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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 | 1.68  | 1.70           |
+| Mean Absolute Error | 1.69  | 1.66           |
 | Pearson Correlation | 0.94  | 0.94  |
 | Spearman Correlation | 0.93 | 0.93  |
-| R² (R-Squared) | 0.87  | 0.87      |
+| R² (R-Squared) | 0.87  | 0.88      |
 
 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.
@@ -66,10 +66,10 @@ preserved by the generated model expression. This value is usually quite high.
 
 | Metric                  | Training Value |
 |-------------------------|----------------|
-| Mean Absolute Error | 5.54   |
+| Mean Absolute Error | 5.33   |
 | Pearson Correlation | 0.92  |
 | Spearman Correlation | 0.98 |
-| R² (R-Squared) | 0.60  |
+| R² (R-Squared) | 0.64  |
 
 </details>
 
@@ -86,22 +86,22 @@ cell-type.
 
 | Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |
 | --- | --- | --- | --- | --- | --- | --- | --- |
-| CD4-positive, alpha-beta T cell | 0.96 | 2.89 | 0.59 | 0.67 | 0.20 | 0.78 | 2872.00 |
-| enterocyte of epithelium of large intestine | 0.96 | 2.58 | 0.56 | 0.82 | 0.23 | 0.77 | 2764.00 |
-| CD8-positive, alpha-beta T cell | 0.93 | 3.54 | 0.60 | 0.69 | 0.22 | 0.80 | 2105.00 |
-| fibroblast | 0.96 | 2.77 | 0.74 | 0.87 | 0.50 | 0.88 | 852.00 |
-| paneth cell of colon | 0.96 | 3.67 | 0.62 | 0.72 | 0.29 | 0.81 | 831.00 |
-| monocyte | 0.94 | 3.53 | 0.72 | 0.80 | 0.38 | 0.86 | 543.00 |
-| B cell | 0.94 | 3.87 | 0.66 | 0.67 | 0.26 | 0.79 | 469.00 |
-| large intestine goblet cell | 0.90 | 4.22 | 0.61 | 0.68 | 0.32 | 0.76 | 385.00 |
-| plasma cell | 0.94 | 3.73 | 0.68 | 0.72 | 0.25 | 0.84 | 330.00 |
-| intestinal crypt stem cell of large intestine | 0.84 | 4.85 | 0.58 | 0.60 | 0.30 | 0.74 | 114.00 |
-| transit amplifying cell of colon | 0.72 | 4.96 | 0.56 | 0.55 | 0.29 | 0.72 | 52.00 |
-| mast cell | 0.83 | 4.62 | 0.58 | 0.55 | 0.36 | 0.79 | 38.00 |
-| gut endothelial cell | 0.72 | 4.72 | 0.65 | 0.64 | 0.38 | 0.77 | 31.00 |
-| neutrophil | 0.69 | 4.21 | 0.68 | 0.67 | 0.34 | 0.78 | 22.00 |
-| intestinal enteroendocrine cell | 0.70 | 4.49 | 0.64 | 0.62 | 0.32 | 0.74 | 19.00 |
-| intestinal tuft cell | 0.69 | 4.94 | 0.50 | 0.49 | 0.33 | 0.78 | 12.00 |
+| CD4-positive, alpha-beta T cell | 0.94 | 2.86 | 0.59 | 0.68 | 0.20 | 0.78 | 2872.00 |
+| enterocyte of epithelium of large intestine | 0.95 | 2.46 | 0.59 | 0.84 | 0.23 | 0.77 | 2764.00 |
+| CD8-positive, alpha-beta T cell | 0.94 | 3.49 | 0.60 | 0.68 | 0.23 | 0.80 | 2105.00 |
+| fibroblast | 0.92 | 2.91 | 0.71 | 0.86 | 0.51 | 0.89 | 852.00 |
+| paneth cell of colon | 0.95 | 3.53 | 0.63 | 0.73 | 0.29 | 0.81 | 831.00 |
+| monocyte | 0.92 | 3.62 | 0.71 | 0.79 | 0.38 | 0.86 | 543.00 |
+| B cell | 0.94 | 4.38 | 0.60 | 0.62 | 0.29 | 0.80 | 469.00 |
+| large intestine goblet cell | 0.87 | 4.21 | 0.61 | 0.67 | 0.33 | 0.76 | 385.00 |
+| plasma cell | 0.93 | 3.68 | 0.68 | 0.72 | 0.24 | 0.84 | 330.00 |
+| intestinal crypt stem cell of large intestine | 0.83 | 5.03 | 0.57 | 0.59 | 0.30 | 0.74 | 114.00 |
+| transit amplifying cell of colon | 0.69 | 4.71 | 0.59 | 0.58 | 0.30 | 0.71 | 52.00 |
+| mast cell | 0.84 | 4.86 | 0.55 | 0.52 | 0.35 | 0.79 | 38.00 |
+| gut endothelial cell | 0.74 | 4.81 | 0.65 | 0.64 | 0.39 | 0.78 | 31.00 |
+| neutrophil | 0.68 | 4.14 | 0.69 | 0.66 | 0.35 | 0.79 | 22.00 |
+| intestinal enteroendocrine cell | 0.70 | 4.38 | 0.64 | 0.63 | 0.31 | 0.74 | 19.00 |
+| intestinal tuft cell | 0.65 | 4.74 | 0.52 | 0.50 | 0.32 | 0.77 | 12.00 |
 
 </details>
 
@@ -196,7 +196,7 @@ 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>