Delete metadata

metadata/Final_V3_manifest.json

@@ -1,10 +0,0 @@
-{
-  "model_name": "Final_V3",
-  "created_at_utc": "2026-04-13T19:53:04Z",
-  "source_checkpoint": "/home/ubuntu/artifacts/nexa_mol/v1_full_pretrain/phase1_blackwell_v3/current_checkpoint.pt",
-  "checkpoint_alias": "/home/ubuntu/artifacts/nexa_mol/v1_full_pretrain/phase1_blackwell_v3/Final_V3.pt",
-  "bytes": 151419519,
-  "run_name": "gems_v1_full_pretrain_blackwell_phase1_v3",
-  "dataset_root": "/home/ubuntu/data/gems_v1_v1_full_pretrain_phase1_v3",
-  "phase": "ssl_structure_foundation_final_v3"
-}

metadata/archive/20260413T201817Z/latest_checkpoint.txt

@@ -1 +0,0 @@
-/home/ubuntu/artifacts/nexa_mol/final_v3_structure_alignment/v26_r1/current_checkpoint.pt

metadata/archive/20260413T202042Z/latest_checkpoint.txt

@@ -1 +0,0 @@
-/home/ubuntu/artifacts/nexa_mol/final_v3_structure_alignment/v26_r1/current_checkpoint.pt

metadata/archive/20260413T213902Z/day1_validation_report.json

@@ -1,2475 +0,0 @@
-{
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-    "docs/projects/msms_pipeline/Engineering.md"
-  ],
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-    "val_structure_clear_hit_at_1": 0.0,
-    "val_structure_confidence_separation": -0.027957430157584895,
-    "val_structure_fingerprint_cosine": 0.4255251376889646,
-    "val_structure_top1_top2_gap_mean": 0.11855697631835938,
-    "val_structure_uncertain_fraction": 0.9922027587890625
-  },
-  "run_name": "final_v3_structure_alignment_v26_r1",
-  "shard_counts": {
-    "test": 2,
-    "train": 4,
-    "val": 2
-  }
-}

metadata/archive/20260413T213902Z/latest_checkpoint.txt

@@ -1 +0,0 @@
-/home/ubuntu/artifacts/nexa_mol/final_v3_structure_alignment/v26_r1/current_checkpoint.pt

