Training in progress, step 5000, checkpoint

last-checkpoint/model.safetensors

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:202104ca90530136dfc5aef3237a8901b67dce6869361dd5d21d130b52994ac1
+oid sha256:27f6f4f2bbcc25fced32c145d81d2403c34d850732d32887a72c1e5cbec02d00
 size 409608164

last-checkpoint/optimizer.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:114101a5ddc6891c4601f118e87976be352560a67e97a74693426ba9727b4e08
+oid sha256:4209b0b9f5deb94ebcf2d92380854c7b631b78404032a5f9332476dfd3d62928
 size 814647162

last-checkpoint/rng_state.pth

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:6d5779b4da1851197cd223f16f614513c70e93f55b710ad47bb6715660cc7b5b
+oid sha256:f56acc8237f33fb7dff2700ce08cc1a1c560666fed07a4192cd682ef5a3c9735
 size 14244

last-checkpoint/scheduler.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:5511dcbb9a364a939bde989e72b2a89b3f896c5bd5c3963fdc057930fd1cbe11
+oid sha256:1541450396138caeedee3557bc5a92a3c638e0b1ec06897e392fc790dab54e7c
 size 1064

last-checkpoint/trainer_state.json

@@ -1,278 +1,124 @@
 {
-  "best_metric": 0.5377817057003977,
-  "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine_restarts-opt25/trial-number=19-learning_rate=4.1e-05-warmup_ratio=0.100-num_cycles=10/checkpoint-10000",
-  "epoch": 0.9863878477017163,
+  "best_metric": 0.0002651347768448962,
+  "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine_restarts-opt25/trial-number=20-learning_rate=4.8e-06-warmup_ratio=0.030-num_cycles=3/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": 0.8329582214355469,
-      "learning_rate": 2.6272899690440636e-05,
-      "loss": 1.4846,
+      "grad_norm": 1.2071019411087036,
+      "learning_rate": 4.590678320024106e-06,
+      "loss": 3.0023,
       "step": 500
     },
     {
       "epoch": 0.09863878477017163,
-      "grad_norm": 0.6239127516746521,
-      "learning_rate": 8.2058780263589e-07,
-      "loss": 0.2772,
+      "grad_norm": 1.287561297416687,
+      "learning_rate": 3.939566284998207e-06,
+      "loss": 1.0049,
       "step": 1000
     },
     {
       "epoch": 0.14795817715525744,
-      "grad_norm": 0.5382785201072693,
-      "learning_rate": 2.5656115903974315e-05,
-      "loss": 0.1826,
+      "grad_norm": 1.2610366344451904,
+      "learning_rate": 2.9418513225048075e-06,
+      "loss": 0.7362,
       "step": 1500
     },
     {
       "epoch": 0.19727756954034326,
-      "grad_norm": 0.2955359220504761,
-      "learning_rate": 6.49292407753829e-07,
-      "loss": 0.0981,
+      "grad_norm": 1.1877018213272095,
+      "learning_rate": 1.819354504895605e-06,
+      "loss": 0.6063,
       "step": 2000
     },
     {
       "epoch": 0.24659696192542907,
-      "grad_norm": 0.30408775806427,
-      "learning_rate": 2.503389658442746e-05,
-      "loss": 0.076,
+      "grad_norm": 1.1616626977920532,
+      "learning_rate": 8.216395424022051e-07,
+      "loss": 0.5432,
       "step": 2500
     },
     {
       "epoch": 0.2959163543105149,
-      "grad_norm": 0.2571639120578766,
-      "learning_rate": 4.977412313142637e-07,
-      "loss": 0.0476,
+      "grad_norm": 1.152053952217102,
+      "learning_rate": 1.7052750737630594e-07,
+      "loss": 0.5186,
       "step": 3000
     },
     {
       "epoch": 0.3452357466956007,
-      "grad_norm": 0.22943373024463654,
-      "learning_rate": 2.4406868253911588e-05,
-      "loss": 0.041,
+      "grad_norm": 1.2023582458496094,
+      "learning_rate": 4.750426273084437e-06,
+      "loss": 0.5091,
       "step": 3500
     },
     {
       "epoch": 0.3945551390806865,
