 0.78 | 0.93 | 0.00 | 0.88 | 0.94 | 0.91 | 0.96 |
44
- | intrahepatic cholangiocyte | 66 | 0.97 | 0.99 | 0.99 | 0.98 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |
45
- | intermediate monocyte | 57 | 0.41 | 0.22 | 0.46 | 0.24 | 0.00 | 0.45 | 0.43 | 0.44 | 0.48 |
46
- | classical monocyte | 25 | 0.08 | 0.00 | 0.15 | 0.26 | 0.00 | 0.26 | 0.18 | 0.24 | 0.16 |
47
- | CD4-positive, alpha-beta T cell | 26 | 0.62 | 0.56 | 0.64 | 0.19 | 0.00 | 0.62 | 0.52 | 0.68 | 0.70 |
48
- | hepatic stellate cell | 18 | 0.64 | 0.56 | 0.61 | 0.73 | 0.00 | 0.84 | 0.94 | 0.89 | 0.91 |
49
- | B cell | 19 | 0.95 | 0.92 | 0.95 | 0.92 | 0.00 | 0.93 | 0.95 | 0.95 | 0.95 |
50
- | fibroblast | 15 | 0.74 | 0.77 | 0.69 | 0.82 | 0.00 | 0.94 | 0.94 | 0.97 | 0.94 |
51
- | non-classical monocyte | 13 | 0.71 | 0.13 | 0.60 | 0.10 | 0.00 | 0.57 | 0.81 | 0.88 | 0.88 |
52
- | myeloid cell | 5 | 0.00 | 0.00 | 0.33 | 0.44 | 0.00 | 0.46 | 0.67 | 0.40 | 0.44 |
53
- | myeloid dendritic cell | 9 | 0.00 | 0.00 | 0.33 | 0.00 | 0.00 | 0.47 | 0.75 | 0.60 | 0.75 |
54
- | hematopoietic precursor cell | 6 | 0.00 | 0.44 | 0.67 | 0.44 | 0.00 | 0.57 | 0.80 | 0.73 | 0.80 |
55
- | T cell | 5 | 0.00 | 0.00 | 0.33 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
56
- | mast cell | 3 | 0.75 | 0.67 | 0.80 | 0.80 | 0.00 | 0.67 | 0.86 | 1.00 | 0.86 |
57
- | plasmacytoid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
58
 
59
  The train accuracies are computed on the training data.
60
 
61
  | Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
62
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
63
- | hepatocyte | 6705 | 0.99 | 0.97 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
64
- | macrophage | 2903 | 0.90 | 0.88 | 0.95 | 0.92 | 0.00 | 0.90 | 0.93 | 0.94 | 0.96 |
65
- | endothelial cell | 1599 | 0.97 | 0.96 | 0.99 | 0.97 | 0.00 | 0.97 | 0.99 | 0.98 | 0.99 |
66
- | monocyte | 1534 | 0.46 | 0.62 | 0.76 | 0.70 | 0.00 | 0.43 | 0.70 | 0.72 | 0.80 |
67
- | CD8-positive, alpha-beta T cell | 1169 | 0.81 | 0.81 | 0.86 | 0.76 | 0.00 | 0.83 | 0.88 | 0.92 | 0.89 |
68
- | erythrocyte | 868 | 0.97 | 0.90 | 0.99 | 0.98 | 0.00 | 0.97 | 0.99 | 0.98 | 0.99 |
69
- | mature NK T cell | 734 | 0.65 | 0.51 | 0.76 | 0.69 | 0.00 | 0.71 | 0.84 | 0.88 | 0.84 |
70
- | plasma cell | 687 | 0.97 | 0.95 | 0.99 | 0.98 | 0.00 | 0.98 | 1.00 | 0.99 | 0.99 |
71
- | natural killer cell | 655 | 0.68 | 0.64 | 0.79 | 0.69 | 0.00 | 0.80 | 0.89 | 0.91 | 0.88 |
72
- | neutrophil | 660 | 0.91 | 0.82 | 0.94 | 0.93 | 0.00 | 0.93 | 0.98 | 0.98 | 0.98 |
73
- | intrahepatic cholangiocyte | 599 | 0.96 | 0.97 | 0.98 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
74
- | intermediate monocyte | 500 | 0.41 | 0.26 | 0.65 | 0.54 | 0.00 | 0.60 | 0.75 | 0.74 | 0.78 |
75
- | classical monocyte | 301 | 0.19 | 0.06 | 0.47 | 0.39 | 0.00 | 0.47 | 0.70 | 0.72 | 0.78 |
76
- | CD4-positive, alpha-beta T cell | 265 | 0.56 | 0.47 | 0.67 | 0.50 | 0.00 | 0.69 | 0.83 | 0.87 | 0.81 |
77
- | hepatic stellate cell | 205 | 0.70 | 0.44 | 0.84 | 0.75 | 0.00 | 0.88 | 0.99 | 0.97 | 0.97 |
78
- | B cell | 144 | 0.94 | 0.95 | 0.96 | 0.92 | 0.00 | 0.95 | 0.99 | 0.99 | 0.98 |
79
- | fibroblast | 146 | 0.74 | 0.69 | 0.80 | 0.82 | 0.00 | 0.97 | 0.99 | 0.99 | 0.97 |
80
- | non-classical monocyte | 100 | 0.64 | 0.18 | 0.82 | 0.47 | 0.00 | 0.74 | 0.87 | 0.88 | 0.89 |
81
- | myeloid cell | 76 | 0.48 | 0.00 | 0.50 | 0.63 | 0.00 | 0.79 | 0.95 | 0.86 | 0.89 |
82
- | myeloid dendritic cell | 47 | 0.00 | 0.00 | 0.48 | 0.30 | 0.00 | 0.43 | 0.82 | 0.76 | 0.91 |
83
- | hematopoietic precursor cell | 35 | 0.00 | 0.40 | 0.68 | 0.55 | 0.00 | 0.73 | 1.00 | 0.99 | 0.92 |
84
- | T cell | 27 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.62 | 1.00 | 1.00 | 0.80 |
85
- | mast cell | 25 | 0.85 | 0.56 | 0.94 | 0.85 | 0.00 | 0.94 | 1.00 | 0.96 | 1.00 |
86
- | plasmacytoid dendritic cell | 8 | 0.00 | 0.00 | 0.88 | 0.93 | 0.00 | 0.59 | 0.94 | 1.00 | 1.00 |
87
 
