Training in progress, step 5000, checkpoint

last-checkpoint/model.safetensors

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:cefca364cb652b250a97253b7dac8a9be9d484cd2b6f4719a5f3abc841b15642
+oid sha256:d5919797ddb0647375bf83938aa7ad57d083597005834cf7c74b2ae2479b17f5
 size 409608164

last-checkpoint/optimizer.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:eb76aa8d697c4b516f54a133000905d318c4e920f1c43ce33421ef2befd40276
+oid sha256:a1492a19f0e514da29d50dd99badee09c341686315e4b279ac45ea7e45eed3af
 size 814647162

last-checkpoint/rng_state.pth

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:7275176284f392a3e940835dd95f85b60a7e2e08932ca0d83052cc5ffd677867
+oid sha256:165d19c8bc2cead0d266eb442d497884e9231bbcb1622fad96b437d39b9984be
 size 14244

last-checkpoint/scheduler.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:2ae632a78fd5514ddc477159922112ccad071a834ab7664a5de8416df1295523
+oid sha256:88281662345f6602ca80f85d210e0abdbe00157634eecda2e1b296acea08077a
 size 1192

last-checkpoint/trainer_state.json

@@ -1,278 +1,124 @@
 {
-  "best_metric": 0.09456473707467963,
-  "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25/trial-number=5-learning_rate=5.4e-06-warmup_ratio=0.050-min_lr=0.000-factor=0.970/checkpoint-10000",
-  "epoch": 0.9863878477017163,
+  "best_metric": 0.5292090145824128,
+  "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25/trial-number=6-learning_rate=1.4e-04-warmup_ratio=0.030-min_lr=0.000-factor=0.870/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": 1.2011727094650269,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 2.2572,
+      "grad_norm": 0.5591509342193604,
+      "learning_rate": 0.00013596662166193572,
+      "loss": 0.8599,
       "step": 500
     },
     {
       "epoch": 0.09863878477017163,
-      "grad_norm": 1.2127913236618042,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.8851,
+      "grad_norm": 0.3582165241241455,
+      "learning_rate": 0.00013596662166193572,
+      "loss": 0.1291,
       "step": 1000
     },
     {
       "epoch": 0.14795817715525744,
-      "grad_norm": 1.1755174398422241,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.6169,
+      "grad_norm": 0.1554139405488968,
+      "learning_rate": 0.00013596662166193572,
+      "loss": 0.0347,
       "step": 1500
     },
     {
       "epoch": 0.19727756954034326,
-      "grad_norm": 0.9869494438171387,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.4677,
+      "grad_norm": 0.12609660625457764,
+      "learning_rate": 0.00013596662166193572,
+      "loss": 0.0174,
       "step": 2000
     },
     {
       "epoch": 0.24659696192542907,
-      "grad_norm": 1.035641074180603,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.3728,
+      "grad_norm": 0.12008047103881836,
+      "learning_rate": 0.00013596662166193572,
+      "loss": 0.0118,
       "step": 2500
     },
     {
       "epoch": 0.2959163543105149,
-      "grad_norm": 0.8810314536094666,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.3065,
+      "grad_norm": 0.10875318944454193,
+      "learning_rate": 0.00013596662166193572,
+      "loss": 0.0087,
       "step": 3000
     },
     {
       "epoch": 0.3452357466956007,
-      "grad_norm": 0.5494240522384644,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.2565,
+      "grad_norm": 0.15160998702049255,
+      "learning_rate": 0.00013596662166193572,
+      "loss": 0.0082,
       "step": 3500
     },
     {
       "epoch": 0.3945551390806865,
-      "grad_norm": 0.6713376045227051,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.2204,
+      "grad_norm": 0.1064407080411911,
+      "learning_rate": 0.00013596662166193572,
+      "loss": 0.0095,
       "step": 4000
     },
     {
       "epoch": 0.4438745314657723,
-      "grad_norm": 0.6078818440437317,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.1916,
+      "grad_norm": 0.10049774497747421,
+      "learning_rate": 0.00013596662166193572,
+      "loss": 0.0058,
       "step": 4500
     },
     {
       "epoch": 0.49319392385085814,
-      "grad_norm": 0.5752325654029846,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.1705,
+      "grad_norm": 0.09324470162391663,
+      "learning_rate": 0.00013596662166193572,
+      "loss": 0.0052,
       "step": 5000
     },
     {
       "epoch": 0.49319392385085814,
-      "eval_all_ligands_equal": 0.0020326999558108703,
-      "eval_e3_equal": 0.318338488731772,
+      "eval_all_ligands_equal": 0.5292090145824128,
+      "eval_e3_equal": 0.803535130357932,
       "eval_e3_graph_edit_distance": 9.999999999999999e+63,
       "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.9946973044631021,
-      "eval_e3_heavy_atoms_difference": -0.895271763146266,
