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README.md +15 -15
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 +1 -1
logs-csv/lightning_logs/version_0/metrics.csv +1208 -946
logs/lightning_logs/version_0/events.out.tfevents.1743272414.cn079.1584376.0 +3 -0
logs/lightning_logs/version_0/hparams.yaml +1 -1
metrics.csv +3 -3
modelbox-config.json +1 -1
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-3beaa410b9731cb0.arrow +3 -0
training-log.csv +604 -473
training-log.png +0 -0

README.md CHANGED Viewed

@@ -12,7 +12,7 @@ datasets:
 # Predictor of _Brucella abortus_ MICs
-_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_).
@@ -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
@@ -41,7 +41,7 @@ by Spearman's $\rho$ on a held-out test set not used in training or early stoppi
     "learning_rate": 1e-05,
     "model_class": "FPMLPModelBox",
     "n_hidden": 3,
-    "n_units": 16,
     "use_2d": true,
     "use_fp": true
 }
@@ -79,39 +79,39 @@ Train (6963 rows):
 ```json
 {
-    "Pearson r": 0.5300446208555996,
-    "RMSE": 0.061959341168403625,
-    "Spearman rho": 0.9393133689615363
 }
 ```
-<img src="predictions-train.png" width=450>
 Validation (1491 rows):
 ```json
 {
-    "Pearson r": 0.4176124412909827,
-    "RMSE": 0.07129787653684616,
-    "Spearman rho": 0.8889606877623673
 }
 ```
-<img src="predictions-validation.png" width=450>
 Test (1492 rows):
 ```json
 {
-    "Pearson r": 0.47702787899824634,
-    "RMSE": 0.08465012907981873,
-    "Spearman rho": 0.9295617687262676
 }
 ```
-<img src="predictions-test.png" width=450>
 ## Training data details

 # Predictor of _Brucella abortus_ MICs
+_Updated:_ Tue  1 Apr 08:02:42 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_).
 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
     "learning_rate": 1e-05,
     "model_class": "FPMLPModelBox",
     "n_hidden": 3,
+    "n_units": 8,
     "use_2d": true,
     "use_fp": true
 }
 ```json
 {
+    "Pearson r": 0.5973702762367811,
+    "RMSE": 0.06257937848567963,
+    "Spearman rho": 0.9137795379778116
 }
 ```
+<img src="predictions_train.png" width=450>
 Validation (1491 rows):
 ```json
 {
+    "Pearson r": 0.4262736927741126,
+    "RMSE": 0.07030162960290909,
+    "Spearman rho": 0.8603014671412592
 }
 ```
+<img src="predictions_validation.png" width=450>
 Test (1492 rows):
 ```json
 {
+    "Pearson r": 0.49197152542126255,
+    "RMSE": 0.07745077461004257,
+    "Spearman rho": 0.9107798729695116
 }
 ```
+<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/Brucella-abortus/107/cache",
     "features": [
         "smiles"
     ],

 {
+    "cache": "/nemo/lab/johnsone/home/users/johnsoe/projects/abx-discovery-strategy/models/spark-dv-2503/Brucella-abortus/105/cache",
     "features": [
         "smiles"
     ],

eval-metrics_test.json CHANGED Viewed

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

 {
+    "Pearson r": 0.49197152542126255,
+    "RMSE": 0.07745077461004257,
+    "Spearman rho": 0.9107798729695116
 }

eval-metrics_train.json CHANGED Viewed

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

 {
+    "Pearson r": 0.5973702762367811,
+    "RMSE": 0.06257937848567963,
+    "Spearman rho": 0.9137795379778116
 }

eval-metrics_validation.json CHANGED Viewed

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

 {
+    "Pearson r": 0.4262736927741126,
+    "RMSE": 0.07030162960290909,
+    "Spearman rho": 0.8603014671412592
 }

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

@@ -5,7 +5,7 @@ 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

 n_hidden: 3
 n_input: 2248
 n_out: 1
+n_units: 8
 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

