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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 | 1.96  | 2.16           |
-| Pearson Correlation | 0.82  | 0.79  |
+| Mean Absolute Error | 1.97  | 2.19           |
+| Pearson Correlation | 0.82  | 0.78  |
 | Spearman Correlation | 0.81 | 0.79  |
-| R² (R-Squared) | 0.60  | 0.50      |
+| R² (R-Squared) | 0.59  | 0.46      |
 
 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 | 13.32   |
-| Pearson Correlation | 0.61  |
-| Spearman Correlation | 0.63 |
-| R² (R-Squared) | -0.45  |
+| Mean Absolute Error | 13.33   |
+| Pearson Correlation | 0.59  |
+| Spearman Correlation | 0.60 |
+| R² (R-Squared) | -0.39  |
 
 </details>
 
@@ -83,33 +83,33 @@ cell-type.
 
 | Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |
 | --- | --- | --- | --- | --- | --- | --- | --- |
-| conjunctival epithelial cell | 0.97 | 0.85 | 0.79 | 0.96 | 0.25 | 0.91 | 4587.00 |
-| corneal epithelial cell | 0.95 | 1.19 | 0.80 | 0.96 | 0.39 | 0.91 | 1488.00 |
-| eye photoreceptor cell | 0.93 | 2.16 | 0.73 | 0.89 | 0.33 | 0.86 | 891.00 |
-| keratocyte | 0.92 | 1.89 | 0.71 | 0.88 | 0.41 | 0.83 | 595.00 |
-| retinal blood vessel endothelial cell | 0.89 | 2.80 | 0.61 | 0.87 | 0.42 | 0.84 | 466.00 |
-| Mueller cell | 0.86 | 2.80 | 0.67 | 0.84 | 0.41 | 0.82 | 360.00 |
-| stromal cell | 0.86 | 1.01 | 0.76 | 0.92 | 0.38 | 0.75 | 325.00 |
-| T cell | 0.83 | 4.76 | 0.53 | 0.68 | 0.20 | 0.73 | 237.00 |
-| microglial cell | 0.88 | 3.28 | 0.62 | 0.78 | 0.31 | 0.73 | 209.00 |
-| radial glial cell | 0.85 | 2.11 | 0.71 | 0.86 | 0.47 | 0.81 | 195.00 |
-| dendritic cell | 0.87 | 4.37 | 0.60 | 0.69 | 0.23 | 0.70 | 182.00 |
-| melanocyte | 0.81 | 3.48 | 0.63 | 0.75 | 0.36 | 0.72 | 144.00 |
-| stem cell | 0.79 | 2.90 | 0.64 | 0.73 | 0.36 | 0.62 | 144.00 |
-| macrophage | 0.84 | 3.38 | 0.65 | 0.76 | 0.36 | 0.73 | 108.00 |
-| endothelial cell | 0.83 | 3.90 | 0.63 | 0.74 | 0.36 | 0.70 | 105.00 |
-| B cell | 0.82 | 5.52 | 0.55 | 0.62 | 0.26 | 0.72 | 102.00 |
-| fibroblast | 0.77 | 3.60 | 0.65 | 0.73 | 0.36 | 0.66 | 95.00 |
-| surface ectodermal cell | 0.69 | 4.63 | 0.61 | 0.61 | 0.39 | 0.69 | 54.00 |
-| epithelial cell of lacrimal sac | 0.72 | 5.08 | 0.54 | 0.48 | 0.39 | 0.67 | 52.00 |
-| retinal pigment epithelial cell | 0.86 | 5.47 | 0.58 | 0.62 | 0.34 | 0.75 | 49.00 |
-| plasma cell | 0.61 | 5.18 | 0.56 | 0.52 | 0.30 | 0.79 | 46.00 |
-| monocyte | 0.72 | 5.11 | 0.58 | 0.59 | 0.33 | 0.68 | 44.00 |
