Training in progress, step 5000, checkpoint

last-checkpoint/model.safetensors

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:a608ff64b48e48b57a79452b34567acbe67a23ada467648f1a5f0c1d6bdcd248
+oid sha256:79b23d719a9479ea9fcf3c40654d6ea53701233b17f0683fa8965acd15e62f82
 size 409608164

last-checkpoint/optimizer.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:4e6cee46d5bf233e52f8dbeb5bd38c5f43127506bc7454b01ea48c9950451f9e
+oid sha256:048c5b45aa055906cac4b47f0ef566aa34a51d5e893f992a7d529f38c51dcde6
 size 814647162

last-checkpoint/rng_state.pth

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:8c6301d04d7e302f9a20d362ab718c250a725ee45dbb7a65cb9261444491d2da
+oid sha256:b675d6df31baeb7c5531251febfde5bc7d1f65613312b004af6d7e748822386d
 size 14244

last-checkpoint/scheduler.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:e48fb3aab7d48713e9e77878b87e09382b75a08326ff8fa709483f3a43dd943f
+oid sha256:e377b6698e9a077ed45bbfd7bfb6e2a8c65b85b0c50e57196e493ab84d34ff36
 size 1064

last-checkpoint/trainer_state.json

@@ -1,278 +1,124 @@
 {
-  "best_metric": 0.4196199734865223,
-  "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25/trial-number=16-learning_rate=2.7e-05-warmup_ratio=0.020-num_cycles=4.000/checkpoint-10000",
-  "epoch": 0.9863878477017163,
+  "best_metric": 0.1456473707467963,
+  "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25/trial-number=17-learning_rate=2.3e-05-warmup_ratio=0.070-num_cycles=5.500/checkpoint-5000",
+  "epoch": 0.49319392385085814,
   "eval_steps": 2500,
-  "global_step": 10000,
+  "global_step": 5000,
   "is_hyper_param_search": true,
   "is_local_process_zero": true,
   "is_world_process_zero": true,
   "log_history": [
     {
       "epoch": 0.049319392385085814,
-      "grad_norm": 1.193555474281311,
-      "learning_rate": 1.9049167867746203e-05,
-      "loss": 2.888,
+      "grad_norm": 1.2309077978134155,
+      "learning_rate": 1.66041292757749e-05,
+      "loss": 3.0087,
       "step": 500
     },
     {
       "epoch": 0.09863878477017163,
-      "grad_norm": 0.8318235278129578,
-      "learning_rate": 2.246394835598448e-05,
-      "loss": 0.5175,
+      "grad_norm": 0.763126790523529,
+      "learning_rate": 1.6680127157646984e-05,
+      "loss": 0.5683,
       "step": 1000
     },
     {
       "epoch": 0.14795817715525744,
-      "grad_norm": 0.5888204574584961,
-      "learning_rate": 5.867106147706695e-06,
-      "loss": 0.2372,
+      "grad_norm": 0.7100871801376343,
+      "learning_rate": 1.586004103408713e-07,
+      "loss": 0.2939,
       "step": 1500
     },
     {
       "epoch": 0.19727756954034326,
-      "grad_norm": 0.4154653251171112,
-      "learning_rate": 9.20011203733316e-07,
-      "loss": 0.1886,
+      "grad_norm": 0.6781579852104187,
+      "learning_rate": 1.3012154594856692e-05,
+      "loss": 0.2607,
       "step": 2000
     },
     {
       "epoch": 0.24659696192542907,
-      "grad_norm": 0.6848288178443909,
-      "learning_rate": 1.536036183614666e-05,
-      "loss": 0.177,
+      "grad_norm": 0.6720414757728577,
+      "learning_rate": 2.2258211750211904e-05,
+      "loss": 0.1925,
       "step": 2500
     },
     {
       "epoch": 0.2959163543105149,
-      "grad_norm": 0.5205318927764893,
-      "learning_rate": 2.660216000372886e-05,
-      "loss": 0.1329,
+      "grad_norm": 0.40102341771125793,
+      "learning_rate": 4.171131747579263e-06,
+      "loss": 0.1259,
       "step": 3000
     },
     {
       "epoch": 0.3452357466956007,
-      "grad_norm": 0.2795868217945099,
-      "learning_rate": 1.7062229379525045e-05,
-      "loss": 0.085,
+      "grad_norm": 0.33403462171554565,
+      "learning_rate": 5.162865531391757e-06,