88
  </details>
89
 
 
5
  - biology
6
  - genomics
7
  - single-cell
8
+ - anndata_version:0.11.3
9
+ - python_version:3.11.11
10
  - popV
11
  - 'tissue: Liver'
12
  ---
 
32
 
33
  | Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
34
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
35
+ | hepatocyte | 739 | 0.99 | 0.98 | 0.97 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |
36
+ | macrophage | 315 | 0.87 | 0.89 | 0.93 | 0.88 | 0.00 | 0.88 | 0.92 | 0.94 | 0.95 |
37
+ | endothelial cell | 180 | 0.97 | 0.97 | 0.98 | 0.98 | 0.00 | 0.98 | 0.97 | 0.97 | 0.98 |
38
+ | monocyte | 174 | 0.50 | 0.61 | 0.62 | 0.61 | 0.00 | 0.48 | 0.43 | 0.46 | 0.62 |
39
+ | CD8-positive, alpha-beta T cell | 119 | 0.82 | 0.82 | 0.82 | 0.58 | 0.00 | 0.82 | 0.76 | 0.82 | 0.86 |
40
+ | erythrocyte | 102 | 0.99 | 0.92 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.97 | 0.99 |
41
+ | mature NK T cell | 63 | 0.59 | 0.47 | 0.62 | 0.47 | 0.00 | 0.57 | 0.53 | 0.62 | 0.63 |
42
+ | plasma cell | 81 | 0.98 | 0.98 | 0.96 | 0.98 | 0.00 | 1.00 | 0.99 | 0.98 | 0.98 |
43
+ | natural killer cell | 84 | 0.74 | 0.72 | 0.74 | 0.44 | 0.00 | 0.74 | 0.74 | 0.78 | 0.78 |
44
+ | neutrophil | 82 | 0.96 | 0.94 | 0.79 | 0.88 | 0.00 | 0.95 | 0.94 | 0.95 | 0.98 |
45
+ | intrahepatic cholangiocyte | 70 | 0.98 | 0.96 | 0.98 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
46
+ | intermediate monocyte | 56 | 0.47 | 0.27 | 0.41 | 0.19 | 0.00 | 0.29 | 0.37 | 0.39 | 0.41 |
47
+ | classical monocyte | 30 | 0.29 | 0.00 | 0.20 | 0.10 | 0.00 | 0.18 | 0.35 | 0.39 | 0.27 |
48
+ | CD4-positive, alpha-beta T cell | 30 | 0.67 | 0.44 | 0.61 | 0.30 | 0.00 | 0.65 | 0.53 | 0.70 | 0.73 |
49
+ | hepatic stellate cell | 25 | 0.75 | 0.44 | 0.64 | 0.42 | 0.00 | 0.76 | 0.94 | 0.90 | 0.86 |
50
+ | B cell | 17 | 0.94 | 0.94 | 0.91 | 0.77 | 0.00 | 0.94 | 0.97 | 0.94 | 0.94 |
51
+ | fibroblast | 15 | 0.73 | 0.65 | 0.61 | 0.59 | 0.00 | 0.79 | 0.94 | 0.86 | 0.86 |
52
+ | non-classical monocyte | 12 | 0.67 | 0.14 | 0.67 | 0.42 | 0.00 | 0.71 | 0.59 | 0.80 | 0.81 |
53
+ | myeloid cell | 5 | 0.50 | 0.00 | 0.33 | 0.50 | 0.00 | 0.62 | 0.67 | 0.77 | 0.80 |
54
+ | myeloid dendritic cell | 6 | 0.00 | 0.00 | 0.25 | 0.00 | 0.00 | 0.62 | 0.60 | 0.67 | 0.60 |
55
+ | hematopoietic precursor cell | 7 | 0.00 | 0.73 | 0.44 | 0.40 | 0.00 | 0.71 | 0.73 | 0.50 | 0.60 |
56
+ | T cell | 5 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.22 | 0.00 | 0.00 | 0.00 |
57
+ | mast cell | 4 | 0.44 | 0.50 | 0.89 | 0.75 | 0.00 | 0.80 | 0.89 | 0.89 | 0.89 |
58
+ | plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 1.00 | 1.00 | 0.00 | 0.50 | 0.00 | 0.00 | 0.00 |
59
 
