Training in progress, step 5000, checkpoint

last-checkpoint/model.safetensors

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:ea6b2a63e760eff0d45b2d57870a9cdfe6e9e18695c39d9e7e147b4c3d883ea4
+oid sha256:e29274006eeab1606993ef4f552a2e753f0dcbae8073f06ec9c3492e660fc53d
 size 409608164

last-checkpoint/optimizer.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:4d006bcf90d1175c35fa2c258bacd4ca60d14976391a619e9ba60990d64dd91e
+oid sha256:d9e4096f1400342314e0a3fe82ac765c1165fd96b2b005d60a0b76c75c5eb0dd
 size 814647162

last-checkpoint/rng_state.pth

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:e986d46d706b3fb91b88a850b06182e639890487ae4440c3df7feb76772997f1
+oid sha256:13f814284b4cdd93d98fab5cf14755225b29b2c0bb2a860806ad9a9487047bfb
 size 14244

last-checkpoint/scheduler.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:f33d61e7faf50026c6df62b1820a4e5e991131d1b2a9f07f2595d907464c4ed2
+oid sha256:d6f447d613c8f23872e44f681809793d7bb3f543c2932bfa3bd7ce8811321e46
 size 1064

last-checkpoint/trainer_state.json

@@ -1,278 +1,124 @@
 {
-  "best_metric": 0.0,
-  "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25-rand-smiles/trial-number=12-learning_rate=2.2e-06-warmup_ratio=0.050-num_cycles=10.000/checkpoint-5000",
-  "epoch": 0.9863878477017163,
+  "best_metric": 8.837825894829872e-05,
+  "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25-rand-smiles/trial-number=13-learning_rate=4.2e-06-warmup_ratio=0.100-num_cycles=6.500/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": 4.169440746307373,
-      "learning_rate": 1.5613799171014363e-06,
-      "loss": 5.9987,
+      "grad_norm": 2.3718929290771484,
+      "learning_rate": 2.989305882911821e-06,
+      "loss": 5.0812,
       "step": 500
     },
     {
       "epoch": 0.09863878477017163,
-      "grad_norm": 1.811974287033081,
-      "learning_rate": 6.043608340530767e-07,
-      "loss": 1.9745,
+      "grad_norm": 1.3658628463745117,
+      "learning_rate": 2.60466910705453e-06,
+      "loss": 1.376,
       "step": 1000
     },
     {
       "epoch": 0.14795817715525744,
-      "grad_norm": 1.5660574436187744,
-      "learning_rate": 1.7934007606188836e-06,
-      "loss": 1.4372,
+      "grad_norm": 1.4346359968185425,
+      "learning_rate": 1.4566522299079576e-07,
+      "loss": 1.0027,
       "step": 1500
     },
     {
       "epoch": 0.19727756954034326,
-      "grad_norm": 1.517979383468628,
-      "learning_rate": 2.134062284657905e-07,
-      "loss": 1.2106,
+      "grad_norm": 1.4034212827682495,
+      "learning_rate": 3.848142336404206e-06,
+      "loss": 0.9352,
       "step": 2000
     },
     {
       "epoch": 0.24659696192542907,
-      "grad_norm": 1.333193063735962,
-      "learning_rate": 2.0966891974916694e-06,
-      "loss": 1.1,
+      "grad_norm": 1.2924391031265259,
+      "learning_rate": 1.9763030136461577e-06,
+      "loss": 0.7403,
       "step": 2500
     },
     {
       "epoch": 0.2959163543105149,
-      "grad_norm": 1.3593288660049438,
-      "learning_rate": 1.4611952262523042e-08,
-      "loss": 0.9629,
+      "grad_norm": 1.2609620094299316,
+      "learning_rate": 4.633445297631418e-07,
+      "loss": 0.6443,
       "step": 3000
     },
     {
       "epoch": 0.3452357466956007,
-      "grad_norm": 1.2619653940200806,
-      "learning_rate": 2.1799591909569794e-06,
-      "loss": 0.9001,
+      "grad_norm": 1.363871693611145,
+      "learning_rate": 4.104914163179973e-06,
+      "loss": 0.6075,
       "step": 3500
     },
     {
       "epoch": 0.3945551390806865,
