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README.md

@@ -12,7 +12,7 @@ datasets:
 
 # Predictor of _Brucella abortus_ MICs 
 
-_Updated:_ cd ..Fri 28 Mar 18:24:49 GMT 2025
+_Updated:_ cd ..Tue Apr  1 03:31:36 BST 2025
 
 Trained on the _Brucella abortus_, WT accumulator phenotype subset of the [human-curated SPARK dataset](https://doi.org/10.1021/acsinfecdis.8b00193) (9946 rows in total for _Brucella abortus_).
 
@@ -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,
+    "learning_rate": 1e-05,
+    "model_class": "FPMLPModelBox",
+    "n_hidden": 3,
     "n_units": 16,
     "use_2d": true,
     "use_fp": true
@@ -79,35 +79,40 @@ Train (6963 rows):
 ```json
 
 {
-    "Pearson r": 0.5503574788961993,
-    "RMSE": 0.053899530321359634,
-    "Spearman rho": 0.9346845985202912
+    "Pearson r": 0.5300446208555996,
+    "RMSE": 0.061959341168403625,
+    "Spearman rho": 0.9393133689615363
 }
 ```
 
+<img src="predictions-train.png" width=450>
+
 Validation (1491 rows):
 
 ```json
 
 {
-    "Pearson r": 0.4224614855497885,
-    "RMSE": 0.06130664795637131,
-    "Spearman rho": 0.88412899537977
+    "Pearson r": 0.4176124412909827,
+    "RMSE": 0.07129787653684616,
+    "Spearman rho": 0.8889606877623673
 }
 ```
 
+<img src="predictions-validation.png" width=450>
 
 Test (1492 rows):
 
 ```json
 
 {
-    "Pearson r": 0.4829411208985374,
-    "RMSE": 0.06526102125644684,
-    "Spearman rho": 0.9303547327209174
+    "Pearson r": 0.47702787899824634,
+    "RMSE": 0.08465012907981873,
+    "Spearman rho": 0.9295617687262676
 }
 ```
 
+<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/Brucella-abortus/71/cache",
+    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark-dv-2503/Brucella-abortus/107/cache",
     "features": [
         "smiles"
     ],

eval-metrics_test.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.4829411208985374,
-    "RMSE": 0.06526102125644684,
-    "Spearman rho": 0.9303547327209174
+    "Pearson r": 0.47702787899824634,
+    "RMSE": 0.08465012907981873,
+    "Spearman rho": 0.9295617687262676
 }

eval-metrics_train.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.5503574788961993,
-    "RMSE": 0.053899530321359634,
-    "Spearman rho": 0.9346845985202912
+    "Pearson r": 0.5300446208555996,
+    "RMSE": 0.061959341168403625,
+    "Spearman rho": 0.9393133689615363
 }

eval-metrics_validation.json

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.4224614855497885,
-    "RMSE": 0.06130664795637131,
-    "Spearman rho": 0.88412899537977
+    "Pearson r": 0.4176124412909827,
+    "RMSE": 0.07129787653684616,
+    "Spearman rho": 0.8889606877623673
 }

logs-csv/lightning_logs/version_0/hparams.yaml

@@ -1 +1,13 @@
-{}
+dropout: 0.2
+ensemble_size: 3
+extra_featurizers: null
+learning_rate: 1.0e-05
+n_hidden: 3
+n_input: 2248
+n_out: 1
+n_units: 16
+optimizer: !!python/name:torch.optim.adam.Adam ''
+reduce_lr_on_plateau: true
+reduce_lr_patience: 10
+use_2d: true
+use_fp: true

logs-csv/lightning_logs/version_0/metrics.csv

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