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README.md +17 -17
data-load-args.json +1 -1
eval-metrics_test.json +3 -3
eval-metrics_train.json +3 -3
eval-metrics_validation.json +3 -3
logs-csv/lightning_logs/version_0/metrics.csv +0 -0
logs/lightning_logs/version_0/events.out.tfevents.1743275074.cn005.1118851.0 +3 -0
metrics.csv +3 -3
modelbox-config.json +3 -3
params.pt +2 -2
predictions_test.csv.gz +2 -2
predictions_test.png +0 -0
predictions_train.csv.gz +2 -2
predictions_train.png +0 -0
predictions_validation.csv.gz +2 -2
predictions_validation.png +0 -0
training-data.hf/cache-c4e479adfed851bd.arrow +3 -0
training-log.csv +1591 -365
training-log.png +0 -0

README.md CHANGED Viewed

@@ -12,7 +12,7 @@ datasets:
 # Predictor of _Staphylococcus aureus_ MICs
-_Updated:_ cd ..Tue Apr  1 03:31:46 BST 2025
 Trained on the _Staphylococcus aureus_, WT accumulator phenotype subset of the [human-curated SPARK dataset](https://doi.org/10.1021/acsinfecdis.8b00193) (2115 rows in total for _Staphylococcus aureus_).
@@ -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.
 ### Model architecture
@@ -35,13 +35,13 @@ by Spearman's $\rho$ on a held-out test set not used in training or early stoppi
 ```json
 {
-    "dropout": 0.2,
     "ensemble_size": 3,
     "extra_featurizers": null,
     "learning_rate": 1e-05,
     "model_class": "ChempropModelBox",
-    "n_hidden": 1,
-    "n_units": 16,
     "use_2d": true,
     "use_fp": true
 }
@@ -79,39 +79,39 @@ Train (1424 rows):
 ```json
 {
-    "Pearson r": 0.9064969320141453,
-    "RMSE": 0.25372380018234253,
-    "Spearman rho": 0.7852081545647585
 }
 ```
-<img src="predictions-train.png" width=450>
 Validation (309 rows):
 ```json
 {
-    "Pearson r": 0.9448327890391637,
-    "RMSE": 0.32256004214286804,
-    "Spearman rho": 0.8618832472295566
 }
 ```
-<img src="predictions-validation.png" width=450>
 Test (316 rows):
 ```json
 {
-    "Pearson r": 0.7412701120900793,
-    "RMSE": 0.7776482701301575,
-    "Spearman rho": 0.8294151050496763
 }
 ```
-<img src="predictions-test.png" width=450>
 ## Training data details

 # Predictor of _Staphylococcus aureus_ MICs
+_Updated:_ Tue  1 Apr 08:02:52 BST 2025
 Trained on the _Staphylococcus aureus_, WT accumulator phenotype subset of the [human-curated SPARK dataset](https://doi.org/10.1021/acsinfecdis.8b00193) (2115 rows in total for _Staphylococcus aureus_).
 based on that training data.
 This model is the best regression model from a hyperparameter search, determined
+by Pearson's $$r$$ on a held-out test set not used in training or early stopping.
 ### Model architecture
 ```json
 {
+    "dropout": 0.0,
     "ensemble_size": 3,
     "extra_featurizers": null,
     "learning_rate": 1e-05,
     "model_class": "ChempropModelBox",
+    "n_hidden": 5,
+    "n_units": 8,
     "use_2d": true,
     "use_fp": true
 }
 ```json
 {
+    "Pearson r": 0.9141987685996613,
+    "RMSE": 0.238382488489151,
+    "Spearman rho": 0.8198319253295027
 }
 ```
+<img src="predictions_train.png" width=450>
 Validation (309 rows):
 ```json
 {
+    "Pearson r": 0.9432814998253994,
+    "RMSE": 0.3496144711971283,
+    "Spearman rho": 0.8553478966171193
 }
 ```
+<img src="predictions_validation.png" width=450>
 Test (316 rows):
 ```json
 {
+    "Pearson r": 0.7588797018977873,
+    "RMSE": 0.7793745398521423,
+    "Spearman rho": 0.8158068476381244
 }
 ```
+<img src="predictions_test.png" width=450>
 ## Training data details

data-load-args.json CHANGED Viewed

@@ -1,5 +1,5 @@
 {
-    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark-dv-2503/Staphylococcus-aureus/123/cache",
     "features": [
         "smiles"
     ],

 {
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     "features": [
         "smiles"
     ],

eval-metrics_test.json CHANGED Viewed

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.7412701120900793,
-    "RMSE": 0.7776482701301575,
-    "Spearman rho": 0.8294151050496763
 }

 {
+    "Pearson r": 0.7588797018977873,
+    "RMSE": 0.7793745398521423,
+    "Spearman rho": 0.8158068476381244
 }

eval-metrics_train.json CHANGED Viewed

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.9064969320141453,
-    "RMSE": 0.25372380018234253,
-    "Spearman rho": 0.7852081545647585
 }

 {
+    "Pearson r": 0.9141987685996613,
+    "RMSE": 0.238382488489151,
+    "Spearman rho": 0.8198319253295027
 }

eval-metrics_validation.json CHANGED Viewed

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.9448327890391637,
-    "RMSE": 0.32256004214286804,
-    "Spearman rho": 0.8618832472295566
 }

 {
+    "Pearson r": 0.9432814998253994,
+    "RMSE": 0.3496144711971283,
+    "Spearman rho": 0.8553478966171193
 }

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The diff for this file is too large to render. See raw diff

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 {
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     "model_class": "ChempropModelBox",
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     "use_2d": true,
     "use_fp": true
 }

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     "model_class": "ChempropModelBox",
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     "use_2d": true,
     "use_fp": true
 }

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