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README.md

@@ -12,7 +12,7 @@ datasets:
 
 # Predictor of _Streptococcus pneumoniae_ MICs 
 
-_Updated:_ cd ..Fri 28 Mar 18:25:19 GMT 2025
+_Updated:_ cd ..Tue Apr  1 03:31:46 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_).
 
@@ -36,11 +36,11 @@ by Spearman's $\rho$ on a held-out test set not used in training or early stoppi
 
 {
     "dropout": 0.2,
-    "ensemble_size": 10,
+    "ensemble_size": 3,
     "extra_featurizers": null,
     "learning_rate": 0.0001,
     "model_class": "ChempropModelBox",
-    "n_hidden": 5,
+    "n_hidden": 3,
     "n_units": 256,
     "use_2d": true,
     "use_fp": true
@@ -79,35 +79,40 @@ Train (6 rows):
 ```json
 
 {
-    "Pearson r": 0.4138370404282536,
-    "RMSE": 0.3910311758518219,
-    "Spearman rho": 0.818181818181818
+    "Pearson r": 0.9972484519866125,
+    "RMSE": 0.05407063290476799,
+    "Spearman rho": 0.9999999999999999
 }
 ```
 
+<img src="predictions-train.png" width=450>
+
 Validation (17 rows):
 
 ```json
 
 {
-    "Pearson r": 0.954468386191219,
-    "RMSE": 1.128600001335144,
-    "Spearman rho": 0.8730841616511641
+    "Pearson r": 0.9390398811962342,
+    "RMSE": 1.1505030393600464,
+    "Spearman rho": 0.7553649488442654
 }
 ```
 
+<img src="predictions-validation.png" width=450>
 
 Test (5 rows):
 
 ```json
 
 {
-    "Pearson r": 0.3867792333436302,
-    "RMSE": 0.8993263244628906,
-    "Spearman rho": 0.09999999999999999
+    "Pearson r": 0.4826536791208014,
+    "RMSE": 0.6846991181373596,
+    "Spearman rho": 0.39999999999999997
 }
 ```
 
+<img src="predictions-test.png" width=450>
+
 ## Training data details
 
 The training data were collated by the authors of:

data-load-args.json

@@ -1,5 +1,5 @@
 {
-    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark/Streptococcus-pneumoniae/79/cache",
+    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark-dv-2503/Streptococcus-pneumoniae/183/cache",
     "features": [
         "smiles"
     ],

eval-metrics_test.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.3867792333436302,
-    "RMSE": 0.8993263244628906,
-    "Spearman rho": 0.09999999999999999
+    "Pearson r": 0.4826536791208014,
+    "RMSE": 0.6846991181373596,
+    "Spearman rho": 0.39999999999999997
 }

eval-metrics_train.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.4138370404282536,
-    "RMSE": 0.3910311758518219,
-    "Spearman rho": 0.818181818181818
+    "Pearson r": 0.9972484519866125,
+    "RMSE": 0.05407063290476799,
+    "Spearman rho": 0.9999999999999999
 }

eval-metrics_validation.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.954468386191219,
-    "RMSE": 1.128600001335144,
-    "Spearman rho": 0.8730841616511641
+    "Pearson r": 0.9390398811962342,
+    "RMSE": 1.1505030393600464,
+    "Spearman rho": 0.7553649488442654
 }

logs-csv/lightning_logs/version_0/metrics.csv

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