-      "eval_e3_heavy_atoms_difference_norm": -0.051160135815713596,
+      "eval_e3_has_attachment_point(s)": 0.9888643393725144,
+      "eval_e3_heavy_atoms_difference": 0.6379142730888202,
+      "eval_e3_heavy_atoms_difference_norm": 0.013342101949007744,
       "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.9946973044631021,
-      "eval_has_all_attachment_points": 0.9414935925762262,
-      "eval_has_three_substructures": 0.9956694653115333,
-      "eval_heavy_atoms_difference": 20.25046398585948,
-      "eval_heavy_atoms_difference_norm": 0.259310979504476,
-      "eval_linker_equal": 0.012814847547503314,
+      "eval_e3_valid": 0.9888643393725144,
+      "eval_has_all_attachment_points": 0.9821475916924437,
+      "eval_has_three_substructures": 0.9989394608926204,
+      "eval_heavy_atoms_difference": 5.095802032699956,
+      "eval_heavy_atoms_difference_norm": 0.06478964207091067,
+      "eval_linker_equal": 0.760936809544852,
       "eval_linker_graph_edit_distance": 9.999999999999999e+63,
       "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9877154220061864,
-      "eval_linker_heavy_atoms_difference": 3.770746796288113,
-      "eval_linker_heavy_atoms_difference_norm": 0.1261414417514629,
+      "eval_linker_has_attachment_point(s)": 0.994962439239947,
+      "eval_linker_heavy_atoms_difference": 0.669818824569156,
+      "eval_linker_heavy_atoms_difference_norm": 0.021724791933184835,
       "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9877154220061864,
-      "eval_loss": 0.35600337386131287,
-      "eval_num_fragments": 2.99584622182943,
-      "eval_poi_equal": 0.3075563411400795,
+      "eval_linker_valid": 0.994962439239947,
+      "eval_loss": 0.3178597092628479,
+      "eval_num_fragments": 2.9992929739284135,
+      "eval_poi_equal": 0.7542200618647813,
       "eval_poi_graph_edit_distance": 9.999999999999999e+63,
       "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.785771100309324,
-      "eval_poi_heavy_atoms_difference": 7.611224038886434,
-      "eval_poi_heavy_atoms_difference_norm": 0.22229839426703232,
+      "eval_poi_has_attachment_point(s)": 0.959169244365886,
+      "eval_poi_heavy_atoms_difference": 1.1574900574458684,
+      "eval_poi_heavy_atoms_difference_norm": 0.027656582487638033,
       "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.785771100309324,
-      "eval_reassembly": 0.0020326999558108703,
-      "eval_reassembly_nostereo": 0.003358373840035351,
-      "eval_runtime": 1463.2337,
-      "eval_samples_per_second": 7.733,
-      "eval_steps_per_second": 0.121,
+      "eval_poi_valid": 0.959169244365886,
+      "eval_reassembly": 0.5365444100751215,
+      "eval_reassembly_nostereo": 0.5646486964206805,
+      "eval_runtime": 1499.2027,
+      "eval_samples_per_second": 7.547,
+      "eval_steps_per_second": 0.118,
       "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.7803800265134777,
+      "eval_valid": 0.946442775077331,
       "step": 5000
-    },
-    {
-      "epoch": 0.542513316235944,
-      "grad_norm": 0.45905882120132446,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.1522,
-      "step": 5500
-    },
-    {
-      "epoch": 0.5918327086210298,
-      "grad_norm": 0.5230804681777954,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.1374,
-      "step": 6000
-    },
-    {
-      "epoch": 0.6411521010061156,
-      "grad_norm": 0.4722335636615753,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.125,
-      "step": 6500
-    },
-    {
-      "epoch": 0.6904714933912014,
-      "grad_norm": 0.48955613374710083,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.1139,
-      "step": 7000
-    },
-    {
-      "epoch": 0.7397908857762873,
-      "grad_norm": 0.36220186948776245,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.104,
-      "step": 7500
-    },
-    {
-      "epoch": 0.7397908857762873,
-      "eval_all_ligands_equal": 0.02129916040653999,
-      "eval_e3_equal": 0.48935041979673,
-      "eval_e3_graph_edit_distance": 9.999999999999999e+63,
-      "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.996464869642068,
-      "eval_e3_heavy_atoms_difference": -0.29482987185152454,
-      "eval_e3_heavy_atoms_difference_norm": -0.026431546412598723,
-      "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.996464869642068,
-      "eval_has_all_attachment_points": 0.9720724701723376,
-      "eval_has_three_substructures": 0.9970835174547061,
-      "eval_heavy_atoms_difference": 12.032081307998233,
-      "eval_heavy_atoms_difference_norm": 0.1589068003485144,
-      "eval_linker_equal": 0.05055236411842687,
-      "eval_linker_graph_edit_distance": 9.999999999999999e+63,
-      "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.991427308882015,