-      "grad_norm": 0.23392128944396973,
-      "learning_rate": 3.6608687250542647e-07,
-      "loss": 0.0277,
+      "grad_norm": 1.0854672193527222,
+      "learning_rate": 4.383293525118708e-06,
+      "loss": 0.4401,
       "step": 4000
     },
     {
       "epoch": 0.4438745314657723,
-      "grad_norm": 0.22501622140407562,
-      "learning_rate": 2.3775662276804576e-05,
-      "loss": 0.0263,
+      "grad_norm": 0.9762827754020691,
+      "learning_rate": 3.5709043705503096e-06,
+      "loss": 0.3614,
       "step": 4500
     },
     {
       "epoch": 0.49319392385085814,
-      "grad_norm": 0.1803915649652481,
-      "learning_rate": 2.5446189610677646e-07,
-      "loss": 0.018,
+      "grad_norm": 0.9475187659263611,
+      "learning_rate": 2.493876561149645e-06,
+      "loss": 0.315,
       "step": 5000
     },
     {
       "epoch": 0.49319392385085814,
-      "eval_all_ligands_equal": 0.43305346884666374,
-      "eval_e3_equal": 0.7778170570039771,
+      "eval_all_ligands_equal": 0.0002651347768448962,
+      "eval_e3_equal": 0.15413168360583296,
       "eval_e3_graph_edit_distance": 9.999999999999999e+63,
       "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.993194874060981,
-      "eval_e3_heavy_atoms_difference": 0.3430844012372956,
-      "eval_e3_heavy_atoms_difference_norm": 0.00442941141209005,
+      "eval_e3_has_attachment_point(s)": 0.9907202828104287,
+      "eval_e3_heavy_atoms_difference": -1.2811312417145382,
+      "eval_e3_heavy_atoms_difference_norm": -0.07662792095249521,
       "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.993194874060981,
-      "eval_has_all_attachment_points": 0.9850640742377376,
-      "eval_has_three_substructures": 0.9992045956694653,
-      "eval_heavy_atoms_difference": 7.4964206805125935,
-      "eval_heavy_atoms_difference_norm": 0.10013163805754127,
-      "eval_linker_equal": 0.6146707909854175,
+      "eval_e3_valid": 0.9907202828104287,
+      "eval_has_all_attachment_points": 0.9022536456031817,
+      "eval_has_three_substructures": 0.9922227132125497,
+      "eval_heavy_atoms_difference": 36.821917808219176,
+      "eval_heavy_atoms_difference_norm": 0.47177577931401626,
+      "eval_linker_equal": 0.003358373840035351,
       "eval_linker_graph_edit_distance": 9.999999999999999e+63,
       "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9961997348652232,
-      "eval_linker_heavy_atoms_difference": 0.447635881573133,
-      "eval_linker_heavy_atoms_difference_norm": -0.0017176987217232774,
+      "eval_linker_has_attachment_point(s)": 0.9817057003977022,
+      "eval_linker_heavy_atoms_difference": 6.612549712770658,
+      "eval_linker_heavy_atoms_difference_norm": 0.29674862948885594,
       "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9961997348652232,
-      "eval_loss": 0.2785375118255615,
-      "eval_num_fragments": 3.0007954043305345,
-      "eval_poi_equal": 0.7222271321254972,
+      "eval_linker_valid": 0.9817057003977022,
+      "eval_loss": 0.4423964321613312,
+      "eval_num_fragments": 2.995934600088378,
+      "eval_poi_equal": 0.07680070702607159,
       "eval_poi_graph_edit_distance": 9.999999999999999e+63,
       "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.9169244365885992,
-      "eval_poi_heavy_atoms_difference": 2.4507291206363235,
-      "eval_poi_heavy_atoms_difference_norm": 0.07988863070947928,
+      "eval_poi_has_attachment_point(s)": 0.6076005302695537,
+      "eval_poi_heavy_atoms_difference": 14.84100751215201,