@@ -1,947 +1,1209 @@
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-471,9.99999993922529e-09,,205791,0.02770700678229332
-471,,0.1632053554058075,205791,
-472,9.99999993922529e-09,,206227,0.027706747874617577
-472,,0.15813755989074707,206227,

 epoch,learning_rate,loss,step,val_loss
+0,9.999999747378752e-06,,435,12.347195625305176
+0,,12.610589027404785,435,
+1,9.999999747378752e-06,,871,11.497300148010254
+1,,11.905877113342285,871,
+2,9.999999747378752e-06,,1307,10.408920288085938
+2,,10.953329086303711,1307,
+3,9.999999747378752e-06,,1743,9.28686237335205
+3,,9.897092819213867,1743,
+4,9.999999747378752e-06,,2179,8.184453010559082
+4,,8.880269050598145,2179,
+5,9.999999747378752e-06,,2615,7.135085105895996
+5,,7.982394218444824,2615,
+6,9.999999747378752e-06,,3051,6.133330821990967
+6,,7.118121147155762,3051,
+7,9.999999747378752e-06,,3487,5.205652236938477
+7,,6.37354040145874,3487,
+8,9.999999747378752e-06,,3923,4.360170841217041
+8,,5.709118843078613,3923,
+9,9.999999747378752e-06,,4359,3.614255905151367
+9,,5.1076812744140625,4359,
+10,9.999999747378752e-06,,4795,2.987230062484741
+10,,4.694294452667236,4795,
+11,9.999999747378752e-06,,5231,2.4890003204345703
+11,,4.328239440917969,5231,
+12,9.999999747378752e-06,,5667,2.0940651893615723
+12,,4.007627487182617,5667,
+13,9.999999747378752e-06,,6103,1.7913615703582764
+13,,3.7759432792663574,6103,
+14,9.999999747378752e-06,,6539,1.5509934425354004
+14,,3.6078121662139893,6539,
+15,9.999999747378752e-06,,6975,1.377376675605774
+15,,3.477191686630249,6975,
+16,9.999999747378752e-06,,7411,1.2540456056594849
+16,,3.310960292816162,7411,
+17,9.999999747378752e-06,,7847,1.1474069356918335
+17,,3.2718238830566406,7847,
+18,9.999999747378752e-06,,8283,1.12093985080719
+18,,3.1689796447753906,8283,
+19,9.999999747378752e-06,,8719,1.0902674198150635
+19,,3.16182804107666,8719,
+20,9.999999747378752e-06,,9155,1.0632402896881104
+20,,3.0953707695007324,9155,
+21,9.999999747378752e-06,,9591,1.0463600158691406
+21,,3.105722188949585,9591,
+22,9.999999747378752e-06,,10027,1.044459342956543
+22,,2.9950764179229736,10027,
+23,9.999999747378752e-06,,10463,1.043411374092102
+23,,2.9842851161956787,10463,
+24,9.999999747378752e-06,,10899,1.0425113439559937
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+25,9.999999747378752e-06,,11335,1.0228697061538696
+25,,2.926400899887085,11335,
+26,9.999999747378752e-06,,11771,1.0265470743179321
+26,,2.8285772800445557,11771,
+27,9.999999747378752e-06,,12207,0.9881733655929565
+27,,2.870560884475708,12207,
+28,9.999999747378752e-06,,12643,0.9908373951911926
+28,,2.8197290897369385,12643,
+29,9.999999747378752e-06,,13079,0.9994473457336426
+29,,2.7508058547973633,13079,
+30,9.999999747378752e-06,,13515,0.9872985482215881
+30,,2.6895697116851807,13515,
+31,9.999999747378752e-06,,13951,0.9874602556228638
+31,,2.675969123840332,13951,
+32,9.999999747378752e-06,,14387,0.9863139390945435
+32,,2.658156394958496,14387,
+33,9.999999747378752e-06,,14823,0.9865542650222778
+33,,2.594906806945801,14823,
+34,9.999999747378752e-06,,15259,0.9714711904525757
+34,,2.5043811798095703,15259,
+35,9.999999747378752e-06,,15695,0.9685059189796448
+35,,2.483637809753418,15695,
+36,9.999999747378752e-06,,16131,0.9707127213478088
+36,,2.4054627418518066,16131,
+37,9.999999747378752e-06,,16567,0.969765305519104
+37,,2.3491575717926025,16567,
+38,9.999999747378752e-06,,17003,0.9744179248809814
+38,,2.2994778156280518,17003,
+39,9.999999747378752e-06,,17439,0.954206109046936
+39,,2.253469228744507,17439,
+40,9.999999747378752e-06,,17875,0.9598492383956909
+40,,2.1906681060791016,17875,
+41,9.999999747378752e-06,,18311,0.941983163356781
+41,,2.1466591358184814,18311,
+42,9.999999747378752e-06,,18747,0.9558475017547607
+42,,2.0937583446502686,18747,
+43,9.999999747378752e-06,,19183,0.9432112574577332
+43,,2.042900323867798,19183,
+44,9.999999747378752e-06,,19619,0.9168140292167664
