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configs:
- config_name: chains
data_files:
- split: train
path: chains/train-*
- split: valid
path: chains/valid-*
- split: test
path: chains/test-*
- config_name: complexes
data_files:
- split: train
path: complexes/train-*
- split: valid
path: complexes/valid-*
- split: test
path: complexes/test-*
---
# PDB-Chain-Complex-Benchmark-Rigor
Rigor rebuild of `Synthyra/PDB-Chain-Complex-Benchmark` with split assignments
recomputed from the published chain and complex parquet artifacts.
## Split Policy
Splits are assigned by connected components over exact sequence, sequence hash,
30% sequence cluster, structure cluster, source split component, same-PDB
asymmetric-unit membership, chain assembly membership, and biological assembly
co-membership from the complex rows. The target is 90/5/5 by component count.
The rebuild hard-fails before upload if any chain or complex member leaks across
train, validation, and test by chain UID, sequence, sequence hash, 30% sequence
cluster, structure cluster, or recomputed split component.
Complex list-valued payload columns are regenerated from the chain table during
the rebuild, then asserted directly from the emitted payloads, including
`asymmetric_unit_chain_uids`.
After writing parquet, the builder reloads the emitted chain and complex shards
and reruns split-routing, payload-consistency, and disjointness checks from the
serialized files.
This artifact-only rebuild does not rerun Foldseek or MMseqs2. It enforces and
verifies the published cluster labels plus optional external sequence
verification edges when supplied.
## Build Metadata
```json
{
"batch_size": 16384,
"chain_scan": {
"assembly_membership_edges_seen": 1138910,
"asymmetric_unit_membership_edges_seen": 1069448,
"chains_scanned": 1069448
},
"chain_write": {
"file_counts": {
"test": 1,
"train": 22,
"valid": 1
},
"row_counts": {
"test": 334,
"train": 1068780,
"valid": 334
}
},
"complex_edge_scan": {
"complex_member_edges_seen": 775327,
"complexes_scanned_for_edges": 363583
},
"complex_write": {
"file_counts": {
"test": 1,
"train": 8,
"valid": 1
},
"member_chain_rows": 1138910,
"member_fields": {
"asymmetric_unit_chain_uids": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 1069448
},
"chain_uid": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 1069448
},
"sequence_clusters_30": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 48857
},
"sequence_hashes": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 183467
},
"sequences": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 183467
},
"split_components": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 6684
},
"structure_clusters": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 66989
}
},
"row_counts": {
"test": 335,
"train": 362909,
"valid": 339
}
},
"component_stats": {
"split_component_count": 6684,
"test_component_count": 334,
"train_component_count": 6016,
"valid_component_count": 334
},
"cpu_count": 32,
"elapsed_seconds": 75.866,
"foldseek_path": "",
"include_source_split_component_edges": true,
"max_rows_per_shard": 50000,
"mmseqs_path": "",
"nvidia-smi_path": "C:\\Windows\\system32\\nvidia-smi.EXE",
"nvidia-smi_version": "Tue Jun 30 18:02:49 2026 \n+-----------------------------------------------------------------------------------------+\n| NVIDIA-SMI 580.88 Driver Version: 580.88 CUDA Version: 13.0 |\n+-----------------------------------------+------------------------+----------------------+\n| GPU Name Driver-Model | Bus-Id Disp.A | Volatile Uncorr. ECC |\n| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |\n| | | MIG M. |\n|=========================================+========================+======================|\n| 0 NVIDIA GeForce RTX 4070 ... WDDM | 00000000:01:00.0 On | N/A |\n| N/A 41C P8 6W / 121W | 984MiB / 8188MiB | 10% Default |\n| | | N/A |\n+-----------------------------------------+------------------------+----------------------+\n\n+-----------------------------------------------------------------------------------------+\n| Processes: |\n| GPU GI CI PID Type Process name GPU Memory |\n| ID ID Usage |\n|=========================================================================================|\n| 0 N/A N/A 8844 C+G ...indows\\System32\\ShellHost.exe N/A |\n| 0 N/A N/A 10456 C+G ..._cw5n1h2txyewy\\SearchHost.exe N/A |\n| 0 N/A N/A 13212 C+G ...5n1h2txyewy\\TextInputHost.exe N/A |\n| 0 N/A N/A 36048 C+G ...Chrome\\Application\\chrome.exe N/A |\n| 0 N/A N/A 41088 C+G ...ntrolPanel\\SystemSettings.exe N/A |\n| 0 N/A N/A 63696 C+G ...8bbwe\\PhoneExperienceHost.exe N/A |\n| 0 N/A N/A 72372 C+G ...y\\StartMenuExperienceHost.exe N/A |\n| 0 N/A N/A 84244 C+G ...xyewy\\ShellExperienceHost.exe N/A |\n| 0 N/A N/A 104536 C+G C:\\Windows\\explorer.exe N/A |\n| 0 N/A N/A 152648 C+G ....0.4022.80\\msedgewebview2.exe N/A |\n| 0 N/A N/A 152984 C+G ...e Experience\\NVIDIA Share.exe N/A |\n| 0 N/A N/A 155976 C+G ...em32\\ApplicationFrameHost.exe N/A |\n| 0 N/A N/A 162800 C+G ...p\\app-3.6.1\\GitHubDesktop.exe N/A |\n| 0 N/A N/A 196292 C+G ...Chrome\\Application\\chrome.exe N/A |\n| 0 N/A N/A 198076 C+G ...