metadata/archive/20260413T213902Z/latest_metrics.json

@@ -1,169 +0,0 @@
-{
-  "backbone_lr": 3.886130904636371e-06,
-  "checkpoint_path": "/home/ubuntu/artifacts/nexa_mol/final_v3_structure_alignment/v26_r1/current_checkpoint.pt",
-  "checkpoint_reloaded": 1.0,
-  "contrastive_loss": 0.5768923759460449,
-  "covariance_loss": 10.012618064880371,
-  "covariance_to_contrastive_ratio": 17.356128252623712,
-  "covariance_weight": 0.0015,
-  "dataloader_time_sec": 0.00035174899676349014,
-  "dataloader_wait_pct_300s": 0.0382592069912683,
-  "dataloader_wait_pct_60s": 0.0961140629935623,
-  "dataloader_wait_pct_900s": 0.066640439237091,
-  "dataloader_wait_pct_run": 0.06717802801040498,
-  "different_inchikey_mean_cosine": 0.004679911238535274,
-  "distributed_rank": 0.0,
-  "distributed_world_size": 1.0,
-  "effective_batch_size": 512.0,
-  "effective_hard_negative_scale": 1.0,
-  "effective_retrieval_weight": 0.6,
-  "effective_structure_bce_weight": 1.0,
-  "embedding_mean_norm": 1.0,
-  "embedding_offdiag_mean_cosine": 0.009513536468148232,
-  "embedding_std": 0.07216806709766388,
-  "final_report": 1.0,
-  "global_batch_size": 512.0,
-  "gpu_active_fraction": 1.0,
-  "gpu_count_observed": 2.0,
-  "gpu_max_memory_gb": 13.279157161712646,
-  "gpu_mem_used_mean_gb": 14.1943359375,
-  "gpu_mem_util_mean_pct": 14.848754175733243,
-  "gpu_memory_stable": true,
-  "gpu_memory_utilization": 0.13982381154325935,
-  "gpu_snapshot_available": 1.0,
-  "gpu_util_max_pct": 54.0,
-  "gpu_util_mean_pct": 36.0,
-  "gpu_util_min_pct": 18.0,
-  "grad_norm": 1.7659728527069092,
-  "holdout_full_coverage": 0.0,
-  "local_batch_size": 512.0,
-  "lr": 3.886130904636371e-06,
-  "mfu_estimate": 0.06267708747552383,
-  "msms_objective": "hybrid",
-  "optimizer_step": 1.0,
-  "regularizer_ramp": 1.0,
-  "resume_checkpoint_path": "/home/ubuntu/artifacts/nexa_mol/final_v3_structure_alignment/v26_r1/current_checkpoint.pt",
-  "resume_start_step": 81002.0,
-  "resumed_from_checkpoint": 1.0,
-  "retrieval_head_lr": 1.9430654523181854e-05,
-  "same_inchikey_mean_cosine": 0.16267980930137343,
-  "samples_per_sec": 1399.0203442084614,
-  "samples_per_sec_300s": 1547.033197547462,
-  "samples_per_sec_60s": 1399.0203442084614,
-  "samples_per_sec_900s": 1512.7885250414204,
-  "samples_per_sec_run_mean": 1533.0231795943853,
-  "step": 91001,
-  "step_time_cv_300s": 0.06743440395418321,
-  "step_time_cv_60s": 0.0,
-  "step_time_cv_900s": 0.09218780075615579,
-  "step_time_sec": 0.3659703749981418,
-  "structure_bce_locked": 0.0,
-  "structure_bce_loss": 0.08383000642061234,
-  "structure_candidate_count": 2126.0,
-  "structure_clear_fraction": 0.0,
-  "structure_clear_hit_at_1": 0.0,
-  "structure_close_fraction": 0.029296875,
-  "structure_close_hit_at_1": 0.0,
-  "structure_confidence_bucket_score_mean": 0.10155132412910461,
-  "structure_confidence_bucket_score_mode": "normalized_gap",
-  "structure_confidence_candidate_count": 2126.0,
-  "structure_confidence_clear_threshold": 1.0,
-  "structure_confidence_close_threshold": 0.35,
-  "structure_confidence_eval_key_mode": "target_identity",
-  "structure_confidence_separation": -0.0040241447277367115,
-  "structure_correct_logit_mean": 9.1875,
-  "structure_fingerprint_cosine": 0.46021854877471924,
-  "structure_hard_negative_bonus_applied": 1.0,
-  "structure_hard_negative_bonus_mean": 0.060302734375,
-  "structure_hard_negative_scale": 1.0,
-  "structure_head_lr": 1.9430654523181854e-05,
-  "structure_hit_at_1": 0.00390625,
-  "structure_hit_at_20": 0.1171875,
-  "structure_hit_at_5": 0.029296875,
-  "structure_local_ce_loss": 3.545562744140625,
-  "structure_local_ce_loss_weight": 0.4,
-  "structure_local_rerank_loss": 0.0,
-  "structure_local_rerank_loss_weight": 0.0,
-  "structure_local_rerank_score_scale": 1.0,
-  "structure_logit_margin_mean": -1.0078125,
-  "structure_margin_loss": 0.0,
-  "structure_margin_loss_weight": 0.0,
-  "structure_missing_formula_fraction": 0.0,
-  "structure_missing_inchikey_fraction": 0.0,
-  "structure_pairwise_logistic_loss": 0.0,
-  "structure_pairwise_logistic_loss_weight": 0.0,
-  "structure_positive_count_mean": 1.0,
-  "structure_post_label_candidate_count": 2126.0,
-  "structure_post_precursor_candidate_count": 2128.0,
-  "structure_prefilter_candidate_count": 2128.0,
-  "structure_retrieval_logit_std": 0.9839304089546204,
-  "structure_retrieval_loss": 10.630162239074707,
-  "structure_retrieval_scorer": "projected_dot",
-  "structure_retrieval_target_mode": "sample",
-  "structure_skipped_query_fraction": 0.0,
-  "structure_soft_target_exact_mix": 0.4,
-  "structure_soft_target_loss": 7.523618221282959,
-  "structure_soft_target_loss_weight": 0.3,
-  "structure_target_backend": "rdkit_morgan",
-  "structure_target_equivalent_count_mean": 1.0,
-  "structure_target_identity_collision_count": 0.0,
-  "structure_target_rank_mean": 314.703125,
-  "structure_to_ssl_ratio": 217.7124787233957,
-  "structure_top1_top2_gap_mean": 0.0986328125,
-  "structure_top1_top2_gap_norm_mean": 0.10155132412910461,
-  "structure_top_negative_logit_mean": 10.1875,
-  "structure_uncertain_fraction": 0.970703125,
-  "structure_uncertain_hit_at_1": 0.0040241447277367115,
-  "structure_valid_query_fraction": 1.0,
-  "test_expected_shard_count": 2.0,
-  "test_full_coverage": 0.0,
-  "test_observed_shard_count": 0.0,
-  "train_loss": 6.491608619689941,
-  "train_loss_ema": 6.519052214060582,
-  "train_retrieval_bank_size": 4096.0,
-  "val_deep_eval_single_view": 0.0,
-  "val_deep_eval_structure_only": 0.0,
-  "val_effective_structure_bce_weight": 1.0,
-  "val_eval_loader_mode": "stream",
-  "val_eval_mode": "deep",
-  "val_expected_shard_count": 2.0,
-  "val_full_coverage": 1.0,
-  "val_hit_at_1": 0.0282135009765625,
-  "val_hit_at_20": 0.15270233154296875,
-  "val_hit_at_5": 0.0726776123046875,
-  "val_loss": 6.646750174145564,
-  "val_observed_eval_batches": 256.0,
-  "val_observed_shard_count": 2.0,
-  "val_ssl_loss": 1.0397093277424574,
-  "val_structure_bce_loss": 0.06532714269997086,
-  "val_structure_candidate_count": 4119.69140625,
-  "val_structure_clear_fraction": 0.0,
-  "val_structure_clear_hit_at_1": 0.0,
-  "val_structure_close_fraction": 0.0077972412109375,
-  "val_structure_close_hit_at_1": 0.014835291571216658,
-  "val_structure_confidence_candidate_count": 4096.0,
-  "val_structure_confidence_separation": -0.027957430157584895,
-  "val_structure_correct_logit_mean": 9.49462890625,
-  "val_structure_fingerprint_cosine": 0.4255251376889646,
-  "val_structure_logit_margin_mean": -1.221923828125,
-  "val_structure_missing_formula_fraction": 0.0,
-  "val_structure_missing_inchikey_fraction": 0.0,
-  "val_structure_retrieval_logit_std": 2.6622845763340592,
-  "val_structure_retrieval_loss": 10.882395941764116,
-  "val_structure_target_equivalent_count_mean": 1.0,
-  "val_structure_target_identity_collision_count": 23.69140625,
-  "val_structure_target_rank_mean": 379.8781280517578,
-  "val_structure_top1_top2_gap_mean": 0.11855697631835938,
-  "val_structure_top1_top2_gap_norm_mean": 0.05411380449368153,
-  "val_structure_top_negative_logit_mean": 10.714599609375,
-  "val_structure_uncertain_fraction": 0.9922027587890625,
-  "val_structure_uncertain_hit_at_1": 0.027957430157584895,
-  "variance_loss": 0.00213623046875,
-  "variance_weight": 0.8,
-  "weighted_covariance_loss": 0.015018927097320557,
-  "weighted_regularizer_to_contrastive_ratio": 0.028996589606316913,
-  "weighted_ssl_loss": 0.02968101501464844,
-  "weighted_structure_bce_loss": 0.08383000642061234,
-  "weighted_structure_retrieval_loss": 6.378097343444824,
-  "weighted_variance_loss": 0.001708984375
-}

metadata/archive/20260413T213902Z/perf_summary.json

@@ -1,16 +0,0 @@
-{
-  "logged_points": 521,
-  "train_loss_min": 3.2278988361358643,
-  "train_loss_max": 7.677141189575195,
-  "train_loss_last": 6.491608619689941,
-  "train_loss_ema_last": 6.519052214060582,
-  "weighted_regularizer_ratio_median": 0.02686493425176378,
-  "weighted_regularizer_ratio_p90": 0.09558363904110317,
-  "samples_per_sec_mean": 1545.3851888056406,
-  "samples_per_sec_min": 930.5498563655322,
-  "samples_per_sec_max": 2247.460787425693,
-  "step_time_mean": 0.33468720350667036,
-  "mfu_mean": 0.06923433462788683,
-  "mfu_max": 0.10068781126337953,
-  "gpu_mem_max_gb": 13.279157161712646
-}

