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README.md

@@ -12,7 +12,7 @@ datasets:
 
 # Predictor of _Escherichia coli_ MICs 
 
-_Updated:_ cd ..Tue Apr  1 03:31:38 BST 2025
+_Updated:_ Tue  1 Apr 08:02:43 BST 2025
 
 Trained on the _Escherichia coli_, WT accumulator phenotype subset of the [human-curated SPARK dataset](https://doi.org/10.1021/acsinfecdis.8b00193) (20451 rows in total for _Escherichia coli_).
 
@@ -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": "FPMLPModelBox",
-    "n_hidden": 5,
+    "n_hidden": 3,
     "n_units": 16,
     "use_2d": true,
     "use_fp": true
@@ -79,39 +79,39 @@ Train (10802 rows):
 ```json
 
 {
-    "Pearson r": 0.8928251051267814,
-    "RMSE": 0.4429602324962616,
-    "Spearman rho": 0.8975456488097212
+    "Pearson r": 0.8981370945321865,
+    "RMSE": 0.43611055612564087,
+    "Spearman rho": 0.8999000632718629
 }
 ```
 
-<img src="predictions-train.png" width=450>
+<img src="predictions_train.png" width=450>
 
 Validation (3348 rows):
 
 ```json
 
 {
-    "Pearson r": 0.5409352944401412,
-    "RMSE": 0.6904200911521912,
-    "Spearman rho": 0.5224176407629412
+    "Pearson r": 0.5463473339778666,
+    "RMSE": 0.6811274290084839,
+    "Spearman rho": 0.521191628774788
 }
 ```
 
-<img src="predictions-validation.png" width=450>
+<img src="predictions_validation.png" width=450>
 
 Test (2959 rows):
 
 ```json
 
 {
-    "Pearson r": 0.6933302354536446,
-    "RMSE": 0.6802275776863098,
-    "Spearman rho": 0.649640116298047
+    "Pearson r": 0.6967744273372313,
+    "RMSE": 0.6774232983589172,
+    "Spearman rho": 0.6465137335847693
 }
 ```
 
-<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/Escherichia-coli/163/cache",
+    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark-dv-2503/Escherichia-coli/155/cache",
     "features": [
         "smiles"
     ],

eval-metrics_test.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.6933302354536446,
-    "RMSE": 0.6802275776863098,
-    "Spearman rho": 0.649640116298047
+    "Pearson r": 0.6967744273372313,
+    "RMSE": 0.6774232983589172,
+    "Spearman rho": 0.6465137335847693
 }

eval-metrics_train.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.8928251051267814,
-    "RMSE": 0.4429602324962616,
-    "Spearman rho": 0.8975456488097212
+    "Pearson r": 0.8981370945321865,
+    "RMSE": 0.43611055612564087,
+    "Spearman rho": 0.8999000632718629
 }

eval-metrics_validation.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.5409352944401412,
-    "RMSE": 0.6904200911521912,
-    "Spearman rho": 0.5224176407629412
+    "Pearson r": 0.5463473339778666,
+    "RMSE": 0.6811274290084839,
+    "Spearman rho": 0.521191628774788
 }

logs-csv/lightning_logs/version_0/hparams.yaml

@@ -2,7 +2,7 @@ dropout: 0.2
 ensemble_size: 3
 extra_featurizers: null
 learning_rate: 0.0001
-n_hidden: 5
+n_hidden: 3
 n_input: 2248
 n_out: 1
 n_units: 16

logs-csv/lightning_logs/version_0/metrics.csv

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metrics.csv

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