| ---
|
| 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
|
| }
|
| }
|
| }
|
| ```
|
|
|
