Training in progress, step 5000, checkpoint

last-checkpoint/model.safetensors

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:95a1e4676557631a08fbea97e286406398a14c1af940a0fd48c328d0cce155f6
+oid sha256:d1bd963d1d2d6a4bcc2a519ccc41848637566544708ba4a8ab620b971086a57f
 size 409608164

last-checkpoint/optimizer.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:4b77c467ed9e190a97774d0e80cea3bc2ceb7238651e85ac65934510d4b88bbc
+oid sha256:6335b8b7868e18edacf471f175ad6a3fef4821ab4663c0c5498d7737dccd3bf6
 size 814647162

last-checkpoint/rng_state.pth

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:b85cd0360d9408a97f595f91b2c2654542a0ab2fe6f214339ae57f297c8e0f4e
+oid sha256:6321b28776ea595b8599b17e72159564c71de2017e660a9954ebb3d3459bc116
 size 14244

last-checkpoint/scheduler.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:89b7730f1bd274eb55646d3cd6eb24e3e89d0753098d21c1629934f850c0c956
+oid sha256:824023b4360ec800e280087115891b2c6432c86d39bc7c6ff8bc6877e138e5ed
 size 1192

last-checkpoint/trainer_state.json

@@ -1,278 +1,124 @@
 {
-  "best_metric": 0.5623508616880247,
-  "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25/trial-number=3-learning_rate=1.1e-04-warmup_ratio=0.050-min_lr=0.000-factor=0.850/checkpoint-10000",
-  "epoch": 0.9863878477017163,
+  "best_metric": 0.1314184710561202,
+  "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25/trial-number=4-learning_rate=1.1e-05-warmup_ratio=0.030-min_lr=0.000-factor=0.940/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": 0.4528912305831909,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.7509,
+      "grad_norm": 1.135282278060913,
+      "learning_rate": 1.0718650414525622e-05,
+      "loss": 1.7205,
       "step": 500
     },
     {
       "epoch": 0.09863878477017163,
-      "grad_norm": 0.36168304085731506,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0993,
+      "grad_norm": 0.9048516750335693,
+      "learning_rate": 1.0718650414525622e-05,
+      "loss": 0.5893,
       "step": 1000
     },
     {
       "epoch": 0.14795817715525744,
-      "grad_norm": 0.21691548824310303,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0324,
+      "grad_norm": 0.8448904156684875,
+      "learning_rate": 1.0718650414525622e-05,
+      "loss": 0.3625,
       "step": 1500
     },
     {
       "epoch": 0.19727756954034326,
-      "grad_norm": 0.14681176841259003,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0176,
+      "grad_norm": 0.67970210313797,
+      "learning_rate": 1.0718650414525622e-05,
+      "loss": 0.2509,
       "step": 2000
     },
     {
       "epoch": 0.24659696192542907,
-      "grad_norm": 0.1438729166984558,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0119,
+      "grad_norm": 0.7555980682373047,
+      "learning_rate": 1.0718650414525622e-05,
+      "loss": 0.1866,
       "step": 2500
     },
     {
       "epoch": 0.2959163543105149,
-      "grad_norm": 0.11427587270736694,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.009,
+      "grad_norm": 0.5226275324821472,
+      "learning_rate": 1.0718650414525622e-05,
+      "loss": 0.147,
       "step": 3000
     },
     {
       "epoch": 0.3452357466956007,
-      "grad_norm": 0.10182422399520874,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0074,
+      "grad_norm": 0.3435736298561096,
+      "learning_rate": 1.0718650414525622e-05,
+      "loss": 0.1174,
       "step": 3500
     },
     {
       "epoch": 0.3945551390806865,
-      "grad_norm": 0.1254289746284485,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0082,
+      "grad_norm": 0.33571186661720276,
+      "learning_rate": 1.0718650414525622e-05,
+      "loss": 0.0952,
       "step": 4000
     },
     {
       "epoch": 0.4438745314657723,
-      "grad_norm": 0.10901518911123276,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0062,
+      "grad_norm": 0.4317052662372589,
+      "learning_rate": 1.0718650414525622e-05,
+      "loss": 0.0774,
       "step": 4500
     },
     {
       "epoch": 0.49319392385085814,
-      "grad_norm": 0.11559788137674332,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0065,
+      "grad_norm": 0.4251234829425812,
+      "learning_rate": 1.0718650414525622e-05,
+      "loss": 0.0646,
       "step": 5000
     },
     {
       "epoch": 0.49319392385085814,
-      "eval_all_ligands_equal": 0.5236411842686699,
-      "eval_e3_equal": 0.8001767565178965,
+      "eval_all_ligands_equal": 0.1314184710561202,
+      "eval_e3_equal": 0.6642509942554131,
       "eval_e3_graph_edit_distance": 9.999999999999999e+63,
       "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.9847989394608926,