+      "loss": 0.1072,
       "step": 3500
     },
     {
       "epoch": 0.3945551390806865,
-      "grad_norm": 0.3321867883205414,
-      "learning_rate": 1.6618734606935415e-06,
-      "loss": 0.0616,
+      "grad_norm": 0.44077345728874207,
+      "learning_rate": 2.2688596596301756e-05,
+      "loss": 0.0983,
       "step": 4000
     },
     {
       "epoch": 0.4438745314657723,
-      "grad_norm": 0.3245985507965088,
-      "learning_rate": 4.48862429344581e-06,
-      "loss": 0.056,
+      "grad_norm": 0.39217662811279297,
+      "learning_rate": 1.1776811003545574e-05,
+      "loss": 0.0716,
       "step": 4500
     },
     {
       "epoch": 0.49319392385085814,
-      "grad_norm": 0.37055209279060364,
-      "learning_rate": 2.1121191121292532e-05,
-      "loss": 0.0536,
+      "grad_norm": 0.33058542013168335,
+      "learning_rate": 4.274544366418573e-07,
+      "loss": 0.0557,
       "step": 5000
     },
     {
       "epoch": 0.49319392385085814,
-      "eval_all_ligands_equal": 0.11842686699072029,
-      "eval_e3_equal": 0.6632788334069819,
+      "eval_all_ligands_equal": 0.1456473707467963,
+      "eval_e3_equal": 0.6572691117984976,
       "eval_e3_graph_edit_distance": 9.999999999999999e+63,
       "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.9943437914273089,
-      "eval_e3_heavy_atoms_difference": -0.12567388422448078,
-      "eval_e3_heavy_atoms_difference_norm": -0.018177922333118175,
+      "eval_e3_has_attachment_point(s)": 0.9968183826778613,
+      "eval_e3_heavy_atoms_difference": -0.38382677861246134,
+      "eval_e3_heavy_atoms_difference_norm": -0.029623813342479082,
       "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.9943437914273089,
-      "eval_has_all_attachment_points": 0.9742819266460451,
-      "eval_has_three_substructures": 0.9975254087494476,
-      "eval_heavy_atoms_difference": 13.662571807335395,
-      "eval_heavy_atoms_difference_norm": 0.17663075672625272,
-      "eval_linker_equal": 0.22253645603181618,
+      "eval_e3_valid": 0.9968183826778613,
+      "eval_has_all_attachment_points": 0.9814405656208572,
+      "eval_has_three_substructures": 0.9990278391515687,
+      "eval_heavy_atoms_difference": 8.372691117984976,
+      "eval_heavy_atoms_difference_norm": 0.11094699556330354,
+      "eval_linker_equal": 0.2407423773751657,
       "eval_linker_graph_edit_distance": 9.999999999999999e+63,
       "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9926646045072912,
-      "eval_linker_heavy_atoms_difference": 3.407954043305347,
-      "eval_linker_heavy_atoms_difference_norm": 0.168941017421816,
+      "eval_linker_has_attachment_point(s)": 0.99584622182943,
+      "eval_linker_heavy_atoms_difference": 1.0983650022094564,
+      "eval_linker_heavy_atoms_difference_norm": 0.01812954549559559,
       "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9926646045072912,
-      "eval_loss": 0.30737200379371643,
-      "eval_num_fragments": 2.9989394608926205,
-      "eval_poi_equal": 0.560053026955369,
+      "eval_linker_valid": 0.99584622182943,
+      "eval_loss": 0.2961718440055847,
+      "eval_num_fragments": 2.999381352187362,
+      "eval_poi_equal": 0.623950508174989,
       "eval_poi_graph_edit_distance": 9.999999999999999e+63,
       "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.875740167918692,
-      "eval_poi_heavy_atoms_difference": 4.594520547945206,
-      "eval_poi_heavy_atoms_difference_norm": 0.14379318801749935,
+      "eval_poi_has_attachment_point(s)": 0.9027839151568714,
+      "eval_poi_heavy_atoms_difference": 2.9172779496243924,
+      "eval_poi_heavy_atoms_difference_norm": 0.09385926668544316,
       "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.875740167918692,
