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README.md

@@ -12,7 +12,7 @@ datasets:
 
 # Predictor of _Streptococcus pneumoniae_ MICs 
 
-_Updated:_ cd ..Tue Apr  1 03:31:46 BST 2025
+_Updated:_ Tue  1 Apr 08:02:53 BST 2025
 
 Trained on the _Streptococcus pneumoniae_, WT accumulator phenotype subset of the [human-curated SPARK dataset](https://doi.org/10.1021/acsinfecdis.8b00193) (1254 rows in total for _Streptococcus pneumoniae_).
 
@@ -26,7 +26,7 @@ Duvida also saves the training data in this checkpoint to allows the calculation
 based on that training data.
 
 This model is the best regression model from a hyperparameter search, determined
-by Spearman's $\rho$ on a held-out test set not used in training or early stopping. 
+by Pearson's $$r$$ on a held-out test set not used in training or early stopping. 
 
 ### Model architecture
 
@@ -40,7 +40,7 @@ by Spearman's $\rho$ on a held-out test set not used in training or early stoppi
     "extra_featurizers": null,
     "learning_rate": 0.0001,
     "model_class": "ChempropModelBox",
-    "n_hidden": 3,
+    "n_hidden": 5,
     "n_units": 256,
     "use_2d": true,
     "use_fp": true
@@ -79,39 +79,39 @@ Train (6 rows):
 ```json
 
 {
-    "Pearson r": 0.9972484519866125,
-    "RMSE": 0.05407063290476799,
-    "Spearman rho": 0.9999999999999999
+    "Pearson r": 0.9940835972030041,
+    "RMSE": 0.06840968132019043,
+    "Spearman rho": 0.9851843661437779
 }
 ```
 
-<img src="predictions-train.png" width=450>
+<img src="predictions_train.png" width=450>
 
 Validation (17 rows):
 
 ```json
 
 {
-    "Pearson r": 0.9390398811962342,
-    "RMSE": 1.1505030393600464,
-    "Spearman rho": 0.7553649488442654
+    "Pearson r": 0.9466036791965707,
+    "RMSE": 1.2293813228607178,
+    "Spearman rho": 0.8179032806479304
 }
 ```
 
-<img src="predictions-validation.png" width=450>
+<img src="predictions_validation.png" width=450>
 
 Test (5 rows):
 
 ```json
 
 {
-    "Pearson r": 0.4826536791208014,
-    "RMSE": 0.6846991181373596,
-    "Spearman rho": 0.39999999999999997
+    "Pearson r": 0.5688338775794037,
+    "RMSE": 0.8309100866317749,
+    "Spearman rho": 0.3
 }
 ```
 
-<img src="predictions-test.png" width=450>
+<img src="predictions_test.png" width=450>
 
 ## Training data details
 

data-load-args.json

@@ -1,5 +1,5 @@
 {
-    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark-dv-2503/Streptococcus-pneumoniae/183/cache",
+    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark-dv-2503/Streptococcus-pneumoniae/191/cache",
     "features": [
         "smiles"
     ],

eval-metrics_test.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.4826536791208014,
-    "RMSE": 0.6846991181373596,
-    "Spearman rho": 0.39999999999999997
+    "Pearson r": 0.5688338775794037,
+    "RMSE": 0.8309100866317749,
+    "Spearman rho": 0.3
 }

eval-metrics_train.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.9972484519866125,
-    "RMSE": 0.05407063290476799,
-    "Spearman rho": 0.9999999999999999
+    "Pearson r": 0.9940835972030041,
+    "RMSE": 0.06840968132019043,
+    "Spearman rho": 0.9851843661437779
 }

eval-metrics_validation.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.9390398811962342,
-    "RMSE": 1.1505030393600464,
-    "Spearman rho": 0.7553649488442654
+    "Pearson r": 0.9466036791965707,
+    "RMSE": 1.2293813228607178,
+    "Spearman rho": 0.8179032806479304
 }

logs-csv/lightning_logs/version_0/metrics.csv

@@ -1,465 +1,467 @@
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