metadata/archive/20260413T213902Z/results.md

@@ -1,171 +0,0 @@
-# MS/MS Training Run Result
-
-- Run name: `final_v3_structure_alignment_v26_r1`
-- Created at: `2026-04-13T21:36:19Z`
-- Dataset root: `/home/ubuntu/data/gems_v1_handoff_labeled_v26`
-- Shard counts: `{'train': 4, 'val': 2, 'test': 2}`
-
-## Primary Metrics
-
-- `train_loss`: `6.491608619689941`
-- `val_loss`: `6.646750174145564`
-- `grad_norm`: `1.7659728527069092`
-- `contrastive_loss`: `0.5768923759460449`
-- `structure_bce_loss`: `0.08383000642061234`
-- `val_structure_bce_loss`: `0.06532714269997086`
-- `val_structure_fingerprint_cosine`: `0.4255251376889646`
-- `different_inchikey_mean_cosine`: `0.004679911238535274`
-- `embedding_std`: `0.07216806709766388`
-- `val_hit_at_20`: `0.15270233154296875`
-- `val_structure_candidate_count`: `4119.69140625`
-- `val_structure_top1_top2_gap_mean`: `0.11855697631835938`
-- `val_structure_uncertain_fraction`: `0.9922027587890625`
-- `val_structure_clear_hit_at_1`: `0.0`
-- `val_structure_confidence_separation`: `-0.027957430157584895`
-- `samples_per_sec`: `1399.0203442084614`
-
-## Failure Mode Assessment
-
-- `dataset_shards_accessible`: pass. Observed shard counts {'train': 4, 'val': 2, 'test': 2}; the canonical Day 1 loader contract requires all splits to be readable.
-- `dataloader_streaming_stable`: pass. Training batches continued to arrive with positive throughput and no iterator stall.
-- `non_finite_loss_or_tensor_failure`: pass. Technical_Plan requires zero NaN or Inf tensors and finite train/val loss.
-- `validation_observability_gap`: pass. Engineering.md expects slope-aware monitoring; missing validation or retrieval metrics make trend judgment weaker.
-- `gpu_memory_instability`: pass. Technical_Plan Day 1 success requires stable GPU memory through the bounded run.
-- `checkpoint_save_reload_failure`: pass. Checkpoint save and reload is an explicit Day 1 success criterion.
-- `embedding_collapse`: pass. Engineering.md expects embedding variance monitoring and non-collapsed representations.
-- `regularizer_dominance`: pass. The current instability mode is regularization overpowering the SSL objective and producing jagged total loss.
-- `structure_supervision_gap`: pass. Once the bridge phase begins, Technical_Plan requires retrieval-oriented validation rather than only augmented contrastive loss.
-- `confidence_surface_gap`: pass. Structure-first qualification now requires explicit confidence diagnostics such as top-1/top-2 separation and uncertainty buckets, not just broader retrieval metrics.
-- `chemistry_target_backend_gap`: pass. The bridge phase should prefer chemistry-grounded fingerprint targets; hashed fallback targets weaken the retrieval signal.
-- `bridge_fit_without_ranking`: pass. Bridge runs must improve retrieval after fingerprint fit saturates; fitting BCE while val Hit@20 stays at candidate-bank baseline means ranking is not generalizing.
-- `metadata_shortcutting`: watch. Engineering.md flags acquisition-artefact shortcut risk; adduct and instrument embeddings remain deliberately down-scaled.
-
-## Pressure Summary
-
-- all metrics overall: `↗ improving (+21.89% weighted)`
-- all metrics weighted improvement: `+21.89%`
-- all metrics average improvement: `+34.52%`
-- all metrics weighted pressure score: `0.284`
-- all metrics counts: `up=21` `none=7` `down=11` `up_fraction=+53.85%`
-- primary metrics overall: `↗ improving (-4.45% weighted)`
-- primary metrics weighted improvement: `-4.45%`
-
-## Metric Pressure
-
-- `train_loss`: `goal ↓ | ↗ +10.57% improving` (early `6.340343519442343`, mid `5.795929590401622`, late `5.670367905463295`, last `6.491608619689941`)
-- `train_loss_ema`: `goal ↓ | ↗ +10.46% improving` (early `6.265581717362126`, mid `5.8371378655061745`, late `5.610470838300897`, last `6.519052214060582`)
-- `contrastive_loss`: `goal ↓ | → -1.64% flat` (early `1.409792113166324`, mid `1.3598130204084982`, late `1.43291388983014`, last `0.5768923759460449`)
-- `val_loss`: `goal ↓ | ↘ -55.82% worsening` (early `1.2876316868363775`, mid `2.20697861268016`, late `2.006446816829876`, last `6.646750174145564`)
-- `val_ssl_loss`: `goal ↓ | → +2.32% flat` (early `1.0849772497183745`, mid `1.0747967428483425`, late `1.0598136518327963`, last `1.0397093277424574`)
-- `structure_bce_loss`: `goal ↓ | ↗ +39.75% improving` (early `0.12293951650489272`, mid `0.07652380578004556`, late `0.07407209518012302`, last `0.08383000642061234`)
-- `val_structure_bce_loss`: `goal ↓ | ↗ +12.20% improving` (early `0.0771060927848642`, mid `0.07029345531468391`, late `0.06769936999660872`, last `0.06532714269997086`)
-- `structure_retrieval_loss`: `goal ↓ | ↗ +10.09% improving` (early `10.237479978903181`, mid `9.41523380775672`, late `9.204101929719421`, last `10.630162239074707`)
-- `val_structure_retrieval_loss`: `goal ↓ | → +4.86% flat` (early `11.562767315655947`, mid `12.150514367967844`, late `11.000247791409492`, last `10.882395941764116`)
-- `structure_fingerprint_cosine`: `goal ↑ | ↗ +17.59% improving` (early `0.3965519580968543`, mid `0.4464927057310336`, late `0.46629545006943846`, last `0.46021854877471924`)
-- `val_structure_fingerprint_cosine`: `goal ↑ | → +0.17% flat` (early `0.4147872725734487`, mid `0.4204998221830465`, late `0.4154996814322658`, last `0.4255251376889646`)
-- `structure_target_rank_mean`: `goal ↓ | ↗ +58.80% improving` (early `351.84337743858384`, mid `176.16389315390174`, late `144.9534280711207`, last `314.703125`)
-- `val_structure_target_rank_mean`: `goal ↓ | ↗ +45.45% improving` (early `760.7540435791016`, mid `683.3385162353516`, late `415.0084457397461`, last `379.8781280517578`)
-- `structure_correct_logit_mean`: `goal ↑ | ↗ +47.31% improving` (early `6.134031791907514`, mid `9.474891618497109`, late `9.035739942528735`, last `9.1875`)
-- `val_structure_correct_logit_mean`: `goal ↑ | ↗ +16.44% improving` (early `8.0311279296875`, mid `8.441162109375`, late `9.3515625`, last `9.49462890625`)
-- `structure_top_negative_logit_mean`: `goal ↓ | ↘ -39.72% worsening` (early `7.262102601156069`, mid `10.490606936416185`, late `10.14691091954023`, last `10.1875`)
-- `val_structure_top_negative_logit_mean`: `goal ↓ | ↘ -16.08% worsening` (early `9.2255859375`, mid `10.51171875`, late `10.708740234375`, last `10.714599609375`)
-- `structure_logit_margin_mean`: `goal ↑ | → +1.23% flat` (early `-1.1263999277456647`, mid `-1.0154725885115607`, late `-1.1125740840517242`, last `-1.0078125`)
-- `val_structure_logit_margin_mean`: `goal ↑ | ↘ -13.67% worsening` (early `-1.194091796875`, mid `-2.0707931518554688`, late `-1.3573150634765625`, last `-1.221923828125`)
-- `structure_retrieval_logit_std`: `goal ↑ | ↗ +112.06% improving` (early `1.0455416592559375`, mid `2.0036371215919537`, late `2.2171744848119803`, last `0.9839304089546204`)
-- `val_structure_retrieval_logit_std`: `goal ↑ | ↗ +102.33% improving` (early `1.2326001720502973`, mid `2.022283688886091`, late `2.49387572822161`, last `2.6622845763340592`)
-- `structure_top1_top2_gap_mean`: `goal ↑ | ↗ +59.22% improving` (early `0.09793567106213873`, mid `0.12284365968208093`, late `0.1559343009159483`, last `0.0986328125`)
-- `val_structure_top1_top2_gap_mean`: `goal ↑ | ↗ +54.91% improving` (early `0.07839679718017578`, mid `0.1310901641845703`, late `0.12144279479980469`, last `0.11855697631835938`)
-- `structure_top1_top2_gap_norm_mean`: `goal ↑ | ↘ -35.65% worsening` (early `0.12215662799301864`, mid `0.07032911504236604`, late `0.07860379065547524`, last `0.10155132412910461`)