-      "eval_reassembly": 0.12152010605391074,
-      "eval_reassembly_nostereo": 0.1375165709235528,
-      "eval_runtime": 1422.6035,
-      "eval_samples_per_second": 7.954,
-      "eval_steps_per_second": 0.124,
+      "eval_poi_valid": 0.9027839151568714,
+      "eval_reassembly": 0.14794520547945206,
+      "eval_reassembly_nostereo": 0.1665046398585948,
+      "eval_runtime": 1567.3459,
+      "eval_samples_per_second": 7.219,
+      "eval_steps_per_second": 0.113,
       "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.8695536897923111,
+      "eval_valid": 0.8985417587273531,
       "step": 5000
-    },
-    {
-      "epoch": 0.542513316235944,
-      "grad_norm": 0.27302974462509155,
-      "learning_rate": 2.554475398889662e-05,
-      "loss": 0.0444,
-      "step": 5500
-    },
-    {
-      "epoch": 0.5918327086210298,
-      "grad_norm": 0.23224854469299316,
-      "learning_rate": 1.0840465507701789e-05,
-      "loss": 0.0319,
-      "step": 6000
-    },
-    {
-      "epoch": 0.6411521010061156,
-      "grad_norm": 0.23858347535133362,
-      "learning_rate": 7.146086424448981e-09,
-      "loss": 0.0252,
-      "step": 6500
-    },
-    {
-      "epoch": 0.6904714933912014,
-      "grad_norm": 0.36267736554145813,
-      "learning_rate": 9.989074812002888e-06,
-      "loss": 0.0243,
-      "step": 7000
-    },
-    {
-      "epoch": 0.7397908857762873,
-      "grad_norm": 0.31655964255332947,
-      "learning_rate": 2.517362368235566e-05,
-      "loss": 0.024,
-      "step": 7500
-    },
-    {
-      "epoch": 0.7397908857762873,
-      "eval_all_ligands_equal": 0.3515687140963323,
-      "eval_e3_equal": 0.7513035793194874,
-      "eval_e3_graph_edit_distance": 9.999999999999999e+63,
-      "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.991427308882015,
-      "eval_e3_heavy_atoms_difference": 0.1234644277507733,
-      "eval_e3_heavy_atoms_difference_norm": -0.003241441692798868,
-      "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.991427308882015,
-      "eval_has_all_attachment_points": 0.9791427308882015,
-      "eval_has_three_substructures": 0.9984091913389306,
-      "eval_heavy_atoms_difference": 8.571277065841803,
-      "eval_heavy_atoms_difference_norm": 0.11408275021017346,
-      "eval_linker_equal": 0.526646045072912,
-      "eval_linker_graph_edit_distance": 9.999999999999999e+63,
-      "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9937251436146708,
-      "eval_linker_heavy_atoms_difference": 0.15510384445426426,
-      "eval_linker_heavy_atoms_difference_norm": -0.03091358477610182,
-      "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9937251436146708,
-      "eval_loss": 0.29450246691703796,
-      "eval_num_fragments": 3.0001767565178965,
-      "eval_poi_equal": 0.6740609809986743,
-      "eval_poi_graph_edit_distance": 9.999999999999999e+63,
-      "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.8986301369863013,
-      "eval_poi_heavy_atoms_difference": 2.8806893504197966,
-      "eval_poi_heavy_atoms_difference_norm": 0.09157872702647427,
-      "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.8986301369863013,
-      "eval_reassembly": 0.35536897923110916,
-      "eval_reassembly_nostereo": 0.3800265134776845,
-      "eval_runtime": 1620.5079,
-      "eval_samples_per_second": 6.982,
-      "eval_steps_per_second": 0.109,
-      "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.8885550154661953,
-      "step": 7500
-    },
-    {
-      "epoch": 0.789110278161373,
-      "grad_norm": 0.2239069789648056,
-      "learning_rate": 2.181080214858652e-05,
-      "loss": 0.0214,
-      "step": 8000
-    },
-    {
