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Build rigor split dataset from published benchmark artifacts

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  1. README.md +196 -0
  2. artifacts/chain_split_assignments.parquet +3 -0
  3. artifacts/composite_clusters.parquet +3 -0
  4. artifacts/leakage_assertions.json +89 -0
  5. artifacts/metadata.json +58 -0
  6. chains/test-00000.parquet +3 -0
  7. chains/train-00000.parquet +3 -0
  8. chains/train-00001.parquet +3 -0
  9. chains/train-00002.parquet +3 -0
  10. chains/train-00003.parquet +3 -0
  11. chains/train-00004.parquet +3 -0
  12. chains/train-00005.parquet +3 -0
  13. chains/train-00006.parquet +3 -0
  14. chains/train-00007.parquet +3 -0
  15. chains/train-00008.parquet +3 -0
  16. chains/train-00009.parquet +3 -0
  17. chains/train-00010.parquet +3 -0
  18. chains/train-00011.parquet +3 -0
  19. chains/train-00012.parquet +3 -0
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  24. chains/train-00017.parquet +3 -0
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  28. chains/train-00021.parquet +3 -0
  29. chains/valid-00000.parquet +3 -0
  30. complexes/test-00000.parquet +3 -0
  31. complexes/train-00000.parquet +3 -0
  32. complexes/train-00001.parquet +3 -0
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  37. complexes/train-00006.parquet +3 -0
  38. complexes/train-00007.parquet +3 -0
  39. complexes/valid-00000.parquet +3 -0
README.md ADDED
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+ ---
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+ configs:
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+ - config_name: chains
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+ data_files:
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+ - split: train
6
+ path: chains/train-*
7
+ - split: valid
8
+ path: chains/valid-*
9
+ - split: test
10
+ path: chains/test-*
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+ - config_name: complexes
12
+ data_files:
13
+ - split: train
14
+ path: complexes/train-*
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+ - split: valid
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+ path: complexes/valid-*
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+ - split: test
18
+ path: complexes/test-*
19
+ ---
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+
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+ # PDB-Chain-Complex-Benchmark-Rigor
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+
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+ Rigor rebuild of `Synthyra/PDB-Chain-Complex-Benchmark` with split assignments
24
+ recomputed from the published chain and complex parquet artifacts.
25
+
26
+ ## Split Policy
27
+
28
+ Splits are assigned by connected components over exact sequence, sequence hash,
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+ 30% sequence cluster, structure cluster, source split component, chain assembly
30
+ membership, and biological assembly co-membership from the complex rows. The
31
+ target is 90/5/5 by component count.
32
+
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+ The rebuild hard-fails before upload if any chain or complex member leaks across
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+ train, validation, and test by chain UID, sequence, sequence hash, 30% sequence
35
+ cluster, structure cluster, or recomputed split component.
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+
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+ This artifact-only rebuild does not rerun Foldseek or MMseqs2. It enforces and
38
+ verifies the published cluster labels plus optional external sequence
39
+ verification edges when supplied.
40
+
41
+ ## Build Metadata
42
+
43
+ ```json
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+ {
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+ "batch_size": 16384,
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+ "chain_scan": {
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+ "assembly_membership_edges_seen": 1138910,
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+ "chains_scanned": 1069448
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+ },
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+ "chain_write": {
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+ "test": 1,
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+ "train": 22,
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+ "valid": 1
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+ },
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+ "test": 337,
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+ "train": 1068774,
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+ "valid": 337
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+ }
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+ },
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+ "complex_edge_scan": {
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+ "complex_member_edges_seen": 775327,
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+ },
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+ "complex_write": {
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+ "file_counts": {
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+ "test": 1,
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+ "train": 8,
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+ "valid": 1
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+ },
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+ "member_chain_rows": 1138910,
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+ "row_counts": {
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+ "train": 362903,
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+ "valid": 342
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+ }
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+ },
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+ "component_stats": {
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+ "split_component_count": 6735,
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+ "test_component_count": 337,
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+ "train_component_count": 6061,
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+ "valid_component_count": 337
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+ },
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+ "cpu_count": 32,
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+ "elapsed_seconds": 91.953,
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+ "foldseek_path": "",
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+ "include_source_split_component_edges": true,
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+ "max_rows_per_shard": 50000,
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+ "mmseqs_path": "",
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+ "nvidia-smi_path": "C:\\Windows\\system32\\nvidia-smi.EXE",
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+ "nvidia-smi_version": "Tue Jun 30 17:17:15 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 43C P5 8W / 117W | 1044MiB / 8188MiB | 40% 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+-----------------------------------------------------------------------------------------+",
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+ "platform": "Windows-11-10.0.26200-SP0",
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+ "python": "3.12.13",
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+ "seed": 42,
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+ "source_repo_id": "Synthyra/PDB-Chain-Complex-Benchmark",
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+ "source_snapshot_dir": "C:\\tmp\\hf_pdb_chain_complex_cache\\datasets--Synthyra--PDB-Chain-Complex-Benchmark\\snapshots\\3eb55ee7289dfedfbddf0cde48b68c5395783ccf",
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+ "target_repo_id": "Synthyra/PDB-Chain-Complex-Benchmark-Rigor",
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+ "test_frac": 0.05,
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+ "valid_frac": 0.05
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+ }
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+ ```
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+
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+ ## Leakage Assertions
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+
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+ ```json
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+ }
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+ }
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+ ```
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