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README.md

@@ -12,7 +12,7 @@ datasets:
 
 # Predictor of _Klebsiella pneumoniae_ MICs 
 
-_Updated:_ cd ..Tue Apr  1 03:31:43 BST 2025
+_Updated:_ Tue  1 Apr 08:02:49 BST 2025
 
 Trained on the _Klebsiella pneumoniae_, WT accumulator phenotype subset of the [human-curated SPARK dataset](https://doi.org/10.1021/acsinfecdis.8b00193) (3920 rows in total for _Klebsiella 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": 1e-05,
     "model_class": "ChempropModelBox",
-    "n_hidden": 5,
+    "n_hidden": 1,
     "n_units": 16,
     "use_2d": true,
     "use_fp": true
@@ -79,39 +79,39 @@ Train (2045 rows):
 ```json
 
 {
-    "Pearson r": 0.8940795429226548,
-    "RMSE": 0.3624576926231384,
-    "Spearman rho": 0.845112973803823
+    "Pearson r": 0.8996679781957766,
+    "RMSE": 0.3616390526294708,
+    "Spearman rho": 0.8527349660329834
 }
 ```
 
-<img src="predictions-train.png" width=450>
+<img src="predictions_train.png" width=450>
 
 Validation (723 rows):
 
 ```json
 
 {
-    "Pearson r": 0.7725444031545016,
-    "RMSE": 0.7004245519638062,
-    "Spearman rho": 0.6222847459695977
+    "Pearson r": 0.7914871274663255,
+    "RMSE": 0.6667208671569824,
+    "Spearman rho": 0.6063974837310576
 }
 ```
 
-<img src="predictions-validation.png" width=450>
+<img src="predictions_validation.png" width=450>
 
 Test (646 rows):
 
 ```json
 
 {
-    "Pearson r": 0.36027280209643125,
-    "RMSE": 0.7164360284805298,
-    "Spearman rho": 0.48359581684441383
+    "Pearson r": 0.3984970954968539,
+    "RMSE": 0.7005582451820374,
+    "Spearman rho": 0.48216191455244684
 }
 ```
 
-<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/Klebsiella-pneumoniae/139/cache",
+    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark-dv-2503/Klebsiella-pneumoniae/123/cache",
     "features": [
         "smiles"
     ],

eval-metrics_test.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.36027280209643125,
-    "RMSE": 0.7164360284805298,
-    "Spearman rho": 0.48359581684441383
+    "Pearson r": 0.3984970954968539,
+    "RMSE": 0.7005582451820374,
+    "Spearman rho": 0.48216191455244684
 }

eval-metrics_train.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.8940795429226548,
-    "RMSE": 0.3624576926231384,
-    "Spearman rho": 0.845112973803823
+    "Pearson r": 0.8996679781957766,
+    "RMSE": 0.3616390526294708,
+    "Spearman rho": 0.8527349660329834
 }

eval-metrics_validation.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.7725444031545016,
-    "RMSE": 0.7004245519638062,
-    "Spearman rho": 0.6222847459695977
+    "Pearson r": 0.7914871274663255,
+    "RMSE": 0.6667208671569824,
+    "Spearman rho": 0.6063974837310576
 }

logs-csv/lightning_logs/version_0/metrics.csv

@@ -1,1103 +1,937 @@
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