-      "epoch": 0.8384296705464589,
-      "grad_norm": 0.19752831757068634,
-      "learning_rate": 5.160363419470711e-06,
-      "loss": 0.0154,
-      "step": 8500
-    },
-    {
-      "epoch": 0.8877490629315447,
-      "grad_norm": 0.192670539021492,
-      "learning_rate": 1.265080700050313e-06,
-      "loss": 0.0129,
-      "step": 9000
-    },
-    {
-      "epoch": 0.9370684553166305,
-      "grad_norm": 0.19295284152030945,
-      "learning_rate": 1.621752404699275e-05,
-      "loss": 0.0131,
-      "step": 9500
-    },
-    {
-      "epoch": 0.9863878477017163,
-      "grad_norm": 0.23245178163051605,
-      "learning_rate": 2.663073667910919e-05,
-      "loss": 0.0142,
-      "step": 10000
-    },
-    {
-      "epoch": 0.9863878477017163,
-      "eval_all_ligands_equal": 0.4196199734865223,
-      "eval_e3_equal": 0.7765797613787009,
-      "eval_e3_graph_edit_distance": 9.999999999999999e+63,
-      "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.9922227132125497,
-      "eval_e3_heavy_atoms_difference": 0.3922227132125497,
-      "eval_e3_heavy_atoms_difference_norm": 0.006326123786719304,
-      "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.9922227132125497,
-      "eval_has_all_attachment_points": 0.9733097657976137,
-      "eval_has_three_substructures": 0.9983208130799823,
-      "eval_heavy_atoms_difference": 9.077684489615555,
-      "eval_heavy_atoms_difference_norm": 0.12011828880330795,
-      "eval_linker_equal": 0.6334953601414052,
-      "eval_linker_graph_edit_distance": 9.999999999999999e+63,
-      "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9942554131683606,
-      "eval_linker_heavy_atoms_difference": 0.6975695978789218,
-      "eval_linker_heavy_atoms_difference_norm": 0.015551211535156739,
-      "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9942554131683606,
-      "eval_loss": 0.30925416946411133,
-      "eval_num_fragments": 3.000618647812638,
-      "eval_poi_equal": 0.6826336721166593,
-      "eval_poi_graph_edit_distance": 9.999999999999999e+63,
-      "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.9060539107379585,
-      "eval_poi_heavy_atoms_difference": 3.0226248342907645,
-      "eval_poi_heavy_atoms_difference_norm": 0.09735135794581425,
-      "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.9060539107379585,
-      "eval_reassembly": 0.4265134776844896,
-      "eval_reassembly_nostereo": 0.4486964206805126,
-      "eval_runtime": 1487.364,
-      "eval_samples_per_second": 7.607,
-      "eval_steps_per_second": 0.119,
-      "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.8972160848431285,
-      "step": 10000
     }
   ],
   "logging_steps": 500,
@@ -287,17 +133,17 @@
         "should_evaluate": false,
         "should_log": false,
         "should_save": true,
-        "should_training_stop": true
+        "should_training_stop": false
       },
       "attributes": {}
     }
   },
-  "total_flos": 8.663036348367667e+16,
+  "total_flos": 4.33139477262336e+16,
   "train_batch_size": 128,
-  "trial_name": "trial-number=16-learning_rate=2.7e-05-warmup_ratio=0.020-num_cycles=4.000",
+  "trial_name": "trial-number=17-learning_rate=2.3e-05-warmup_ratio=0.070-num_cycles=5.500",
   "trial_params": {
-    "learning_rate": 2.663073667910919e-05,
-    "num_cycles": 4.0,
-    "warmup_ratio": 0.02
+    "learning_rate": 2.321257272753331e-05,
+    "num_cycles": 5.5,
+    "warmup_ratio": 0.06999999999999999
   }
 }

last-checkpoint/training_args.bin

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:31978025e93efda8b0ad609eee57a99711e64540e52af23213d222e4dc7d2484
+oid sha256:5f210b06f27913c2673bfd7d2d682546273265dd19b3943552ec0e3bed293fbd
 size 7416