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README.md

@@ -51,10 +51,10 @@ space might still be useful for analysis.
 
 | Metric                  | Training Value | Validation Value |
 |-------------------------|----------------|------------------|
-| Mean Absolute Error | 2.39  | 2.45           |
+| Mean Absolute Error | 2.38  | 2.47           |
 | Pearson Correlation | 0.84  | 0.81  |
 | Spearman Correlation | 0.86 | 0.84  |
-| R² (R-Squared) | 0.52  | 0.49      |
+| R² (R-Squared) | 0.54  | 0.48      |
 
 The gene-wise coefficient of variation summarizes how well variation between different genes is
 preserved by the generated model expression. This value is usually quite high.
@@ -63,10 +63,10 @@ preserved by the generated model expression. This value is usually quite high.
 
 | Metric                  | Training Value |
 |-------------------------|----------------|
-| Mean Absolute Error | 13.48   |
-| Pearson Correlation | 0.59  |
-| Spearman Correlation | 0.66 |
-| R² (R-Squared) | -1.49  |
+| Mean Absolute Error | 13.58   |
+| Pearson Correlation | 0.58  |
+| Spearman Correlation | 0.65 |
+| R² (R-Squared) | -1.50  |
 
 </details>
 
@@ -83,20 +83,20 @@ cell-type.
 
 | Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |
 | --- | --- | --- | --- | --- | --- | --- | --- |
-| neutrophil | 0.94 | 2.25 | 0.64 | 0.87 | 0.19 | 0.84 | 2911.00 |
-| CD4-positive, alpha-beta T cell | 0.94 | 1.96 | 0.62 | 0.90 | 0.34 | 0.79 | 2025.00 |
-| monocyte | 0.87 | 1.79 | 0.64 | 0.88 | 0.40 | 0.77 | 1389.00 |
-| CD8-positive, alpha-beta T cell | 0.86 | 2.95 | 0.58 | 0.85 | 0.32 | 0.74 | 1147.00 |
-| granulocyte | 0.79 | 2.38 | 0.64 | 0.89 | 0.46 | 0.83 | 853.00 |
-| plasma cell | 0.75 | 2.35 | 0.71 | 0.91 | 0.19 | 0.85 | 825.00 |
-| erythroid progenitor cell | 0.64 | 2.46 | 0.67 | 0.91 | 0.49 | 0.89 | 757.00 |
-| mature NK T cell | 0.78 | 3.77 | 0.58 | 0.76 | 0.33 | 0.69 | 678.00 |
-| hematopoietic stem cell | 0.89 | 2.27 | 0.65 | 0.87 | 0.53 | 0.85 | 617.00 |
-| memory B cell | 0.87 | 4.54 | 0.56 | 0.68 | 0.33 | 0.70 | 310.00 |
-| common myeloid progenitor | 0.72 | 2.72 | 0.69 | 0.89 | 0.54 | 0.88 | 287.00 |
-| macrophage | 0.86 | 4.43 | 0.63 | 0.70 | 0.34 | 0.78 | 265.00 |
-| naive B cell | 0.88 | 5.59 | 0.57 | 0.66 | 0.27 | 0.66 | 142.00 |
-| erythrocyte | 0.90 | 5.34 | 0.53 | 0.47 | 0.33 | 0.90 | 87.00 |
+| neutrophil | 0.94 | 2.21 | 0.66 | 0.88 | 0.19 | 0.84 | 2911.00 |
+| CD4-positive, alpha-beta T cell | 0.94 | 1.93 | 0.64 | 0.91 | 0.33 | 0.79 | 2025.00 |
+| monocyte | 0.87 | 1.70 | 0.68 | 0.89 | 0.40 | 0.78 | 1389.00 |
+| CD8-positive, alpha-beta T cell | 0.85 | 2.94 | 0.58 | 0.84 | 0.32 | 0.74 | 1147.00 |
+| granulocyte | 0.76 | 2.42 | 0.63 | 0.87 | 0.47 | 0.84 | 853.00 |
+| plasma cell | 0.76 | 2.29 | 0.72 | 0.92 | 0.19 | 0.85 | 825.00 |
+| erythroid progenitor cell | 0.62 | 2.48 | 0.67 | 0.91 | 0.49 | 0.89 | 757.00 |
+| mature NK T cell | 0.81 | 3.78 | 0.57 | 0.77 | 0.33 | 0.69 | 678.00 |
+| hematopoietic stem cell | 0.89 | 2.25 | 0.65 | 0.87 | 0.53 | 0.85 | 617.00 |
+| memory B cell | 0.89 | 4.68 | 0.55 | 0.68 | 0.33 | 0.70 | 310.00 |
+| common myeloid progenitor | 0.73 | 2.48 | 0.73 | 0.89 | 0.54 | 0.88 | 287.00 |
+| macrophage | 0.84 | 4.55 | 0.62 | 0.69 | 0.34 | 0.79 | 265.00 |
+| naive B cell | 0.89 | 5.33 | 0.60 | 0.68 | 0.26 | 0.66 | 142.00 |
+| erythrocyte | 0.91 | 5.13 | 0.55 | 0.49 | 0.33 | 0.90 | 87.00 |
 
 </details>
 
@@ -188,7 +188,7 @@ scvi-tools documentation for details. -->
 If provided by the original uploader, for those interested in understanding or replicating the
 training process, the code is available at the link below.
 
-**Training Code URL**: Not provided by uploader
+**Training Code URL**: https://github.com/YosefLab/scvi-hub-models/blob/main/src/scvi_hub_models/TS_train_all_tissues.ipynb
 
 </details>