+44,,2.0295207500457764,19619,
+45,9.999999747378752e-06,,20055,0.9057791829109192
+45,,1.9492710828781128,20055,
+46,9.999999747378752e-06,,20491,0.8864799737930298
+46,,1.947975754737854,20491,
+47,9.999999747378752e-06,,20927,0.8704744577407837
+47,,1.9288501739501953,20927,
+48,9.999999747378752e-06,,21363,0.8524640798568726
+48,,1.8628989458084106,21363,
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+53,,1.7118741273880005,23543,
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+55,9.999999747378752e-06,,24415,0.8205669522285461
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+56,9.999999747378752e-06,,24851,0.8181902170181274
+56,,1.6603578329086304,24851,
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+57,,1.657749056816101,25287,
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+58,,1.6273260116577148,25723,
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+59,,1.5864617824554443,26159,
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+60,,1.5745919942855835,26595,
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+61,,1.5481845140457153,27031,
+62,9.999999747378752e-06,,27467,0.7787193059921265
+62,,1.533064365386963,27467,
+63,9.999999747378752e-06,,27903,0.7615450620651245
+63,,1.5285077095031738,27903,
+64,9.999999747378752e-06,,28339,0.7560862302780151
+64,,1.5362216234207153,28339,
+65,9.999999747378752e-06,,28775,0.7480394244194031
+65,,1.4711854457855225,28775,
+66,9.999999747378752e-06,,29211,0.7197772860527039
+66,,1.509401559829712,29211,
+67,9.999999747378752e-06,,29647,0.7148717641830444
+67,,1.464417815208435,29647,
+68,9.999999747378752e-06,,30083,0.7201829552650452
+68,,1.4654011726379395,30083,
+69,9.999999747378752e-06,,30519,0.6977061033248901
+69,,1.44647216796875,30519,
+70,9.999999747378752e-06,,30955,0.706938624382019
+70,,1.441315770149231,30955,
+71,9.999999747378752e-06,,31391,0.693871259689331
+71,,1.3945173025131226,31391,
+72,9.999999747378752e-06,,31827,0.6893923282623291
+72,,1.4102041721343994,31827,
+73,9.999999747378752e-06,,32263,0.6832123398780823
+73,,1.3481693267822266,32263,
+74,9.999999747378752e-06,,32699,0.6770223379135132
+74,,1.383002758026123,32699,
+75,9.999999747378752e-06,,33135,0.6723833084106445
+75,,1.3444722890853882,33135,
+76,9.999999747378752e-06,,33571,0.6630107760429382
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+77,,1.2902066707611084,34007,
+78,9.999999747378752e-06,,34443,0.6463503837585449
+78,,1.3141063451766968,34443,
+79,9.999999747378752e-06,,34879,0.6398874521255493
+79,,1.3067352771759033,34879,
+80,9.999999747378752e-06,,35315,0.6314529180526733
+80,,1.292785882949829,35315,
+81,9.999999747378752e-06,,35751,0.63086998462677
+81,,1.2664560079574585,35751,
+82,9.999999747378752e-06,,36187,0.6311241984367371
+82,,1.2600841522216797,36187,
+83,9.999999747378752e-06,,36623,0.61506587266922
+83,,1.2331231832504272,36623,
+84,9.999999747378752e-06,,37059,0.6155656576156616
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+86,9.999999747378752e-06,,37931,0.5980408191680908
+86,,1.2175074815750122,37931,
+87,9.999999747378752e-06,,38367,0.5873793363571167
+87,,1.194711685180664,38367,
+88,9.999999747378752e-06,,38803,0.5889610648155212
+88,,1.2069380283355713,38803,
+89,9.999999747378752e-06,,39239,0.5733702778816223
+89,,1.1841886043548584,39239,
+90,9.999999747378752e-06,,39675,0.5708132982254028
+90,,1.184841275215149,39675,
+91,9.999999747378752e-06,,40111,0.5667516589164734
+91,,1.1692787408828735,40111,
+92,9.999999747378752e-06,,40547,0.5660102367401123
+92,,1.1503732204437256,40547,
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+94,9.999999747378752e-06,,41419,0.5462523102760315
+94,,1.1226993799209595,41419,
+95,9.999999747378752e-06,,41855,0.5522202253341675
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+98,9.999999747378752e-06,,43163,0.5273721814155579
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