-| fat cell | 0.79 | 3.79 | 0.65 | 0.75 | 0.35 | 0.69 | 44.00 |
-| retinal bipolar neuron | 0.74 | 4.76 | 0.60 | 0.65 | 0.39 | 0.70 | 34.00 |
-| erythroid lineage cell | 0.29 | 6.96 | 0.25 | 0.26 | 0.25 | 0.93 | 30.00 |
-| CD4-positive, alpha-beta T cell | 0.40 | 6.50 | 0.45 | 0.35 | 0.31 | 0.54 | 23.00 |
-| pigmented ciliary epithelial cell | 0.63 | 5.26 | 0.58 | 0.53 | 0.33 | 0.63 | 17.00 |
+| conjunctival epithelial cell | 0.98 | 0.88 | 0.77 | 0.96 | 0.25 | 0.91 | 4587.00 |
+| corneal epithelial cell | 0.93 | 1.32 | 0.76 | 0.95 | 0.39 | 0.91 | 1488.00 |
+| eye photoreceptor cell | 0.94 | 2.09 | 0.74 | 0.90 | 0.32 | 0.86 | 891.00 |
+| keratocyte | 0.93 | 1.83 | 0.72 | 0.88 | 0.41 | 0.83 | 595.00 |
+| retinal blood vessel endothelial cell | 0.90 | 2.79 | 0.60 | 0.88 | 0.41 | 0.84 | 466.00 |
+| Mueller cell | 0.86 | 2.77 | 0.68 | 0.85 | 0.40 | 0.82 | 360.00 |
+| stromal cell | 0.84 | 1.05 | 0.74 | 0.92 | 0.38 | 0.75 | 325.00 |
+| T cell | 0.78 | 4.66 | 0.54 | 0.68 | 0.21 | 0.73 | 237.00 |
+| microglial cell | 0.87 | 3.46 | 0.59 | 0.77 | 0.31 | 0.73 | 209.00 |
+| radial glial cell | 0.86 | 2.11 | 0.71 | 0.85 | 0.47 | 0.81 | 195.00 |
+| dendritic cell | 0.87 | 4.56 | 0.58 | 0.67 | 0.24 | 0.70 | 182.00 |
+| melanocyte | 0.82 | 3.28 | 0.65 | 0.76 | 0.35 | 0.72 | 144.00 |
+| stem cell | 0.82 | 2.80 | 0.66 | 0.73 | 0.37 | 0.63 | 144.00 |
+| macrophage | 0.82 | 3.45 | 0.65 | 0.76 | 0.36 | 0.73 | 108.00 |
+| endothelial cell | 0.81 | 3.65 | 0.66 | 0.76 | 0.36 | 0.71 | 105.00 |
+| B cell | 0.84 | 5.53 | 0.55 | 0.62 | 0.26 | 0.72 | 102.00 |
+| fibroblast | 0.76 | 3.36 | 0.68 | 0.74 | 0.35 | 0.65 | 95.00 |
+| surface ectodermal cell | 0.66 | 4.59 | 0.61 | 0.62 | 0.38 | 0.69 | 54.00 |
+| epithelial cell of lacrimal sac | 0.68 | 5.19 | 0.53 | 0.48 | 0.40 | 0.67 | 52.00 |
+| retinal pigment epithelial cell | 0.86 | 5.64 | 0.57 | 0.62 | 0.34 | 0.75 | 49.00 |
+| plasma cell | 0.59 | 5.37 | 0.54 | 0.50 | 0.29 | 0.79 | 46.00 |
+| monocyte | 0.69 | 5.03 | 0.58 | 0.59 | 0.33 | 0.68 | 44.00 |
+| fat cell | 0.82 | 3.73 | 0.66 | 0.76 | 0.34 | 0.68 | 44.00 |
+| retinal bipolar neuron | 0.68 | 4.76 | 0.60 | 0.64 | 0.39 | 0.70 | 34.00 |
+| erythroid lineage cell | 0.33 | 7.35 | 0.23 | 0.24 | 0.23 | 0.93 | 30.00 |
+| CD4-positive, alpha-beta T cell | 0.40 | 6.72 | 0.44 | 0.35 | 0.31 | 0.54 | 23.00 |
+| pigmented ciliary epithelial cell | 0.59 | 5.24 | 0.58 | 0.53 | 0.34 | 0.63 | 17.00 |
 
 </details>
 
@@ -201,7 +201,7 @@ 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>