-- `val_structure_top1_top2_gap_norm_mean`: `goal ↑ | ↘ -16.83% worsening` (early `0.06950851557485294`, mid `0.07577372609375743`, late `0.0578127475164365`, last `0.05411380449368153`)
-- `structure_uncertain_fraction`: `goal ↓ | ↘ -6.11% worsening` (early `0.924663565751445`, mid `0.984747561416185`, late `0.9811422413793104`, last `0.970703125`)
-- `val_structure_uncertain_fraction`: `goal ↓ | → -0.03% flat` (early `0.9941177368164062`, mid `0.9762382507324219`, late `0.9944419860839844`, last `0.9922027587890625`)
-- `structure_confidence_separation`: `goal ↑ | ↘ -531.56% worsening` (early `-0.007918493679557749`, mid `-0.032136323077151974`, late `-0.05001017991881603`, last `-0.0040241447277367115`)
-- `val_structure_confidence_separation`: `goal ↑ | ↘ -204.85% worsening` (early `-0.00795668972114072`, mid `-0.01309866098972634`, late `-0.024256365849851136`, last `-0.027957430157584895`)
-- `structure_hit_at_1`: `goal ↑ | ↗ +549.68% improving` (early `0.007880238439306358`, mid `0.032706376445086706`, late `0.051196569683908046`, last `0.00390625`)
-- `structure_hit_at_5`: `goal ↑ | ↗ +402.47% improving` (early `0.03360955563583815`, mid `0.11673591040462428`, late `0.16887796336206898`, last `0.029296875`)
-- `structure_hit_at_20`: `goal ↑ | ↗ +239.46% improving` (early `0.10721865968208093`, mid `0.28105807442196534`, late `0.3639659662356322`, last `0.1171875`)
-- `val_hit_at_1`: `goal ↑ | → +207.79% flat` (early `0.0079345703125`, mid `0.01372528076171875`, late `0.02442169189453125`, last `0.0282135009765625`)
-- `val_hit_at_5`: `goal ↑ | ↗ +134.85% improving` (early `0.0288543701171875`, mid `0.0425567626953125`, late `0.0677642822265625`, last `0.0726776123046875`)
-- `val_hit_at_20`: `goal ↑ | ↗ +76.67% improving` (early `0.08158111572265625`, mid `0.094146728515625`, late `0.14413070678710938`, last `0.15270233154296875`)
-- `weighted_regularizer_to_contrastive_ratio`: `goal ↓ | ↗ +54.61% improving` (early `0.0667222202939108`, mid `0.0329437448262181`, late `0.03028750823471251`, last `0.028996589606316913`)
-- `samples_per_sec`: `goal ↑ | ↘ -2.88% worsening` (early `1575.5664566260843`, mid `1531.3735887168505`, late `1530.1496274666802`, last `1399.0203442084614`)
-- `gpu_max_memory_gb`: `goal ≈ | ↗ +100.00% improving` (early `13.252925169950275`, mid `13.279059082097401`, late `13.279157161712646`, last `13.279157161712646`)
-- `grad_norm`: `goal ≈ | ↘ -100.00% worsening` (early `4.638080189338309`, mid `4.979553528603791`, late `6.072961742165445`, last `1.7659728527069092`)
-
-## Primary Metric Pressure
-
-- `train_loss`: `goal ↓ | ↗ +10.57% improving` (early `6.340343519442343`, mid `5.795929590401622`, late `5.670367905463295`, last `6.491608619689941`)
-- `val_loss`: `goal ↓ | ↘ -55.82% worsening` (early `1.2876316868363775`, mid `2.20697861268016`, late `2.006446816829876`, last `6.646750174145564`)
-- `grad_norm`: `goal ≈ | ↘ -100.00% worsening` (early `4.638080189338309`, mid `4.979553528603791`, late `6.072961742165445`, last `1.7659728527069092`)
-- `contrastive_loss`: `goal ↓ | → -1.64% flat` (early `1.409792113166324`, mid `1.3598130204084982`, late `1.43291388983014`, last `0.5768923759460449`)
-- `structure_bce_loss`: `goal ↓ | ↗ +39.75% improving` (early `0.12293951650489272`, mid `0.07652380578004556`, late `0.07407209518012302`, last `0.08383000642061234`)
-- `val_structure_bce_loss`: `goal ↓ | ↗ +12.20% improving` (early `0.0771060927848642`, mid `0.07029345531468391`, late `0.06769936999660872`, last `0.06532714269997086`)
-- `val_structure_fingerprint_cosine`: `goal ↑ | → +0.17% flat` (early `0.4147872725734487`, mid `0.4204998221830465`, late `0.4154996814322658`, last `0.4255251376889646`)
-- `val_hit_at_20`: `goal ↑ | ↗ +76.67% improving` (early `0.08158111572265625`, mid `0.094146728515625`, late `0.14413070678710938`, last `0.15270233154296875`)
-- `val_structure_top1_top2_gap_mean`: `goal ↑ | ↗ +54.91% improving` (early `0.07839679718017578`, mid `0.1310901641845703`, late `0.12144279479980469`, last `0.11855697631835938`)
-- `val_structure_uncertain_fraction`: `goal ↓ | → -0.03% flat` (early `0.9941177368164062`, mid `0.9762382507324219`, late `0.9944419860839844`, last `0.9922027587890625`)
-- `val_structure_confidence_separation`: `goal ↑ | ↘ -204.85% worsening` (early `-0.00795668972114072`, mid `-0.01309866098972634`, late `-0.024256365849851136`, last `-0.027957430157584895`)
-- `samples_per_sec`: `goal ↑ | ↘ -2.88% worsening` (early `1575.5664566260843`, mid `1531.3735887168505`, late `1530.1496274666802`, last `1399.0203442084614`)
-
-## Debug Metrics
-
-- `train_loss`: `6.491608619689941`
-- `train_loss_ema`: `6.519052214060582`
-- `val_loss`: `6.646750174145564`
-- `contrastive_loss`: `0.5768923759460449`
-- `val_ssl_loss`: `1.0397093277424574`
-- `variance_loss`: `0.00213623046875`
-- `covariance_loss`: `10.012618064880371`
-- `structure_bce_loss`: `0.08383000642061234`
-- `structure_retrieval_loss`: `10.630162239074707`
-- `val_structure_retrieval_loss`: `10.882395941764116`
-- `structure_fingerprint_cosine`: `0.46021854877471924`
-- `structure_hit_at_1`: `0.00390625`
-- `structure_hit_at_5`: `0.029296875`
-- `structure_hit_at_20`: `0.1171875`
-- `structure_target_rank_mean`: `314.703125`
-- `structure_logit_margin_mean`: `-1.0078125`
-- `structure_retrieval_logit_std`: `0.9839304089546204`
-- `val_structure_retrieval_logit_std`: `2.6622845763340592`
-- `structure_correct_logit_mean`: `9.1875`
-- `structure_top_negative_logit_mean`: `10.1875`
-- `val_structure_correct_logit_mean`: `9.49462890625`
-- `val_structure_top_negative_logit_mean`: `10.714599609375`
-- `structure_top1_top2_gap_mean`: `0.0986328125`
-- `structure_top1_top2_gap_norm_mean`: `0.10155132412910461`
-- `structure_confidence_candidate_count`: `2126.0`
-- `structure_close_fraction`: `0.029296875`
-- `structure_uncertain_fraction`: `0.970703125`
-- `structure_uncertain_hit_at_1`: `0.0040241447277367115`
-- `structure_confidence_separation`: `-0.0040241447277367115`
-- `val_structure_top1_top2_gap_mean`: `0.11855697631835938`
-- `val_structure_top1_top2_gap_norm_mean`: `0.05411380449368153`
-- `val_structure_confidence_candidate_count`: `4096.0`
-- `val_structure_close_fraction`: `0.0077972412109375`
-- `val_structure_uncertain_fraction`: `0.9922027587890625`
-- `val_structure_close_hit_at_1`: `0.014835291571216658`
-- `val_structure_uncertain_hit_at_1`: `0.027957430157584895`
-- `val_structure_confidence_separation`: `-0.027957430157584895`
-- `grad_norm`: `1.7659728527069092`
-- `weighted_regularizer_to_contrastive_ratio`: `0.028996589606316913`
-- `samples_per_sec`: `1399.0203442084614`
-- `samples_per_sec_60s`: `1399.0203442084614`
-- `samples_per_sec_300s`: `1547.033197547462`
-- `samples_per_sec_900s`: `1512.7885250414204`
-- `samples_per_sec_run_mean`: `1533.0231795943853`
-- `gpu_max_memory_gb`: `13.279157161712646`
-- `gpu_util_mean_pct`: `36.0`
-- `gpu_util_min_pct`: `18.0`
-- `gpu_util_max_pct`: `54.0`
-- `gpu_active_fraction`: `1.0`
-- `gpu_mem_used_mean_gb`: `14.1943359375`
-- `gpu_mem_util_mean_pct`: `14.848754175733243`
-- `gpu_snapshot_available`: `1.0`
-- `step_time_sec`: `0.3659703749981418`
-- `step_time_cv_300s`: `0.06743440395418321`
-- `step_time_cv_900s`: `0.09218780075615579`
-- `dataloader_wait_pct_60s`: `0.0961140629935623`
-- `dataloader_wait_pct_300s`: `0.0382592069912683`
-- `dataloader_wait_pct_900s`: `0.066640439237091`
-- `dataloader_wait_pct_run`: `0.06717802801040498`
-- `mfu_estimate`: `0.06267708747552383`