+      "eval_poi_heavy_atoms_difference_norm": 0.4345841106935927,
       "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.9169244365885992,
-      "eval_reassembly": 0.4402121078214759,
-      "eval_reassembly_nostereo": 0.46425099425541316,
-      "eval_runtime": 1542.5148,
-      "eval_samples_per_second": 7.335,
-      "eval_steps_per_second": 0.115,
-      "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.9092355280600972,
-      "step": 5000
-    },
-    {
-      "epoch": 0.542513316235944,
-      "grad_norm": 0.20737028121948242,
-      "learning_rate": 2.3140914224020417e-05,
-      "loss": 0.0186,
-      "step": 5500
-    },
-    {
-      "epoch": 0.5918327086210298,
-      "grad_norm": 0.15458911657333374,
-      "learning_rate": 1.6297869900751245e-07,
-      "loss": 0.0124,
-      "step": 6000
-    },
-    {
-      "epoch": 0.6411521010061156,
-      "grad_norm": 0.14841268956661224,
-      "learning_rate": 2.2503263233042807e-05,
-      "loss": 0.0138,
-      "step": 6500
-    },
-    {
-      "epoch": 0.6904714933912014,
-      "grad_norm": 0.12427664548158646,
-      "learning_rate": 9.17293970323937e-08,
-      "loss": 0.0091,
-      "step": 7000
-    },
-    {
-      "epoch": 0.7397908857762873,
-      "grad_norm": 0.1593613624572754,
-      "learning_rate": 2.1863351364368523e-05,
-      "loss": 0.0106,
-      "step": 7500
-    },
-    {
-      "epoch": 0.7397908857762873,
-      "eval_all_ligands_equal": 0.4937693327441449,
-      "eval_e3_equal": 0.7898365002209456,
-      "eval_e3_graph_edit_distance": 9.999999999999999e+63,
-      "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.9818824569155987,
-      "eval_e3_heavy_atoms_difference": 0.7626159964648697,
-      "eval_e3_heavy_atoms_difference_norm": 0.01952838555738377,
-      "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.9818824569155987,
-      "eval_has_all_attachment_points": 0.9794078656650465,
-      "eval_has_three_substructures": 0.9978789217852408,
-      "eval_heavy_atoms_difference": 8.318780380026514,
-      "eval_heavy_atoms_difference_norm": 0.11057632558865749,
-      "eval_linker_equal": 0.7052585064074238,
-      "eval_linker_graph_edit_distance": 9.999999999999999e+63,
-      "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9941670349094123,
-      "eval_linker_heavy_atoms_difference": 0.4478126380910296,
-      "eval_linker_heavy_atoms_difference_norm": 0.004455464636486706,
-      "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9941670349094123,
-      "eval_loss": 0.2852873206138611,
-      "eval_num_fragments": 3.001414052143173,
-      "eval_poi_equal": 0.7374281926646045,
-      "eval_poi_graph_edit_distance": 9.999999999999999e+63,
-      "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.9178965974370304,
-      "eval_poi_heavy_atoms_difference": 2.421210782147592,
-      "eval_poi_heavy_atoms_difference_norm": 0.07977257687171646,
-      "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.9178965974370304,
-      "eval_reassembly": 0.5018117543084402,
-      "eval_reassembly_nostereo": 0.5254971277065842,
-      "eval_runtime": 1500.952,
-      "eval_samples_per_second": 7.539,
+      "eval_poi_valid": 0.6076005302695537,
+      "eval_reassembly": 0.0002651347768448962,
+      "eval_reassembly_nostereo": 0.0002651347768448962,
+      "eval_runtime": 1495.3687,
+      "eval_samples_per_second": 7.567,
       "eval_steps_per_second": 0.118,
       "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.8995139195757843,
-      "step": 7500
-    },
-    {
-      "epoch": 0.789110278161373,