-      "grad_norm": 1.375174641609192,
-      "learning_rate": 5.1486486192622186e-08,
-      "loss": 0.801,
+      "grad_norm": 1.2903954982757568,
+      "learning_rate": 1.3582738363327274e-06,
+      "loss": 0.5113,
       "step": 4000
     },
     {
       "epoch": 0.4438745314657723,
-      "grad_norm": 1.445817470550537,
-      "learning_rate": 2.024986117163073e-06,
-      "loss": 0.7564,
+      "grad_norm": 1.1472790241241455,
+      "learning_rate": 9.294907338615516e-07,
+      "loss": 0.4674,
       "step": 4500
     },
     {
       "epoch": 0.49319392385085814,
-      "grad_norm": 1.337365746498108,
-      "learning_rate": 3.159594019707261e-07,
-      "loss": 0.6855,
+      "grad_norm": 1.1475571393966675,
+      "learning_rate": 4.177685109431936e-06,
+      "loss": 0.4428,
       "step": 5000
     },
     {
       "epoch": 0.49319392385085814,
-      "eval_all_ligands_equal": 0.0,
-      "eval_e3_equal": 0.037384003535130356,
+      "eval_all_ligands_equal": 8.837825894829872e-05,
+      "eval_e3_equal": 0.1028722934158197,
       "eval_e3_graph_edit_distance": 9.999999999999999e+63,
       "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.9461776403004861,
-      "eval_e3_heavy_atoms_difference": 1.7942554131683606,
-      "eval_e3_heavy_atoms_difference_norm": 0.009207668134979698,
+      "eval_e3_has_attachment_point(s)": 0.9854175872735307,
+      "eval_e3_heavy_atoms_difference": -0.5527176314626602,
+      "eval_e3_heavy_atoms_difference_norm": -0.05577837939951782,
       "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.9461776403004861,
-      "eval_has_all_attachment_points": 0.6704374723817941,
-      "eval_has_three_substructures": 0.9482103402562969,
-      "eval_heavy_atoms_difference": 64.90022094564738,
-      "eval_heavy_atoms_difference_norm": 0.8422759977934355,
-      "eval_linker_equal": 0.0007070260715863897,
+      "eval_e3_valid": 0.9854175872735307,
+      "eval_has_all_attachment_points": 0.8555015466195316,
+      "eval_has_three_substructures": 0.9873619089703933,
+      "eval_heavy_atoms_difference": 46.67167476800707,
+      "eval_heavy_atoms_difference_norm": 0.5948913274228967,
+      "eval_linker_equal": 0.0017675651789659744,
       "eval_linker_graph_edit_distance": 9.999999999999999e+63,
       "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9129474149359258,
-      "eval_linker_heavy_atoms_difference": 9.08882015024304,
-      "eval_linker_heavy_atoms_difference_norm": 0.45784852428455797,
+      "eval_linker_has_attachment_point(s)": 0.9801148917366328,
+      "eval_linker_heavy_atoms_difference": 7.120106053910738,
+      "eval_linker_heavy_atoms_difference_norm": 0.3211703879057646,
       "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9129474149359258,
-      "eval_loss": 0.7413397431373596,
-      "eval_num_fragments": 3.0321696862571805,
-      "eval_poi_equal": 8.837825894829872e-05,
+      "eval_linker_valid": 0.9801148917366328,
+      "eval_loss": 0.5266121029853821,
+      "eval_num_fragments": 2.9908970393283254,
+      "eval_poi_equal": 0.02209456473707468,
       "eval_poi_graph_edit_distance": 9.999999999999999e+63,
       "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.3013698630136986,
-      "eval_poi_heavy_atoms_difference": 26.02792752982766,
-      "eval_poi_heavy_atoms_difference_norm": 0.7980199520836797,
+      "eval_poi_has_attachment_point(s)": 0.49368095448519667,
+      "eval_poi_heavy_atoms_difference": 19.568095448519664,
+      "eval_poi_heavy_atoms_difference_norm": 0.567172306807292,
