| { |
| "architecture_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 |
| }, |
| "architectures": [ |
| "NexaMassSpectralEncoder" |
| ], |
| "evaluation_adapters": { |
| "massspecgym": { |
| "benchmark": "MassSpecGym molecule retrieval", |
| "claim_boundary": "top-k transfer signal; ranking and confidence remain open decision-layer problems", |
| "path": "evaluation/massspecgym/run_massspecgym_retrieval_hf.py", |
| "reference_result": "test Hit@20 0.3505 with frozen V3 projected-dot scorer under Hit@k-only evaluation" |
| } |
| }, |
| "foundation_checkpoint": "weights/Final_V3-model_state.safetensors", |
| "foundation_checkpoint_format": "safetensors", |
| "full_training_checkpoints": { |
| "location": "Wasabi object storage", |
| "note": "Optimizer-bearing full training checkpoints are intentionally not part of the public Hugging Face payload; the public release contains model-state weights only." |
| }, |
| "input_contract": { |
| "feature_width": 8, |
| "mask": "boolean valid-peak mask, shape [batch, max_peaks]", |
| "max_peaks": 256, |
| "metadata_embeddings": [ |
| "adduct_id", |
| "instrument_id" |
| ], |
| "per_peak_features": [ |
| "mz", |
| "intensity", |
| "mz_to_precursor", |
| "peak_rank", |
| "precursor_mz", |
| "charge", |
| "collision_energy", |
| "peak_count" |
| ] |
| }, |
| "library_name": "pytorch", |
| "model_type": "nexamass", |
| "not_supported": [ |
| "unrestricted de novo molecule generation", |
| "calibrated top-1 molecular identification without external validation" |
| ], |
| "object_storage_pytorch_weights": { |
| "files": [ |
| "weights/Final_V3-model_state.pt", |
| "weights/NexaMass-V3-Struct-model_state.pt" |
| ], |
| "location": "Wasabi object storage", |
| "note": "PyTorch .pt model-state files are retained in object storage. The public Hugging Face payload is safetensors-only.", |
| "path": "wasabi:nexa-ms/models/dreams_pretrain_v1/checkpoints/NexaMass-V3-Struct/hf_release/weights/" |
| }, |
| "outputs": { |
| "morgan_fingerprint_logits": 2048, |
| "retrieval_target_dim": 256, |
| "ssl_projection_dim": 192, |
| "structure_query_dim": 256 |
| }, |
| "parameter_count": 14106690, |
| "primary_checkpoint": "weights/NexaMass-V3-Struct-model_state.safetensors", |
| "primary_checkpoint_format": "safetensors", |
| "public_weight_files": [ |
| "weights/NexaMass-V3-Struct-model_state.safetensors", |
| "weights/Final_V3-model_state.safetensors" |
| ], |
| "public_weight_format": "safetensors", |
| "recommended_inference": "Use the structure-aligned model-state checkpoint for spectrum embeddings and Morgan fingerprint probability vectors, then compare against a candidate molecular fingerprint bank.", |
| "task": "MS/MS spectral representation learning and RDKit Morgan fingerprint alignment" |
| } |
|
|