-      "eval_linker_heavy_atoms_difference": 2.3915156871409633,
-      "eval_linker_heavy_atoms_difference_norm": 0.07977087082546026,
-      "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.991427308882015,
-      "eval_loss": 0.32415854930877686,
-      "eval_num_fragments": 2.9999116217410515,
-      "eval_poi_equal": 0.49332744144940344,
-      "eval_poi_graph_edit_distance": 9.999999999999999e+63,
-      "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.8737958462218294,
-      "eval_poi_heavy_atoms_difference": 4.038267786124614,
-      "eval_poi_heavy_atoms_difference_norm": 0.12759997053490574,
-      "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.8737958462218294,
-      "eval_reassembly": 0.021741051701281485,
-      "eval_reassembly_nostereo": 0.028722934158197082,
-      "eval_runtime": 1531.3373,
-      "eval_samples_per_second": 7.389,
-      "eval_steps_per_second": 0.116,
-      "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.868935041979673,
-      "step": 7500
-    },
-    {
-      "epoch": 0.789110278161373,
-      "grad_norm": 0.46921494603157043,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.0955,
-      "step": 8000
-    },
-    {
-      "epoch": 0.8384296705464589,
-      "grad_norm": 0.4087197482585907,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.0874,
-      "step": 8500
-    },
-    {
-      "epoch": 0.8877490629315447,
-      "grad_norm": 0.4746197462081909,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.0797,
-      "step": 9000
-    },
-    {
-      "epoch": 0.9370684553166305,
-      "grad_norm": 0.37426093220710754,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.0731,
-      "step": 9500
-    },
-    {
-      "epoch": 0.9863878477017163,
-      "grad_norm": 0.40007445216178894,
-      "learning_rate": 5.3589822732989715e-06,
-      "loss": 0.0669,
-      "step": 10000
-    },
-    {
-      "epoch": 0.9863878477017163,
-      "eval_all_ligands_equal": 0.09456473707467963,
-      "eval_e3_equal": 0.6007954043305347,
-      "eval_e3_graph_edit_distance": 9.999999999999999e+63,
-      "eval_e3_graph_edit_distance_norm": 1.0,
-      "eval_e3_has_attachment_point(s)": 0.9971718957136544,
-      "eval_e3_heavy_atoms_difference": -0.43243482103402564,
-      "eval_e3_heavy_atoms_difference_norm": -0.031573210575467435,
-      "eval_e3_tanimoto_similarity": 0.0,
-      "eval_e3_valid": 0.9971718957136544,
-      "eval_has_all_attachment_points": 0.982235969951392,
-      "eval_has_three_substructures": 0.9982324348210341,
-      "eval_heavy_atoms_difference": 8.169155987627043,
-      "eval_heavy_atoms_difference_norm": 0.10747551064018938,
-      "eval_linker_equal": 0.171895713654441,
-      "eval_linker_graph_edit_distance": 9.999999999999999e+63,
-      "eval_linker_graph_edit_distance_norm": 1.0,
-      "eval_linker_has_attachment_point(s)": 0.9944321696862571,
-      "eval_linker_heavy_atoms_difference": 1.0428634555899248,
-      "eval_linker_heavy_atoms_difference_norm": 0.013365477460276531,
-      "eval_linker_tanimoto_similarity": 0.0,
-      "eval_linker_valid": 0.9944321696862571,
-      "eval_loss": 0.3112289011478424,
-      "eval_num_fragments": 3.000353513035793,
-      "eval_poi_equal": 0.5798497569597879,
-      "eval_poi_graph_edit_distance": 9.999999999999999e+63,
-      "eval_poi_graph_edit_distance_norm": 1.0,
-      "eval_poi_has_attachment_point(s)": 0.9041979673000442,
-      "eval_poi_heavy_atoms_difference": 2.963411400795404,
-      "eval_poi_heavy_atoms_difference_norm": 0.09370426729833506,
-      "eval_poi_tanimoto_similarity": 0.0,
-      "eval_poi_valid": 0.9041979673000442,
-      "eval_reassembly": 0.0965974370304905,
-      "eval_reassembly_nostereo": 0.11542200618647813,
-      "eval_runtime": 1544.4156,
-      "eval_samples_per_second": 7.326,
-      "eval_steps_per_second": 0.115,
-      "eval_tanimoto_similarity": 0.0,
-      "eval_valid": 0.9008395934600089,
-      "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=5-learning_rate=5.4e-06-warmup_ratio=0.050-min_lr=0.000-factor=0.970",
+  "trial_name": "trial-number=6-learning_rate=1.4e-04-warmup_ratio=0.030-min_lr=0.000-factor=0.870",
   "trial_params": {
-    "factor": 0.9700000000000001,
-    "learning_rate": 5.3589822732989715e-06,
-    "min_lr": 1.0903925608555295e-10,
-    "warmup_ratio": 0.05
+    "factor": 0.8700000000000001,
+    "learning_rate": 0.00013596662166193572,
+    "min_lr": 6.431829535567748e-09,
+    "warmup_ratio": 0.03
   }
 }

last-checkpoint/training_args.bin

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:2cf30ccdd8d52d502c1a40017b44c18b685251fc6be624b49b6045f779dc20fd
+oid sha256:865624014eb48b5ea34b378e8ae120892c934c317cd5d4fa5e183be5aa03040f
 size 7480