       "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.3013698630136986,
-      "eval_reassembly": 0.0,
-      "eval_reassembly_nostereo": 0.0,
-      "eval_runtime": 1500.6368,
-      "eval_samples_per_second": 7.54,
-      "eval_steps_per_second": 0.118,
-      "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.2844896155545736,
-      "step": 5000
-    },
-    {
-      "epoch": 0.542513316235944,
-      "grad_norm": 1.2575222253799438,
-      "learning_rate": 1.6656876679399406e-06,
-      "loss": 0.6502,
-      "step": 5500
-    },
-    {
-      "epoch": 0.5918327086210298,
-      "grad_norm": 1.1440157890319824,
-      "learning_rate": 7.501476710478152e-07,
-      "loss": 0.5992,
-      "step": 6000
-    },
-    {
-      "epoch": 0.6411521010061156,
-      "grad_norm": 1.0409629344940186,
-      "learning_rate": 1.1807005624117962e-06,
-      "loss": 0.5677,
-      "step": 6500
-    },
-    {
-      "epoch": 0.6904714933912014,
-      "grad_norm": 1.311508059501648,
-      "learning_rate": 1.2590240506504755e-06,
-      "loss": 0.5325,
-      "step": 7000
-    },
-    {
-      "epoch": 0.7397908857762873,
-      "grad_norm": 0.9935227632522583,
-      "learning_rate": 6.761699700853001e-07,
-      "loss": 0.5017,
-      "step": 7500
-    },
-    {
-      "epoch": 0.7397908857762873,
-      "eval_all_ligands_equal": 0.0,
-      "eval_e3_equal": 0.0827220503756076,
-      "eval_e3_graph_edit_distance": 9.999999999999999e+63,
-      "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.9852408307556341,
-      "eval_e3_heavy_atoms_difference": -0.6676977463543968,
-      "eval_e3_heavy_atoms_difference_norm": -0.06390924999730649,
-      "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.9852408307556341,
-      "eval_has_all_attachment_points": 0.8275740167918691,
-      "eval_has_three_substructures": 0.9867432611577552,
-      "eval_heavy_atoms_difference": 53.99496243923995,
-      "eval_heavy_atoms_difference_norm": 0.692721967350773,
-      "eval_linker_equal": 0.0020326999558108703,
-      "eval_linker_graph_edit_distance": 9.999999999999999e+63,
-      "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9718073353954927,
-      "eval_linker_heavy_atoms_difference": 7.161290322580645,
-      "eval_linker_heavy_atoms_difference_norm": 0.31956488397760113,
-      "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9718073353954927,
-      "eval_loss": 0.5782048106193542,
-      "eval_num_fragments": 3.0007070260715865,
-      "eval_poi_equal": 0.011489173663278833,
-      "eval_poi_graph_edit_distance": 9.999999999999999e+63,
-      "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.3986743261157755,
-      "eval_poi_heavy_atoms_difference": 22.559699513919576,
-      "eval_poi_heavy_atoms_difference_norm": 0.672502934449603,
-      "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.3986743261157755,
-      "eval_reassembly": 0.0,
-      "eval_reassembly_nostereo": 0.0,
-      "eval_runtime": 1422.689,
-      "eval_samples_per_second": 7.953,
+      "eval_poi_valid": 0.49368095448519667,
+      "eval_reassembly": 8.837825894829872e-05,
+      "eval_reassembly_nostereo": 8.837825894829872e-05,
+      "eval_runtime": 1422.3857,
+      "eval_samples_per_second": 7.955,
       "eval_steps_per_second": 0.124,
       "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.3926646045072912,
-      "step": 7500
-    },
-    {
-      "epoch": 0.789110278161373,
-      "grad_norm": 1.2995916604995728,
-      "learning_rate": 1.7312149208305083e-06,
