NexaMass-V3-Struct / configs /structure_alignment_config.json
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{
"checkpoint": {
"bytes": 160482975,
"config": {
"collision_max": 200.0,
"dropout": 0.1,
"fingerprint_dim": 2048,
"heads": 8,
"layers": 6,
"max_peaks": 256,
"metadata_scale": 0.02,
"model_dim": 384,
"mz_max": 2000.0,
"projection_dim": 192,
"retrieval_mlp_hidden_dim": 512,
"target_projection_dim": 256
},
"created_at": "2026-04-13T21:34:38Z",
"file": "weights/NexaMass-V3-Struct.pt",
"metrics_keys": [
"backbone_lr",
"contrastive_loss",
"covariance_loss",
"covariance_to_contrastive_ratio",
"covariance_weight",
"dataloader_time_sec",
"dataloader_wait_pct_300s",
"dataloader_wait_pct_60s",
"dataloader_wait_pct_900s",
"dataloader_wait_pct_run",
"distributed_rank",
"distributed_world_size",
"effective_batch_size",
"effective_hard_negative_scale",
"effective_retrieval_weight",
"effective_structure_bce_weight",
"embedding_std",
"global_batch_size",
"gpu_active_fraction",
"gpu_count_observed",
"gpu_max_memory_gb",
"gpu_mem_used_mean_gb",
"gpu_mem_util_mean_pct",
"gpu_memory_utilization",
"gpu_snapshot_available",
"gpu_util_max_pct",
"gpu_util_mean_pct",
"gpu_util_min_pct",
"grad_norm",
"local_batch_size",
"lr",
"mfu_estimate",
"msms_objective",
"optimizer_step",
"regularizer_ramp",
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"retrieval_head_lr",
"samples_per_sec",
"samples_per_sec_300s",
"samples_per_sec_60s",
"samples_per_sec_900s",
"samples_per_sec_run_mean",
"step_time_cv_300s",
"step_time_cv_60s",
"step_time_cv_900s",
"step_time_sec",
"structure_bce_locked",
"structure_bce_loss",
"structure_candidate_count",
"structure_clear_fraction",
"structure_clear_hit_at_1",
"structure_close_fraction",
"structure_close_hit_at_1",
"structure_confidence_bucket_score_mean",
"structure_confidence_bucket_score_mode",
"structure_confidence_candidate_count",
"structure_confidence_clear_threshold",
"structure_confidence_close_threshold",
"structure_confidence_eval_key_mode",
"structure_confidence_separation",
"structure_correct_logit_mean",
"structure_fingerprint_cosine",
"structure_hard_negative_bonus_applied",
"structure_hard_negative_bonus_mean",
"structure_hard_negative_scale",
"structure_head_lr",
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"structure_hit_at_20",
"structure_hit_at_5",
"structure_local_ce_loss",
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"structure_local_rerank_loss",
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"structure_local_rerank_score_scale",
"structure_logit_margin_mean",
"structure_margin_loss",
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"structure_prefilter_candidate_count",
"structure_retrieval_logit_std",
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"structure_skipped_query_fraction",
"structure_soft_target_exact_mix",
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"structure_soft_target_loss_weight",
"structure_target_backend",
"structure_target_equivalent_count_mean",
"structure_target_identity_collision_count",
"structure_target_rank_mean",
"structure_to_ssl_ratio",
"structure_top1_top2_gap_mean",
"structure_top1_top2_gap_norm_mean",
"structure_top_negative_logit_mean",
"structure_uncertain_fraction",
"structure_uncertain_hit_at_1",
"structure_valid_query_fraction",
"train_loss",
"train_loss_ema",
"train_retrieval_bank_size",
"variance_loss",
"variance_weight",
"weighted_covariance_loss",
"weighted_regularizer_to_contrastive_ratio",
"weighted_ssl_loss",
"weighted_structure_bce_loss",
"weighted_structure_retrieval_loss",
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],
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"model_state_file": "weights/NexaMass-V3-Struct-model_state.pt",
"param_count": 14106690,
"state_tensors": 103,
"step": 91001
},
"dataset": "corrected labeled GeMS handoff surface with enforced molecular labels",
"evaluation_summary": {
"embedding_std": 0.0722,
"gallery_exact_fingerprint_decodes": 11,
"gallery_size": 20,
"massspecgym_test_hit20_adapter": 0.3505,
"validation_fingerprint_cosine": 0.4255,
"validation_structure_bce": 0.0653
},
"name": "NexaMass-V3-Struct alignment checkpoint",
"objective_weights": {
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"retrieval_soft_target_loss_weight": 0.3,
"retrieval_weight": 0.6,
"ssl_preservation_weight": 0.05,
"structure_bce_weight": 1.0
},
"parent_checkpoint": "weights/Final_V3-model_state.pt",
"phase": "RDKit Morgan fingerprint structure alignment"
}