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-  "run_name": "final_v3_structure_alignment_v26_r1"
-}

metadata/day1_validation_report.json

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-{
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-  "created_at": "2026-04-13T21:36:19Z",
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metadata/eval_coverage.json

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metadata/latest_checkpoint.txt

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metadata/latest_metrics.json

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-  "val_structure_target_equivalent_count_mean": 1.0,
-  "val_structure_target_identity_collision_count": 23.69140625,
-  "val_structure_target_rank_mean": 379.8781280517578,
-  "val_structure_top1_top2_gap_mean": 0.11855697631835938,
-  "val_structure_top1_top2_gap_norm_mean": 0.05411380449368153,
-  "val_structure_top_negative_logit_mean": 10.714599609375,
-  "val_structure_uncertain_fraction": 0.9922027587890625,
-  "val_structure_uncertain_hit_at_1": 0.027957430157584895,
-  "variance_loss": 0.00213623046875,
-  "variance_weight": 0.8,
-  "weighted_covariance_loss": 0.015018927097320557,
-  "weighted_regularizer_to_contrastive_ratio": 0.028996589606316913,
-  "weighted_ssl_loss": 0.02968101501464844,
-  "weighted_structure_bce_loss": 0.08383000642061234,
-  "weighted_structure_retrieval_loss": 6.378097343444824,
-  "weighted_variance_loss": 0.001708984375
-}

metadata/perf_summary.json

@@ -1,16 +0,0 @@
-{
-  "logged_points": 521,
-  "train_loss_min": 3.2278988361358643,
-  "train_loss_max": 7.677141189575195,
-  "train_loss_last": 6.491608619689941,
-  "train_loss_ema_last": 6.519052214060582,
-  "weighted_regularizer_ratio_median": 0.02686493425176378,
-  "weighted_regularizer_ratio_p90": 0.09558363904110317,
-  "samples_per_sec_mean": 1545.3851888056406,
-  "samples_per_sec_min": 930.5498563655322,
-  "samples_per_sec_max": 2247.460787425693,
-  "step_time_mean": 0.33468720350667036,
-  "mfu_mean": 0.06923433462788683,
-  "mfu_max": 0.10068781126337953,
-  "gpu_mem_max_gb": 13.279157161712646
-}

