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README.md

@@ -54,10 +54,10 @@ space might still be useful for analysis.
 
 | Metric                  | Training Value | Validation Value |
 |-------------------------|----------------|------------------|
-| Mean Absolute Error | 2.28  | 2.26           |
-| Pearson Correlation | 0.85  | 0.85  |
-| Spearman Correlation | 0.86 | 0.86  |
-| R² (R-Squared) | 0.54  | 0.55      |
+| Mean Absolute Error | 2.29  | 2.31           |
+| Pearson Correlation | 0.85  | 0.84  |
+| Spearman Correlation | 0.86 | 0.85  |
+| R² (R-Squared) | 0.54  | 0.57      |
 
 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.
@@ -66,9 +66,9 @@ preserved by the generated model expression. This value is usually quite high.
 
 | Metric                  | Training Value |
 |-------------------------|----------------|
-| Mean Absolute Error | 12.58   |
-| Pearson Correlation | 0.61  |
-| Spearman Correlation | 0.68 |
+| Mean Absolute Error | 12.66   |
+| Pearson Correlation | 0.62  |
+| Spearman Correlation | 0.69 |
 | R² (R-Squared) | -0.87  |
 
 </details>
@@ -86,20 +86,20 @@ cell-type.
 
 | Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |
 | --- | --- | --- | --- | --- | --- | --- | --- |
-| neutrophil | 0.94 | 2.13 | 0.68 | 0.89 | 0.18 | 0.84 | 2911.00 |
-| CD4-positive, alpha-beta T cell | 0.93 | 1.95 | 0.62 | 0.91 | 0.34 | 0.79 | 2025.00 |
-| monocyte | 0.88 | 1.76 | 0.65 | 0.90 | 0.39 | 0.78 | 1389.00 |
-| CD8-positive, alpha-beta T cell | 0.87 | 3.04 | 0.55 | 0.84 | 0.32 | 0.74 | 1147.00 |
-| granulocyte | 0.77 | 2.38 | 0.64 | 0.89 | 0.45 | 0.83 | 853.00 |
-| plasma cell | 0.79 | 2.25 | 0.73 | 0.92 | 0.19 | 0.85 | 825.00 |
-| erythroid progenitor cell | 0.59 | 2.34 | 0.70 | 0.93 | 0.48 | 0.89 | 757.00 |
-| mature NK T cell | 0.78 | 3.76 | 0.58 | 0.78 | 0.33 | 0.69 | 678.00 |
-| hematopoietic stem cell | 0.90 | 2.20 | 0.67 | 0.89 | 0.53 | 0.85 | 617.00 |
-| memory B cell | 0.87 | 4.15 | 0.61 | 0.72 | 0.32 | 0.69 | 310.00 |
-| common myeloid progenitor | 0.70 | 2.72 | 0.70 | 0.89 | 0.55 | 0.88 | 287.00 |
-| macrophage | 0.85 | 4.31 | 0.64 | 0.71 | 0.34 | 0.78 | 265.00 |
-| naive B cell | 0.88 | 5.38 | 0.59 | 0.67 | 0.26 | 0.66 | 142.00 |
-| erythrocyte | 0.90 | 4.94 | 0.57 | 0.52 | 0.31 | 0.90 | 87.00 |
+| neutrophil | 0.94 | 1.88 | 0.72 | 0.90 | 0.18 | 0.84 | 2911.00 |
+| CD4-positive, alpha-beta T cell | 0.94 | 2.03 | 0.59 | 0.90 | 0.33 | 0.79 | 2025.00 |
+| monocyte | 0.89 | 1.68 | 0.68 | 0.90 | 0.39 | 0.77 | 1389.00 |
+| CD8-positive, alpha-beta T cell | 0.87 | 2.92 | 0.59 | 0.86 | 0.32 | 0.74 | 1147.00 |
+| granulocyte | 0.78 | 2.44 | 0.61 | 0.89 | 0.45 | 0.83 | 853.00 |
+| plasma cell | 0.80 | 2.29 | 0.72 | 0.92 | 0.19 | 0.85 | 825.00 |
+| erythroid progenitor cell | 0.61 | 2.36 | 0.70 | 0.92 | 0.49 | 0.89 | 757.00 |
+| mature NK T cell | 0.80 | 3.67 | 0.59 | 0.79 | 0.33 | 0.69 | 678.00 |
+| hematopoietic stem cell | 0.87 | 2.24 | 0.66 | 0.89 | 0.53 | 0.85 | 617.00 |
+| memory B cell | 0.85 | 4.27 | 0.59 | 0.71 | 0.32 | 0.69 | 310.00 |
+| common myeloid progenitor | 0.76 | 2.67 | 0.71 | 0.90 | 0.54 | 0.88 | 287.00 |
+| macrophage | 0.87 | 4.32 | 0.64 | 0.70 | 0.34 | 0.78 | 265.00 |
+| naive B cell | 0.91 | 5.25 | 0.60 | 0.67 | 0.26 | 0.66 | 142.00 |
+| erythrocyte | 0.91 | 4.97 | 0.57 | 0.52 | 0.31 | 0.90 | 87.00 |
 
 </details>
 
@@ -194,7 +194,7 @@ 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>