60
  The train accuracies are computed on the training data.
61
 
62
  | Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
63
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
64
+ | hepatocyte | 6675 | 0.99 | 0.97 | 0.99 | 1.00 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
65
+ | macrophage | 2917 | 0.89 | 0.89 | 0.95 | 0.92 | 0.00 | 0.91 | 0.93 | 0.94 | 0.96 |
66
+ | endothelial cell | 1594 | 0.96 | 0.96 | 0.98 | 0.97 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
67
+ | monocyte | 1547 | 0.52 | 0.64 | 0.77 | 0.72 | 0.00 | 0.63 | 0.69 | 0.71 | 0.82 |
68
+ | CD8-positive, alpha-beta T cell | 1171 | 0.79 | 0.81 | 0.87 | 0.74 | 0.00 | 0.85 | 0.89 | 0.92 | 0.89 |
69
+ | erythrocyte | 878 | 0.99 | 0.88 | 0.99 | 0.98 | 0.00 | 0.96 | 0.99 | 0.98 | 0.99 |
70
+ | mature NK T cell | 745 | 0.63 | 0.50 | 0.76 | 0.66 | 0.00 | 0.72 | 0.85 | 0.87 | 0.84 |
71
+ | plasma cell | 685 | 0.98 | 0.96 | 0.99 | 0.97 | 0.00 | 0.99 | 1.00 | 0.99 | 0.99 |
72
+ | natural killer cell | 661 | 0.70 | 0.64 | 0.78 | 0.64 | 0.00 | 0.77 | 0.88 | 0.89 | 0.88 |
73
+ | neutrophil | 657 | 0.94 | 0.80 | 0.94 | 0.92 | 0.00 | 0.97 | 0.98 | 0.97 | 0.98 |
74
+ | intrahepatic cholangiocyte | 595 | 0.96 | 0.96 | 0.98 | 0.99 | 0.00 | 0.97 | 0.99 | 0.99 | 0.99 |
75
+ | intermediate monocyte | 501 | 0.44 | 0.22 | 0.65 | 0.54 | 0.00 | 0.50 | 0.74 | 0.74 | 0.79 |
76
+ | classical monocyte | 296 | 0.21 | 0.02 | 0.43 | 0.37 | 0.00 | 0.54 | 0.68 | 0.71 | 0.76 |
77
+ | CD4-positive, alpha-beta T cell | 261 | 0.51 | 0.51 | 0.67 | 0.55 | 0.00 | 0.71 | 0.82 | 0.87 | 0.80 |
78
+ | hepatic stellate cell | 198 | 0.55 | 0.27 | 0.82 | 0.79 | 0.00 | 0.91 | 0.97 | 0.97 | 0.96 |
79
+ | B cell | 146 | 0.94 | 0.95 | 0.96 | 0.84 | 0.00 | 0.94 | 0.99 | 0.98 | 0.97 |
80
+ | fibroblast | 146 | 0.61 | 0.64 | 0.78 | 0.85 | 0.00 | 0.93 | 0.99 | 0.99 | 0.97 |
81
+ | non-classical monocyte | 101 | 0.63 | 0.22 | 0.83 | 0.46 | 0.00 | 0.80 | 0.87 | 0.86 | 0.89 |
82
+ | myeloid cell | 76 | 0.72 | 0.00 | 0.59 | 0.58 | 0.00 | 0.82 | 0.93 | 0.89 | 0.90 |
83
+ | myeloid dendritic cell | 50 | 0.00 | 0.04 | 0.51 | 0.13 | 0.00 | 0.68 | 0.89 | 0.87 | 0.91 |
84
+ | hematopoietic precursor cell | 34 | 0.00 | 0.38 | 0.64 | 0.55 | 0.00 | 0.83 | 1.00 | 0.99 | 0.90 |
85
+ | T cell | 27 | 0.00 | 0.00 | 0.13 | 0.18 | 0.00 | 0.68 | 1.00 | 1.00 | 0.94 |
86
+ | mast cell | 24 | 0.34 | 0.46 | 0.89 | 0.69 | 0.00 | 0.98 | 1.00 | 0.96 | 1.00 |
87
+ | plasmacytoid dendritic cell | 7 | 0.00 | 0.00 | 0.86 | 0.83 | 0.00 | 0.61 | 1.00 | 1.00 | 1.00 |
88
 
89
  </details>
90