-      "loss": 0.4783,
-      "step": 8000
-    },
-    {
-      "epoch": 0.8384296705464589,
-      "grad_norm": 1.1670758724212646,
-      "learning_rate": 2.625183839161817e-07,
-      "loss": 0.4483,
-      "step": 8500
-    },
-    {
-      "epoch": 0.8877490629315447,
-      "grad_norm": 1.0538517236709595,
-      "learning_rate": 2.0633757196738724e-06,
-      "loss": 0.4319,
-      "step": 9000
-    },
-    {
-      "epoch": 0.9370684553166305,
-      "grad_norm": 1.168967843055725,
-      "learning_rate": 3.027835050239297e-08,
-      "loss": 0.4054,
-      "step": 9500
-    },
-    {
-      "epoch": 0.9863878477017163,
-      "grad_norm": 0.8473185300827026,
-      "learning_rate": 2.182809124107808e-06,
-      "loss": 0.3918,
-      "step": 10000
-    },
-    {
-      "epoch": 0.9863878477017163,
-      "eval_all_ligands_equal": 0.0,
-      "eval_e3_equal": 0.11321254971277066,
-      "eval_e3_graph_edit_distance": 9.999999999999999e+63,
-      "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.9885992045956694,
-      "eval_e3_heavy_atoms_difference": -1.165090587715422,
-      "eval_e3_heavy_atoms_difference_norm": -0.0760775265425178,
-      "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.9885992045956694,
-      "eval_has_all_attachment_points": 0.8649580203269995,
-      "eval_has_three_substructures": 0.9895713654441007,
-      "eval_heavy_atoms_difference": 42.39593460008838,
-      "eval_heavy_atoms_difference_norm": 0.5396815683959801,
-      "eval_linker_equal": 0.0021210782147591694,
-      "eval_linker_graph_edit_distance": 9.999999999999999e+63,
-      "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9826778612461334,
-      "eval_linker_heavy_atoms_difference": 6.7108263367211665,
-      "eval_linker_heavy_atoms_difference_norm": 0.2914348823794422,
-      "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9826778612461334,
-      "eval_loss": 0.5012893080711365,
-      "eval_num_fragments": 2.996818382677861,
-      "eval_poi_equal": 0.03049049933716306,
-      "eval_poi_graph_edit_distance": 9.999999999999999e+63,
-      "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.5458241272646929,
-      "eval_poi_heavy_atoms_difference": 18.0181175430844,
-      "eval_poi_heavy_atoms_difference_norm": 0.519674391987532,
-      "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.5458241272646929,
-      "eval_reassembly": 0.0,
-      "eval_reassembly_nostereo": 0.0,
-      "eval_runtime": 1411.5279,
-      "eval_samples_per_second": 8.016,
-      "eval_steps_per_second": 0.125,
-      "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.5427308882015024,
-      "step": 10000
+      "eval_valid": 0.4899690676093681,
+      "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": 8.729673191023411e+16,
+  "total_flos": 4.364959997072179e+16,
   "train_batch_size": 128,
-  "trial_name": "trial-number=12-learning_rate=2.2e-06-warmup_ratio=0.050-num_cycles=10.000",
+  "trial_name": "trial-number=13-learning_rate=4.2e-06-warmup_ratio=0.100-num_cycles=6.500",
   "trial_params": {
-    "learning_rate": 2.182809124107808e-06,
-    "num_cycles": 10.0,
-    "warmup_ratio": 0.05
+    "learning_rate": 4.179049624310726e-06,
+    "num_cycles": 6.5,
+    "warmup_ratio": 0.09999999999999999
   }
 }

last-checkpoint/training_args.bin

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:5ab795fe306a3df71aedd0af760cbeb1cc92edd3774292b1be2346e1f0dde464
+oid sha256:819a2ebf29508b71d8eace90a1047d07f6b339e1026de9ca7ae90f3b7aa1b43e
 size 7480