__2p2nqsd0c76g0\\app\\Codex.exe N/A |\n| 0 N/A N/A 206536 C+G ...2txyewy\\CrossDeviceResume.exe N/A |\n| 0 N/A N/A 221536 C+G ...Files\\Notepad++\\notepad++.exe N/A |\n+-----------------------------------------------------------------------------------------+",
"platform": "Windows-11-10.0.26200-SP0",
"python": "3.12.13",
"seed": 42,
"sequence_verification_max_unknown_fraction": 0.0,
"source_chain_rows": 1069448,
"source_complex_rows": 363583,
"source_repo_id": "Synthyra/PDB-Chain-Complex-Benchmark",
"source_snapshot_dir": "C:\\tmp\\hf_pdb_chain_complex_cache\\datasets--Synthyra--PDB-Chain-Complex-Benchmark\\snapshots\\3eb55ee7289dfedfbddf0cde48b68c5395783ccf",
"target_repo_id": "Synthyra/PDB-Chain-Complex-Benchmark-Rigor",
"test_frac": 0.05,
"valid_frac": 0.05
}
```
## Leakage Assertions
```json
{
"chains": {
"fields": {
"chain_uid": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 1069448
},
"seqs": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 183467
},
"sequence_cluster_30": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 48857
},
"sequence_hash": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 183467
},
"split_component": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 6684
},
"structure_cluster": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 66989
}
},
"post_write": {
"fields": {
"chain_uid": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 1069448
},
"seqs": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 183467
},
"sequence_cluster_30": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 48857
},
"sequence_hash": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 183467
},
"split_component": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 6684
},
"structure_cluster": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 66989
}
},
"rows": 1069448,
"split_counts": {
"test": 334,
"train": 1068780,
"valid": 334
}
},
"rows": 1069448,
"sequence_verification_edges": {
"checked_edges": 0,
"cross_split_edges": 0,
"provided": false,
"skipped_self_edges": 0,
"skipped_unknown_edges": 0,
"total_edges": 0
},
"split_counts": {
"test": 334,
"train": 1068780,
"valid": 334
}
},
"complexes": {
"member_chain_rows": 1138910,
"member_fields": {
"asymmetric_unit_chain_uids": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 1069448
},
"chain_uid": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 1069448
},
"sequence_clusters_30": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 48857
},
"sequence_hashes": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 183467
},
"sequences": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 183467
},
"split_components": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 6684
},
"structure_clusters": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 66989
}
},
"member_split_consistency": "passed",
"payload_columns_regenerated_from_chains": true,
"post_write": {
"asymmetric_unit_chain_rows": 1760175,
"member_chain_rows": 1138910,
"member_fields": {
"asymmetric_unit_chain_uids": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 1069448
},
"chain_uid": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 1069448
},
"sequence_clusters_30": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 48857
},
"sequence_hashes": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 183467
},
"sequences": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 183467
},
"split_components": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 6684
},
"structure_clusters": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 66989
}
},
"payload_columns_match_chain_rows": true,
"rows": 363583,
"shard_split_routing": "passed",
"split_counts": {
"test": 335,
"train": 362909,
"valid": 339
}
},
"rows": 363583,
"split_counts": {
"test": 335,
"train": 362909,
"valid": 339
}
}
}
```
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