metadata/results.md

@@ -1,171 +0,0 @@
-# MS/MS Training Run Result
-
-- Run name: `final_v3_structure_alignment_v26_r1`
-- Created at: `2026-04-13T21:36:19Z`
-- Dataset root: `/home/ubuntu/data/gems_v1_handoff_labeled_v26`
-- Shard counts: `{'train': 4, 'val': 2, 'test': 2}`
-
-## Primary Metrics
-
-- `train_loss`: `6.491608619689941`
-- `val_loss`: `6.646750174145564`
-- `grad_norm`: `1.7659728527069092`
-- `contrastive_loss`: `0.5768923759460449`
-- `structure_bce_loss`: `0.08383000642061234`
-- `val_structure_bce_loss`: `0.06532714269997086`
-- `val_structure_fingerprint_cosine`: `0.4255251376889646`
-- `different_inchikey_mean_cosine`: `0.004679911238535274`
-- `embedding_std`: `0.07216806709766388`
-- `val_hit_at_20`: `0.15270233154296875`
-- `val_structure_candidate_count`: `4119.69140625`
-- `val_structure_top1_top2_gap_mean`: `0.11855697631835938`
-- `val_structure_uncertain_fraction`: `0.9922027587890625`
-- `val_structure_clear_hit_at_1`: `0.0`
-- `val_structure_confidence_separation`: `-0.027957430157584895`
-- `samples_per_sec`: `1399.0203442084614`
-
-## Failure Mode Assessment
-
-- `dataset_shards_accessible`: pass. Observed shard counts {'train': 4, 'val': 2, 'test': 2}; the canonical Day 1 loader contract requires all splits to be readable.
-- `dataloader_streaming_stable`: pass. Training batches continued to arrive with positive throughput and no iterator stall.
-- `non_finite_loss_or_tensor_failure`: pass. Technical_Plan requires zero NaN or Inf tensors and finite train/val loss.
-- `validation_observability_gap`: pass. Engineering.md expects slope-aware monitoring; missing validation or retrieval metrics make trend judgment weaker.
-- `gpu_memory_instability`: pass. Technical_Plan Day 1 success requires stable GPU memory through the bounded run.
-- `checkpoint_save_reload_failure`: pass. Checkpoint save and reload is an explicit Day 1 success criterion.
-- `embedding_collapse`: pass. Engineering.md expects embedding variance monitoring and non-collapsed representations.
-- `regularizer_dominance`: pass. The current instability mode is regularization overpowering the SSL objective and producing jagged total loss.
-- `structure_supervision_gap`: pass. Once the bridge phase begins, Technical_Plan requires retrieval-oriented validation rather than only augmented contrastive loss.
-- `confidence_surface_gap`: pass. Structure-first qualification now requires explicit confidence diagnostics such as top-1/top-2 separation and uncertainty buckets, not just broader retrieval metrics.
-- `chemistry_target_backend_gap`: pass. The bridge phase should prefer chemistry-grounded fingerprint targets; hashed fallback targets weaken the retrieval signal.
-- `bridge_fit_without_ranking`: pass. Bridge runs must improve retrieval after fingerprint fit saturates; fitting BCE while val Hit@20 stays at candidate-bank baseline means ranking is not generalizing.
-- `metadata_shortcutting`: watch. Engineering.md flags acquisition-artefact shortcut risk; adduct and instrument embeddings remain deliberately down-scaled.
-
-## Pressure Summary
-
-- all metrics overall: `↗ improving (+21.89% weighted)`
-- all metrics weighted improvement: `+21.89%`
-- all metrics average improvement: `+34.52%`
-- all metrics weighted pressure score: `0.284`
-- all metrics counts: `up=21` `none=7` `down=11` `up_fraction=+53.85%`
-- primary metrics overall: `↗ improving (-4.45% weighted)`
-- primary metrics weighted improvement: `-4.45%`
-
-## Metric Pressure
-
-- `train_loss`: `goal ↓ | ↗ +10.57% improving` (early `6.340343519442343`, mid `5.795929590401622`, late `5.670367905463295`, last `6.491608619689941`)
-- `train_loss_ema`: `goal ↓ | ↗ +10.46% improving` (early `6.265581717362126`, mid `5.8371378655061745`, late `5.610470838300897`, last `6.519052214060582`)
-- `contrastive_loss`: `goal ↓ | → -1.64% flat` (early `1.409792113166324`, mid `1.3598130204084982`, late `1.43291388983014`, last `0.5768923759460449`)
-- `val_loss`: `goal ↓ | ↘ -55.82% worsening` (early `1.2876316868363775`, mid `2.20697861268016`, late `2.006446816829876`, last `6.646750174145564`)
-- `val_ssl_loss`: `goal ↓ | → +2.32% flat` (early `1.0849772497183745`, mid `1.0747967428483425`, late `1.0598136518327963`, last `1.0397093277424574`)
-- `structure_bce_loss`: `goal ↓ | ↗ +39.75% improving` (early `0.12293951650489272`, mid `0.07652380578004556`, late `0.07407209518012302`, last `0.08383000642061234`)
-- `val_structure_bce_loss`: `goal ↓ | ↗ +12.20% improving` (early `0.0771060927848642`, mid `0.07029345531468391`, late `0.06769936999660872`, last `0.06532714269997086`)
-- `structure_retrieval_loss`: `goal ↓ | ↗ +10.09% improving` (early `10.237479978903181`, mid `9.41523380775672`, late `9.204101929719421`, last `10.630162239074707`)
-- `val_structure_retrieval_loss`: `goal ↓ | → +4.86% flat` (early `11.562767315655947`, mid `12.150514367967844`, late `11.000247791409492`, last `10.882395941764116`)
-- `structure_fingerprint_cosine`: `goal ↑ | ↗ +17.59% improving` (early `0.3965519580968543`, mid `0.4464927057310336`, late `0.46629545006943846`, last `0.46021854877471924`)
-- `val_structure_fingerprint_cosine`: `goal ↑ | → +0.17% flat` (early `0.4147872725734487`, mid `0.4204998221830465`, late `0.4154996814322658`, last `0.4255251376889646`)
-- `structure_target_rank_mean`: `goal ↓ | ↗ +58.80% improving` (early `351.84337743858384`, mid `176.16389315390174`, late `144.9534280711207`, last `314.703125`)
-- `val_structure_target_rank_mean`: `goal ↓ | ↗ +45.45% improving` (early `760.7540435791016`, mid `683.3385162353516`, late `415.0084457397461`, last `379.8781280517578`)
-- `structure_correct_logit_mean`: `goal ↑ | ↗ +47.31% improving` (early `6.134031791907514`, mid `9.474891618497109`, late `9.035739942528735`, last `9.1875`)
-- `val_structure_correct_logit_mean`: `goal ↑ | ↗ +16.44% improving` (early `8.0311279296875`, mid `8.441162109375`, late `9.3515625`, last `9.49462890625`)
-- `structure_top_negative_logit_mean`: `goal ↓ | ↘ -39.72% worsening` (early `7.262102601156069`, mid `10.490606936416185`, late `10.14691091954023`, last `10.1875`)
-- `val_structure_top_negative_logit_mean`: `goal ↓ | ↘ -16.08% worsening` (early `9.2255859375`, mid `10.51171875`, late `10.708740234375`, last `10.714599609375`)
-- `structure_logit_margin_mean`: `goal ↑ | → +1.23% flat` (early `-1.1263999277456647`, mid `-1.0154725885115607`, late `-1.1125740840517242`, last `-1.0078125`)
-- `val_structure_logit_margin_mean`: `goal ↑ | ↘ -13.67% worsening` (early `-1.194091796875`, mid `-2.0707931518554688`, late `-1.3573150634765625`, last `-1.221923828125`)
-- `structure_retrieval_logit_std`: `goal ↑ | ↗ +112.06% improving` (early `1.0455416592559375`, mid `2.0036371215919537`, late `2.2171744848119803`, last `0.9839304089546204`)
-- `val_structure_retrieval_logit_std`: `goal ↑ | ↗ +102.33% improving` (early `1.2326001720502973`, mid `2.022283688886091`, late `2.49387572822161`, last `2.6622845763340592`)
-- `structure_top1_top2_gap_mean`: `goal ↑ | ↗ +59.22% improving` (early `0.09793567106213873`, mid `0.12284365968208093`, late `0.1559343009159483`, last `0.0986328125`)
-- `val_structure_top1_top2_gap_mean`: `goal ↑ | ↗ +54.91% improving` (early `0.07839679718017578`, mid `0.1310901641845703`, late `0.12144279479980469`, last `0.11855697631835938`)
-- `structure_top1_top2_gap_norm_mean`: `goal ↑ | ↘ -35.65% worsening` (early `0.12215662799301864`, mid `0.07032911504236604`, late `0.07860379065547524`, last `0.10155132412910461`)
