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README.md +19 -14
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/hparams.yaml +4 -4
logs-csv/lightning_logs/version_0/metrics.csv +794 -152
logs/lightning_logs/version_0/events.out.tfevents.1743277072.cn077.1935888.0 +3 -0
logs/lightning_logs/version_0/hparams.yaml +4 -4
metrics.csv +3 -3
modelbox-config.json +4 -4
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-args.json +1 -1
training-data.hf/cache-9f30da37a0ffe0fd.arrow +3 -0
training-log.csv +397 -76
training-log.png +0 -0

README.md CHANGED Viewed

@@ -12,7 +12,7 @@ datasets:
 # Predictor of _Yersinia pestis_ MICs
-_Updated:_ cd ..Fri 28 Mar 18:25:28 GMT 2025
 Trained on the _Yersinia pestis_, WT accumulator phenotype subset of the [human-curated SPARK dataset](https://doi.org/10.1021/acsinfecdis.8b00193) (10002 rows in total for _Yersinia pestis_).
@@ -36,12 +36,12 @@ by Spearman's $\rho$ on a held-out test set not used in training or early stoppi
 {
     "dropout": 0.2,
-    "ensemble_size": 10,
     "extra_featurizers": null,
-    "learning_rate": 0.0001,
     "model_class": "FPMLPModelBox",
-    "n_hidden": 2,
-    "n_units": 16,
     "use_2d": true,
     "use_fp": true
 }
@@ -79,35 +79,40 @@ Train (7002 rows):
 ```json
 {
-    "Pearson r": 0.8516616817450599,
-    "RMSE": 0.037040311843156815,
-    "Spearman rho": 0.97379069361196
 }
 ```
 Validation (1499 rows):
 ```json
 {
-    "Pearson r": 0.7403999692649684,
-    "RMSE": 0.041353218257427216,
-    "Spearman rho": 0.9332247081913623
 }
 ```
 Test (1501 rows):
 ```json
 {
-    "Pearson r": 0.7870136836550153,
-    "RMSE": 0.042944587767124176,
-    "Spearman rho": 0.9723500084144376
 }
 ```
 ## Training data details
 The training data were collated by the authors of:

 # Predictor of _Yersinia pestis_ MICs
+_Updated:_ cd ..Tue Apr  1 03:31:50 BST 2025
 Trained on the _Yersinia pestis_, WT accumulator phenotype subset of the [human-curated SPARK dataset](https://doi.org/10.1021/acsinfecdis.8b00193) (10002 rows in total for _Yersinia pestis_).
 {
     "dropout": 0.2,
+    "ensemble_size": 3,
     "extra_featurizers": null,
+    "learning_rate": 1e-05,
     "model_class": "FPMLPModelBox",
+    "n_hidden": 5,
+    "n_units": 64,
     "use_2d": true,
     "use_fp": true
 }
 ```json
 {
+    "Pearson r": 0.8172829331255921,
+    "RMSE": 0.031726885586977005,
+    "Spearman rho": 0.9709886269987218
 }
 ```
+<img src="predictions-train.png" width=450>
 Validation (1499 rows):
 ```json
 {
+    "Pearson r": 0.722565134551274,
+    "RMSE": 0.038165923207998276,
+    "Spearman rho": 0.9247149302918276
 }
 ```
+<img src="predictions-validation.png" width=450>
 Test (1501 rows):
 ```json
 {
+    "Pearson r": 0.7763133307532436,
+    "RMSE": 0.035939376801252365,
+    "Spearman rho": 0.9701919932392147
 }
 ```
+<img src="predictions-test.png" width=450>
 ## Training data details
 The training data were collated by the authors of:

data-load-args.json CHANGED Viewed

@@ -1,5 +1,5 @@
 {
-    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark/Yersinia-pestis/11/cache",
     "features": [
         "smiles"
     ],

 {
+    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark-dv-2503/Yersinia-pestis/117/cache",
     "features": [
         "smiles"
     ],

eval-metrics_test.json CHANGED Viewed

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.7870136836550153,
-    "RMSE": 0.042944587767124176,
-    "Spearman rho": 0.9723500084144376
 }

 {
+    "Pearson r": 0.7763133307532436,
+    "RMSE": 0.035939376801252365,
+    "Spearman rho": 0.9701919932392147
 }

eval-metrics_train.json CHANGED Viewed

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.8516616817450599,
-    "RMSE": 0.037040311843156815,
-    "Spearman rho": 0.97379069361196
 }

 {
+    "Pearson r": 0.8172829331255921,
+    "RMSE": 0.031726885586977005,
+    "Spearman rho": 0.9709886269987218
 }

eval-metrics_validation.json CHANGED Viewed

@@ -1,5 +1,5 @@
 {
-    "Pearson r": 0.7403999692649684,
-    "RMSE": 0.041353218257427216,
-    "Spearman rho": 0.9332247081913623
 }

 {
+    "Pearson r": 0.722565134551274,
+    "RMSE": 0.038165923207998276,
+    "Spearman rho": 0.9247149302918276
 }

logs-csv/lightning_logs/version_0/hparams.yaml CHANGED Viewed

@@ -1,11 +1,11 @@
 dropout: 0.2
-ensemble_size: 10
 extra_featurizers: null
-learning_rate: 0.0001
-n_hidden: 2
 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

 dropout: 0.2
+ensemble_size: 3
 extra_featurizers: null
+learning_rate: 1.0e-05
+n_hidden: 5
 n_input: 2248
 n_out: 1
+n_units: 64
 optimizer: !!python/name:torch.optim.adam.Adam ''
 reduce_lr_on_plateau: true
 reduce_lr_patience: 10

logs-csv/lightning_logs/version_0/metrics.csv CHANGED Viewed

@@ -1,153 +1,795 @@
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