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README.md

@@ -12,7 +12,7 @@ datasets:
 
 # Predictor of _Yersinia enterocolitica_ MICs 
 
-_Updated:_ cd ..Tue Apr  1 03:31:48 BST 2025
+_Updated:_ Tue  1 Apr 08:02:53 BST 2025
 
 Trained on the _Yersinia enterocolitica_, WT accumulator phenotype subset of the [human-curated SPARK dataset](https://doi.org/10.1021/acsinfecdis.8b00193) (1405 rows in total for _Yersinia enterocolitica_).
 
@@ -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
 
@@ -42,7 +42,7 @@ by Spearman's $\rho$ on a held-out test set not used in training or early stoppi
     "model_class": "ChempropModelBox",
     "n_hidden": 5,
     "n_units": 8,
-    "use_2d": true,
+    "use_2d": false,
     "use_fp": true
 }
 ```
@@ -79,39 +79,39 @@ Train (984 rows):
 ```json
 
 {
-    "Pearson r": 0.9618103873465654,
-    "RMSE": 0.2396148145198822,
-    "Spearman rho": 0.9586278151088848
+    "Pearson r": 0.9610046864345855,
+    "RMSE": 0.24681584537029266,
+    "Spearman rho": 0.9570068923333792
 }
 ```
 
-<img src="predictions-train.png" width=450>
+<img src="predictions_train.png" width=450>
 
 Validation (210 rows):
 
 ```json
 
 {
-    "Pearson r": 0.6479210242024951,
-    "RMSE": 0.5957785248756409,
-    "Spearman rho": 0.6402976188003731
+    "Pearson r": 0.6104635893879058,
+    "RMSE": 0.618925929069519,
+    "Spearman rho": 0.6049210503171903
 }
 ```
 
-<img src="predictions-validation.png" width=450>
+<img src="predictions_validation.png" width=450>
 
 Test (211 rows):
 
 ```json
 
 {
-    "Pearson r": 0.6504082120678273,
-    "RMSE": 0.6142442226409912,
-    "Spearman rho": 0.7049102788615442
+    "Pearson r": 0.6665680561527187,
+    "RMSE": 0.607518196105957,
+    "Spearman rho": 0.6959985257844904
 }
 ```
 
-<img src="predictions-test.png" width=450>
+<img src="predictions_test.png" width=450>
 
 ## Training data details
 

data-config.json

@@ -9,7 +9,7 @@
     ],
     "_out_key": "labels",
     "input_shape": [
-        2248
+        2048
     ],
     "output_shape": [
         1

data-load-args.json

@@ -1,5 +1,5 @@
 {
-    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark-dv-2503/Yersinia-enterocolitica/185/cache",
+    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark-dv-2503/Yersinia-enterocolitica/184/cache",
     "features": [
         "smiles"
     ],

eval-metrics_test.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.6504082120678273,
-    "RMSE": 0.6142442226409912,
-    "Spearman rho": 0.7049102788615442
+    "Pearson r": 0.6665680561527187,
+    "RMSE": 0.607518196105957,
+    "Spearman rho": 0.6959985257844904
 }

eval-metrics_train.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.9618103873465654,
-    "RMSE": 0.2396148145198822,
-    "Spearman rho": 0.9586278151088848
+    "Pearson r": 0.9610046864345855,
+    "RMSE": 0.24681584537029266,
+    "Spearman rho": 0.9570068923333792
 }

eval-metrics_validation.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.6479210242024951,
-    "RMSE": 0.5957785248756409,
-    "Spearman rho": 0.6402976188003731
+    "Pearson r": 0.6104635893879058,
+    "RMSE": 0.618925929069519,
+    "Spearman rho": 0.6049210503171903
 }

logs-csv/lightning_logs/version_0/metrics.csv

@@ -1,625 +1,663 @@
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