-- `val_structure_top1_top2_gap_norm_mean`: `goal ↑ | ↘ -16.83% worsening` (early `0.06950851557485294`, mid `0.07577372609375743`, late `0.0578127475164365`, last `0.05411380449368153`)
-- `structure_uncertain_fraction`: `goal ↓ | ↘ -6.11% worsening` (early `0.924663565751445`, mid `0.984747561416185`, late `0.9811422413793104`, last `0.970703125`)
-- `val_structure_uncertain_fraction`: `goal ↓ | → -0.03% flat` (early `0.9941177368164062`, mid `0.9762382507324219`, late `0.9944419860839844`, last `0.9922027587890625`)
-- `structure_confidence_separation`: `goal ↑ | ↘ -531.56% worsening` (early `-0.007918493679557749`, mid `-0.032136323077151974`, late `-0.05001017991881603`, last `-0.0040241447277367115`)
-- `val_structure_confidence_separation`: `goal ↑ | ↘ -204.85% worsening` (early `-0.00795668972114072`, mid `-0.01309866098972634`, late `-0.024256365849851136`, last `-0.027957430157584895`)
-- `structure_hit_at_1`: `goal ↑ | ↗ +549.68% improving` (early `0.007880238439306358`, mid `0.032706376445086706`, late `0.051196569683908046`, last `0.00390625`)
-- `structure_hit_at_5`: `goal ↑ | ↗ +402.47% improving` (early `0.03360955563583815`, mid `0.11673591040462428`, late `0.16887796336206898`, last `0.029296875`)
-- `structure_hit_at_20`: `goal ↑ | ↗ +239.46% improving` (early `0.10721865968208093`, mid `0.28105807442196534`, late `0.3639659662356322`, last `0.1171875`)
-- `val_hit_at_1`: `goal ↑ | → +207.79% flat` (early `0.0079345703125`, mid `0.01372528076171875`, late `0.02442169189453125`, last `0.0282135009765625`)
-- `val_hit_at_5`: `goal ↑ | ↗ +134.85% improving` (early `0.0288543701171875`, mid `0.0425567626953125`, late `0.0677642822265625`, last `0.0726776123046875`)
-- `val_hit_at_20`: `goal ↑ | ↗ +76.67% improving` (early `0.08158111572265625`, mid `0.094146728515625`, late `0.14413070678710938`, last `0.15270233154296875`)
-- `weighted_regularizer_to_contrastive_ratio`: `goal ↓ | ↗ +54.61% improving` (early `0.0667222202939108`, mid `0.0329437448262181`, late `0.03028750823471251`, last `0.028996589606316913`)
-- `samples_per_sec`: `goal ↑ | ↘ -2.88% worsening` (early `1575.5664566260843`, mid `1531.3735887168505`, late `1530.1496274666802`, last `1399.0203442084614`)
-- `gpu_max_memory_gb`: `goal ≈ | ↗ +100.00% improving` (early `13.252925169950275`, mid `13.279059082097401`, late `13.279157161712646`, last `13.279157161712646`)
-- `grad_norm`: `goal ≈ | ↘ -100.00% worsening` (early `4.638080189338309`, mid `4.979553528603791`, late `6.072961742165445`, last `1.7659728527069092`)
-
-## Primary Metric Pressure
-
-- `train_loss`: `goal ↓ | ↗ +10.57% improving` (early `6.340343519442343`, mid `5.795929590401622`, late `5.670367905463295`, last `6.491608619689941`)
-- `val_loss`: `goal ↓ | ↘ -55.82% worsening` (early `1.2876316868363775`, mid `2.20697861268016`, late `2.006446816829876`, last `6.646750174145564`)
-- `grad_norm`: `goal ≈ | ↘ -100.00% worsening` (early `4.638080189338309`, mid `4.979553528603791`, late `6.072961742165445`, last `1.7659728527069092`)
-- `contrastive_loss`: `goal ↓ | → -1.64% flat` (early `1.409792113166324`, mid `1.3598130204084982`, late `1.43291388983014`, last `0.5768923759460449`)
-- `structure_bce_loss`: `goal ↓ | ↗ +39.75% improving` (early `0.12293951650489272`, mid `0.07652380578004556`, late `0.07407209518012302`, last `0.08383000642061234`)
-- `val_structure_bce_loss`: `goal ↓ | ↗ +12.20% improving` (early `0.0771060927848642`, mid `0.07029345531468391`, late `0.06769936999660872`, last `0.06532714269997086`)
-- `val_structure_fingerprint_cosine`: `goal ↑ | → +0.17% flat` (early `0.4147872725734487`, mid `0.4204998221830465`, late `0.4154996814322658`, last `0.4255251376889646`)
-- `val_hit_at_20`: `goal ↑ | ↗ +76.67% improving` (early `0.08158111572265625`, mid `0.094146728515625`, late `0.14413070678710938`, last `0.15270233154296875`)
-- `val_structure_top1_top2_gap_mean`: `goal ↑ | ↗ +54.91% improving` (early `0.07839679718017578`, mid `0.1310901641845703`, late `0.12144279479980469`, last `0.11855697631835938`)
-- `val_structure_uncertain_fraction`: `goal ↓ | → -0.03% flat` (early `0.9941177368164062`, mid `0.9762382507324219`, late `0.9944419860839844`, last `0.9922027587890625`)
-- `val_structure_confidence_separation`: `goal ↑ | ↘ -204.85% worsening` (early `-0.00795668972114072`, mid `-0.01309866098972634`, late `-0.024256365849851136`, last `-0.027957430157584895`)
-- `samples_per_sec`: `goal ↑ | ↘ -2.88% worsening` (early `1575.5664566260843`, mid `1531.3735887168505`, late `1530.1496274666802`, last `1399.0203442084614`)
-
-## Debug Metrics
-
-- `train_loss`: `6.491608619689941`
-- `train_loss_ema`: `6.519052214060582`
-- `val_loss`: `6.646750174145564`
-- `contrastive_loss`: `0.5768923759460449`
-- `val_ssl_loss`: `1.0397093277424574`
-- `variance_loss`: `0.00213623046875`
-- `covariance_loss`: `10.012618064880371`
-- `structure_bce_loss`: `0.08383000642061234`
-- `structure_retrieval_loss`: `10.630162239074707`
-- `val_structure_retrieval_loss`: `10.882395941764116`
-- `structure_fingerprint_cosine`: `0.46021854877471924`
-- `structure_hit_at_1`: `0.00390625`
-- `structure_hit_at_5`: `0.029296875`
-- `structure_hit_at_20`: `0.1171875`
-- `structure_target_rank_mean`: `314.703125`
-- `structure_logit_margin_mean`: `-1.0078125`
-- `structure_retrieval_logit_std`: `0.9839304089546204`
-- `val_structure_retrieval_logit_std`: `2.6622845763340592`
-- `structure_correct_logit_mean`: `9.1875`
-- `structure_top_negative_logit_mean`: `10.1875`
-- `val_structure_correct_logit_mean`: `9.49462890625`
-- `val_structure_top_negative_logit_mean`: `10.714599609375`
-- `structure_top1_top2_gap_mean`: `0.0986328125`
-- `structure_top1_top2_gap_norm_mean`: `0.10155132412910461`
-- `structure_confidence_candidate_count`: `2126.0`
-- `structure_close_fraction`: `0.029296875`
-- `structure_uncertain_fraction`: `0.970703125`
-- `structure_uncertain_hit_at_1`: `0.0040241447277367115`
-- `structure_confidence_separation`: `-0.0040241447277367115`
-- `val_structure_top1_top2_gap_mean`: `0.11855697631835938`
-- `val_structure_top1_top2_gap_norm_mean`: `0.05411380449368153`
-- `val_structure_confidence_candidate_count`: `4096.0`
-- `val_structure_close_fraction`: `0.0077972412109375`
-- `val_structure_uncertain_fraction`: `0.9922027587890625`
-- `val_structure_close_hit_at_1`: `0.014835291571216658`
-- `val_structure_uncertain_hit_at_1`: `0.027957430157584895`
-- `val_structure_confidence_separation`: `-0.027957430157584895`
-- `grad_norm`: `1.7659728527069092`
-- `weighted_regularizer_to_contrastive_ratio`: `0.028996589606316913`
-- `samples_per_sec`: `1399.0203442084614`
-- `samples_per_sec_60s`: `1399.0203442084614`
-- `samples_per_sec_300s`: `1547.033197547462`
-- `samples_per_sec_900s`: `1512.7885250414204`
-- `samples_per_sec_run_mean`: `1533.0231795943853`
-- `gpu_max_memory_gb`: `13.279157161712646`
-- `gpu_util_mean_pct`: `36.0`
-- `gpu_util_min_pct`: `18.0`
-- `gpu_util_max_pct`: `54.0`
-- `gpu_active_fraction`: `1.0`
-- `gpu_mem_used_mean_gb`: `14.1943359375`
-- `gpu_mem_util_mean_pct`: `14.848754175733243`
-- `gpu_snapshot_available`: `1.0`
-- `step_time_sec`: `0.3659703749981418`
-- `step_time_cv_300s`: `0.06743440395418321`
-- `step_time_cv_900s`: `0.09218780075615579`
-- `dataloader_wait_pct_60s`: `0.0961140629935623`
-- `dataloader_wait_pct_300s`: `0.0382592069912683`
-- `dataloader_wait_pct_900s`: `0.066640439237091`
-- `dataloader_wait_pct_run`: `0.06717802801040498`
-- `mfu_estimate`: `0.06267708747552383`