-      "eval_e3_heavy_atoms_difference": 0.6638091029606716,
-      "eval_e3_heavy_atoms_difference_norm": 0.014836414397080187,
+      "eval_e3_has_attachment_point(s)": 0.9954927087936367,
+      "eval_e3_heavy_atoms_difference": -0.1652673442333186,
+      "eval_e3_heavy_atoms_difference_norm": -0.0189775084827908,
       "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.9847989394608926,
-      "eval_has_all_attachment_points": 0.9811754308440124,
-      "eval_has_three_substructures": 0.9996464869642068,
-      "eval_heavy_atoms_difference": 6.973221387538666,
-      "eval_heavy_atoms_difference_norm": 0.09065782983430724,
-      "eval_linker_equal": 0.7539549270879363,
+      "eval_e3_valid": 0.9954927087936367,
+      "eval_has_all_attachment_points": 0.9818824569155987,
+      "eval_has_three_substructures": 0.9983208130799823,
+      "eval_heavy_atoms_difference": 9.841184268669908,
+      "eval_heavy_atoms_difference_norm": 0.1288377887017133,
+      "eval_linker_equal": 0.21767565178965975,
       "eval_linker_graph_edit_distance": 9.999999999999999e+63,
       "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9969951391957579,
-      "eval_linker_heavy_atoms_difference": 0.559169244365886,
-      "eval_linker_heavy_atoms_difference_norm": 0.012528181856226664,
+      "eval_linker_has_attachment_point(s)": 0.9942554131683606,
+      "eval_linker_heavy_atoms_difference": 2.058241272646929,
+      "eval_linker_heavy_atoms_difference_norm": 0.07612205467495885,
       "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9969951391957579,
-      "eval_loss": 0.30445051193237305,
-      "eval_num_fragments": 3.0001767565178965,
-      "eval_poi_equal": 0.7479452054794521,
+      "eval_linker_valid": 0.9942554131683606,
+      "eval_loss": 0.300495982170105,
+      "eval_num_fragments": 2.999381352187362,
+      "eval_poi_equal": 0.5985859478568272,
       "eval_poi_graph_edit_distance": 9.999999999999999e+63,
       "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.9374281926646045,
-      "eval_poi_heavy_atoms_difference": 1.8859036676977463,
-      "eval_poi_heavy_atoms_difference_norm": 0.05362304789611469,
+      "eval_poi_has_attachment_point(s)": 0.900309323906319,
+      "eval_poi_heavy_atoms_difference": 3.2072470172337604,
+      "eval_poi_heavy_atoms_difference_norm": 0.10008980427814149,
       "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.9374281926646045,
-      "eval_reassembly": 0.5313300927971719,
-      "eval_reassembly_nostereo": 0.5539549270879364,
-      "eval_runtime": 1550.2145,
-      "eval_samples_per_second": 7.299,
-      "eval_steps_per_second": 0.114,
+      "eval_poi_valid": 0.900309323906319,
+      "eval_reassembly": 0.13442333186036234,
+      "eval_reassembly_nostereo": 0.1504197967300044,
+      "eval_runtime": 1571.3971,
+      "eval_samples_per_second": 7.201,
+      "eval_steps_per_second": 0.113,
       "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.921608484312859,
+      "eval_valid": 0.8950066283694211,
       "step": 5000
-    },
-    {
-      "epoch": 0.542513316235944,
-      "grad_norm": 0.11470098048448563,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0042,
-      "step": 5500
-    },
-    {
-      "epoch": 0.5918327086210298,
-      "grad_norm": 0.11638347059488297,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0042,
-      "step": 6000
-    },
-    {
-      "epoch": 0.6411521010061156,
-      "grad_norm": 0.07129918038845062,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0059,
-      "step": 6500
-    },
-    {
-      "epoch": 0.6904714933912014,
-      "grad_norm": 0.044687844812870026,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0034,
-      "step": 7000
-    },
-    {
-      "epoch": 0.7397908857762873,
-      "grad_norm": 0.0823349729180336,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0031,
-      "step": 7500
-    },
-    {
-      "epoch": 0.7397908857762873,
-      "eval_all_ligands_equal": 0.5498895271763147,
-      "eval_e3_equal": 0.8119310649580204,
-      "eval_e3_graph_edit_distance": 9.999999999999999e+63,
-      "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.9771100309323907,
-      "eval_e3_heavy_atoms_difference": 0.8516129032258064,
-      "eval_e3_heavy_atoms_difference_norm": 0.02148143499541932,
-      "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.9771100309323907,
-      "eval_has_all_attachment_points": 0.9779938135218736,
-      "eval_has_three_substructures": 0.9984091913389306,
-      "eval_heavy_atoms_difference": 7.066725585505965,
-      "eval_heavy_atoms_difference_norm": 0.09269971150883742,
-      "eval_linker_equal": 0.7787892178524083,
