Add SST2 binding affinity results

.gitattributes

@@ -36,3 +36,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 assets/HELM-BERT.png filter=lfs diff=lfs merge=lfs -text
 assets/tsne_ppi_splits.png filter=lfs diff=lfs merge=lfs -text
 assets/tsne_permeability_splits.png filter=lfs diff=lfs merge=lfs -text
+assets/tsne_sst2_splits.png filter=lfs diff=lfs merge=lfs -text

README.md

@@ -75,17 +75,17 @@ Pre-trained on deduplicated peptide sequences from:
 
 | Split | R² | Pearson | RMSE | MAE |
 |:-----:|:--:|:-------:|:----:|:---:|
-| Random | 0.751 | 0.867 | 0.398 | 0.263 |
-| Scaffold | 0.655 | 0.821 | 0.398 | 0.305 |
+| Random | 0.769 | 0.878 | 0.388 | 0.269 |
+| Scaffold | 0.643 | 0.812 | 0.380 | 0.284 |
 
 **Multi-Assay** (separate PAMPA and Caco-2 heads):
 
 | Split | Assay | R² | Pearson | RMSE | MAE |
 |:-----:|:-----:|:--:|:-------:|:----:|:---:|
-| Random | PAMPA | 0.740 | 0.862 | 0.399 | 0.281 |
-| Random | Caco-2 | 0.694 | 0.833 | 0.412 | 0.274 |
-| Scaffold | PAMPA | 0.629 | 0.815 | 0.406 | 0.317 |
-| Scaffold | Caco-2 | 0.625 | 0.822 | 0.426 | 0.316 |
+| Random | PAMPA | 0.711 | 0.844 | 0.426 | 0.298 |
+| Random | Caco-2 | 0.772 | 0.878 | 0.402 | 0.305 |
+| Scaffold | PAMPA | 0.584 | 0.788 | 0.393 | 0.299 |
+| Scaffold | Caco-2 | 0.701 | 0.846 | 0.381 | 0.287 |
 
 Train/test 9:1, val 10% from train. Scaffold split by Murcko scaffolds.
 
@@ -95,8 +95,8 @@ Train/test 9:1, val 10% from train. Scaffold split by Murcko scaffolds.
 
 | Split | ROC-AUC | PR-AUC | F1 | MCC | Balanced Acc |
 |:-----:|:-------:|:------:|:--:|:---:|:------------:|
-| Random | 0.972 | 0.913 | 0.855 | 0.819 | 0.909 |
-| aCSM | 0.870 | 0.701 | 0.604 | 0.547 | 0.731 |
+| Random | 0.972 | 0.912 | 0.859 | 0.824 | 0.911 |
+| aCSM | 0.868 | 0.702 | 0.613 | 0.559 | 0.735 |
 
 Train/test 8:2, val 10% from train, 1:4 positive:negative ratio.
 - **Random**: random split
@@ -104,6 +104,17 @@ Train/test 8:2, val 10% from train, 1:4 positive:negative ratio.
 
 <p align="center"><img src="assets/tsne_ppi_splits.png" width="800"></p>
 
+### SST2 Binding Affinity (pChEMBL)
+
+| Split | R² | Pearson | RMSE | MAE |
+|:-----:|:--:|:-------:|:----:|:---:|
+| Random | 0.312 | 0.600 | 0.742 | 0.499 |
+| Scaffold | 0.078 | 0.532 | 1.154 | 0.821 |
+
+Train/test 9:1, val 10% from train. Scaffold split by Murcko scaffolds.
+
+<p align="center"><img src="assets/tsne_sst2_splits.png" width="800"></p>
+
 ## Citation
 
 ```bibtex