metadata/training_surface.json

@@ -1,68 +0,0 @@
-{
-  "created_at": "2026-04-13T20:20:55Z",
-  "run_name": "final_v3_structure_alignment_v26_r1",
-  "wandb_project": "Nexa_Mol",
-  "wandb_run_name": "final_v3_structure_alignment_v26_r1",
-  "wandb_group": "Structure-Alignment",
-  "dataset_root": "/home/ubuntu/data/gems_v1_handoff_labeled_v26",
-  "selected_shards_json": "/home/ubuntu/data/gems_v1_handoff_labeled_v26/selected_shards.json",
-  "selected_shards_exists": true,
-  "phase_ready_marker": "",
-  "phase_ready_exists": false,
-  "phase_receipt_path": "",
-  "phase_receipt_exists": false,
-  "train_shard_surface_mode": "train_only",
-  "refresh_selected_shards_on_iterator_reset": false,
-  "parent_policy": "local_only",
-  "labeled_eval_root": "",
-  "query_dataset_root": "",
-  "bank_dataset_root": "",
-  "primary_checkpoint_run_name": "",
-  "fallback_checkpoint_run_name": "",
-  "local_parent_checkpoint": "/home/ubuntu/artifacts/nexa_mol/v1_full_pretrain/phase1_blackwell_v3/Final_V3.pt",
-  "current_checkpoint_path": "",
-  "current_checkpoint_exists": true,
-  "disable_auto_resume": true,
-  "resume_model_only": true,
-  "objective": "hybrid",
-  "ssl_weight": 0.05,
-  "structure_weight": 1.0,
-  "structure_post_saturation_weight": 0.0,
-  "structure_threshold": 0.0,
-  "structure_lock_patience": 0,
-  "train_retrieval_watch_only": false,
-  "freeze_retrieval_head": false,
-  "retrieval_weight": 0.6,
-  "batch_size": 512,
-  "eval_batch_size": 512,
-  "num_workers": 12,
-  "grad_accum_steps": 1,
-  "loader_prefetch_factor": 4,
-  "log_every": 20,
-  "sync_every": 1000,
-  "amp_mode": "",
-  "additional_steps": 10000,
-  "max_steps": 91001,
-  "eval_batches": 24,
-  "eval_batches_per_shard": 0,
-  "eval_start_after_steps": 0,
-  "deep_eval_every": 2000,
-  "deep_eval_start_after_steps": 2000,
-  "deep_eval_batches": 256,
-  "deep_eval_single_view": false,
-  "deep_eval_structure_only": false,
-  "active_train_shards": 0,
-  "prefetch_train_shards": 0,
-  "val_shards": 0,
-  "test_shards": 0,
-  "train_offset": 0,
-  "val_offset": 0,
-  "test_offset": 0,
-  "selected_shards_summary": {
-    "train_count": 4,
-    "val_count": 2,
-    "test_count": 2,
-    "prefetch_count": 0,
-    "subset_strategy": "v26_native_confidence_policy_subset"
-  }
-}