-      "eval_linker_graph_edit_distance": 9.999999999999999e+63,
-      "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9923994697304463,
-      "eval_linker_heavy_atoms_difference": 0.4481661511268228,
-      "eval_linker_heavy_atoms_difference_norm": 0.006821181166453098,
-      "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9923994697304463,
-      "eval_loss": 0.31453314423561096,
-      "eval_num_fragments": 2.9998232434821035,
-      "eval_poi_equal": 0.7662395050817499,
-      "eval_poi_graph_edit_distance": 9.999999999999999e+63,
-      "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.9374281926646045,
-      "eval_poi_heavy_atoms_difference": 1.763057887759611,
-      "eval_poi_heavy_atoms_difference_norm": 0.05254183317720355,
-      "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.9374281926646045,
-      "eval_reassembly": 0.5576668139637649,
-      "eval_reassembly_nostereo": 0.5741051701281484,
-      "eval_runtime": 1494.0608,
-      "eval_samples_per_second": 7.573,
-      "eval_steps_per_second": 0.118,
-      "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.9133009279717189,
-      "step": 7500
-    },
-    {
-      "epoch": 0.789110278161373,
-      "grad_norm": 0.0743485540151596,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0034,
-      "step": 8000
-    },
-    {
-      "epoch": 0.8384296705464589,
-      "grad_norm": 0.08227942138910294,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0035,
-      "step": 8500
-    },
-    {
-      "epoch": 0.8877490629315447,
-      "grad_norm": 0.07675650715827942,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.004,
-      "step": 9000
-    },
-    {
-      "epoch": 0.9370684553166305,
-      "grad_norm": 0.060432229191064835,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.003,
-      "step": 9500
-    },
-    {
-      "epoch": 0.9863878477017163,
-      "grad_norm": 0.06841175258159637,
-      "learning_rate": 0.00010780369551982127,
-      "loss": 0.0024,
-      "step": 10000
-    },
-    {
-      "epoch": 0.9863878477017163,
-      "eval_all_ligands_equal": 0.5623508616880247,
-      "eval_e3_equal": 0.8172337604949182,
-      "eval_e3_graph_edit_distance": 9.999999999999999e+63,
-      "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.9732213875386655,
-      "eval_e3_heavy_atoms_difference": 0.8075121520106054,
-      "eval_e3_heavy_atoms_difference_norm": 0.02178934615008687,
-      "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.9732213875386655,
-      "eval_has_all_attachment_points": 0.9811754308440124,
-      "eval_has_three_substructures": 0.9995581087052585,
-      "eval_heavy_atoms_difference": 7.874414494034467,
-      "eval_heavy_atoms_difference_norm": 0.10424160867591652,
-      "eval_linker_equal": 0.8018559434379142,
-      "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": 0.41741051701281484,
-      "eval_linker_heavy_atoms_difference_norm": 0.008801670643119743,
-      "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9961997348652232,
-      "eval_loss": 0.3179270923137665,
-      "eval_num_fragments": 2.9999116217410515,
-      "eval_poi_equal": 0.771895713654441,
-      "eval_poi_graph_edit_distance": 9.999999999999999e+63,
-      "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.9324790101634998,
-      "eval_poi_heavy_atoms_difference": 1.9437030490499336,
-      "eval_poi_heavy_atoms_difference_norm": 0.059822219414631145,
-      "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.9324790101634998,
-      "eval_reassembly": 0.5704816615112682,
-      "eval_reassembly_nostereo": 0.5938135218736191,
-      "eval_runtime": 1488.581,
-      "eval_samples_per_second": 7.601,
-      "eval_steps_per_second": 0.119,
-      "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.9044631020768891,
-      "step": 10000
     }
   ],
   "logging_steps": 500,
@@ -287,18 +133,18 @@
         "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=3-learning_rate=1.1e-04-warmup_ratio=0.050-min_lr=0.000-factor=0.850",
+  "trial_name": "trial-number=4-learning_rate=1.1e-05-warmup_ratio=0.030-min_lr=0.000-factor=0.940",
   "trial_params": {
-    "factor": 0.8500000000000001,
-    "learning_rate": 0.00010780369551982127,
-    "min_lr": 1.8229175490752733e-09,
-    "warmup_ratio": 0.05
+    "factor": 0.9400000000000001,
+    "learning_rate": 1.0718650414525622e-05,
+    "min_lr": 3.3284513007278865e-10,
+    "warmup_ratio": 0.03
   }
 }

last-checkpoint/training_args.bin

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:56b45b5b99bb8c5156b9bb3f2256bfde36b4a1aad0a9e68d5f17b356acd18a39
+oid sha256:f29f15ae3259a93d42ac696f28d2c0b8196a389c2575004f411b5c6a07b26402
 size 7480