-      "grad_norm": 0.15298856794834137,
-      "learning_rate": 4.078573218899062e-08,
-      "loss": 0.0069,
-      "step": 8000
-    },
-    {
-      "epoch": 0.8384296705464589,
-      "grad_norm": 0.13901959359645844,
-      "learning_rate": 2.1221822955006206e-05,
-      "loss": 0.0094,
-      "step": 8500
-    },
-    {
-      "epoch": 0.8877490629315447,
-      "grad_norm": 0.13829457759857178,
-      "learning_rate": 1.0199000429473975e-08,
-      "loss": 0.0055,
-      "step": 9000
-    },
-    {
-      "epoch": 0.9370684553166305,
-      "grad_norm": 0.1309487521648407,
-      "learning_rate": 2.0579323969683986e-05,
-      "loss": 0.0073,
-      "step": 9500
-    },
-    {
-      "epoch": 0.9863878477017163,
-      "grad_norm": 0.12091012299060822,
-      "learning_rate": 0.0,
-      "loss": 0.0045,
-      "step": 10000
-    },
-    {
-      "epoch": 0.9863878477017163,
-      "eval_all_ligands_equal": 0.5377817057003977,
-      "eval_e3_equal": 0.8026513477684489,
-      "eval_e3_graph_edit_distance": 9.999999999999999e+63,
-      "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.9797613787008396,
-      "eval_e3_heavy_atoms_difference": 0.7304463102076889,
-      "eval_e3_heavy_atoms_difference_norm": 0.01900045264389891,
-      "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.9797613787008396,
-      "eval_has_all_attachment_points": 0.9812638091029606,
-      "eval_has_three_substructures": 0.9984975695978789,
-      "eval_heavy_atoms_difference": 7.356252761820592,
-      "eval_heavy_atoms_difference_norm": 0.0992063786357022,
-      "eval_linker_equal": 0.7575784357048166,
-      "eval_linker_graph_edit_distance": 9.999999999999999e+63,
-      "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9953159522757402,
-      "eval_linker_heavy_atoms_difference": 0.33398144056562085,
-      "eval_linker_heavy_atoms_difference_norm": 0.000855128969353191,
-      "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9953159522757402,
-      "eval_loss": 0.29665082693099976,
-      "eval_num_fragments": 3.000265134776845,
-      "eval_poi_equal": 0.7650022094564737,
-      "eval_poi_graph_edit_distance": 9.999999999999999e+63,
-      "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.9282368537339815,
-      "eval_poi_heavy_atoms_difference": 2.0986301369863014,
-      "eval_poi_heavy_atoms_difference_norm": 0.0700343135603784,
-      "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.9282368537339815,
-      "eval_reassembly": 0.5460892620415377,
-      "eval_reassembly_nostereo": 0.5688908528501988,
-      "eval_runtime": 1498.7882,
-      "eval_samples_per_second": 7.549,
-      "eval_steps_per_second": 0.118,
-      "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.907998232434821,
-      "step": 10000
+      "eval_valid": 0.6027397260273972,
+      "step": 5000
     }
   ],
   "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=19-learning_rate=4.1e-05-warmup_ratio=0.100-num_cycles=10",
+  "trial_name": "trial-number=20-learning_rate=4.8e-06-warmup_ratio=0.030-num_cycles=3",
   "trial_params": {
-    "learning_rate": 4.051582532010182e-05,
-    "num_cycles": 10,
-    "warmup_ratio": 0.09999999999999999
+    "learning_rate": 4.7612058274004114e-06,
+    "num_cycles": 3,
+    "warmup_ratio": 0.03
   }
 }

last-checkpoint/training_args.bin

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:30c24aa130bb589f26c14c76ff3e1402a059dbf6cb4c501dd80b4d1553ff8b07
+oid sha256:0f8057f0c2567833fc528c645484091b445fc667ccf97f1a0356c8ff90208876
 size 7480