metadata
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.
Chains shorter than min_sequence_length or containing X residues when
exclude_sequences_with_x=true are removed before graph construction. Biological
assembly rows containing any removed member chain are dropped rather than
published as partial complexes.
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.
Cluster-Balanced PyTorch Sampling
The training split can be loaded with streaming=False and sampled as one
random row per sequence-cluster group per epoch. Chain mode groups by
sequence_cluster_30. Complex mode defaults to one sample per member sequence
cluster from sequence_clusters_30; set complex_grouping="cluster_set" to
sample one row per unique complex cluster signature instead.
import collections
import random
from typing import Any, Mapping, Optional
from datasets import load_dataset
from torch.utils.data import DataLoader, Dataset
DEFAULT_REPO_ID = "Synthyra/PDB-Chain-Complex-Benchmark-Rigor"
class PDBClusteredDataset(Dataset):
"""One randomly selected row per sequence-cluster group per epoch."""
def __init__(
self,
repo_id: str = DEFAULT_REPO_ID,
mode: str = "chains",
split: str = "train",
seed: int = 0,
epoch: int = 0,
cluster_key: Optional[str] = None,
complex_grouping: str = "member_cluster",
load_kwargs: Optional[Mapping[str, Any]] = None,
) -> None:
mode_to_config = {
"single": "chains",
"chains": "chains",
"complex": "complexes",
"complexes": "complexes",
}
self.config = mode_to_config[mode]
self.seed = int(seed)
self.cluster_key = cluster_key or (
"sequence_cluster_30" if self.config == "chains" else "sequence_clusters_30"
)
self.complex_grouping = complex_grouping
self.dataset = load_dataset(
repo_id,
self.config,
split=split,
streaming=False,
**dict(load_kwargs or {}),
)
self.groups = self._build_groups()
self.group_keys = sorted(self.groups)
self.set_epoch(epoch)
def _group_keys_for_value(self, value: Any) -> tuple[tuple[str, ...], ...]:
if self.config == "chains":
return ((str(value),),)
clusters = tuple(sorted({str(cluster) for cluster in value if str(cluster)}))
if not clusters:
raise ValueError("complex row has no sequence cluster labels")
if self.complex_grouping == "cluster_set":
return (clusters,)
if self.complex_grouping == "member_cluster":
return tuple((cluster,) for cluster in clusters)
raise ValueError("complex_grouping must be 'member_cluster' or 'cluster_set'")
def _build_groups(self) -> dict[tuple[str, ...], list[int]]:
groups = collections.defaultdict(list)
for row_idx, value in enumerate(self.dataset[self.cluster_key]):
for key in self._group_keys_for_value(value):
groups[key].append(row_idx)
if not groups:
raise ValueError("dataset split contains no rows")
return dict(groups)
def set_epoch(self, epoch: int) -> None:
self.epoch = int(epoch)
rng = random.Random(self.seed + self.epoch)
self.indices = [rng.choice(self.groups[key]) for key in self.group_keys]
def __len__(self) -> int:
return len(self.indices)
def __getitem__(self, index: int) -> Mapping[str, Any]:
return self.dataset[self.indices[index]]
def identity_collate(batch: list[Mapping[str, Any]]) -> list[Mapping[str, Any]]:
return batch
chains = PDBClusteredDataset(mode="single", split="train", seed=42)
complexes = PDBClusteredDataset(mode="complex", split="train", seed=42)
chains_loader = DataLoader(chains, batch_size=8, shuffle=False, collate_fn=identity_collate)
complex_loader = DataLoader(complexes, batch_size=2, shuffle=False, collate_fn=identity_collate)
for epoch in range(3):
chains.set_epoch(epoch)
complexes.set_epoch(epoch)
first_chain_batch = next(iter(chains_loader))
first_complex_batch = next(iter(complex_loader))
Build Metadata
{
"batch_size": 16384,
"chain_scan": {
"assembly_membership_edges_seen": 1105293,
"asymmetric_unit_membership_edges_seen": 1037226,
"chains_excluded_contains_x": 24118,
"chains_excluded_too_short": 13084,
"chains_excluded_total": 32222,
"chains_retained": 1037226,
"chains_scanned": 1069448
},
"chain_write": {
"file_counts": {
"test": 1,
"train": 21,
"valid": 1
},
"row_counts": {
"test": 302,
"train": 1036622,
"valid": 302
}
},
"complex_edge_scan": {
"complex_member_edges_seen": 642454,
"complexes_dropped_by_filtered_member": 18838,
"complexes_scanned_for_edges": 344745,
"source_complex_rows_seen": 363583
},
"complex_write": {
"complexes_dropped_by_filtered_member": 18838,
"file_counts": {
"test": 1,
"train": 7,
"valid": 1
},
"member_chain_rows": 987199,
"member_fields": {
"asymmetric_unit_chain_uids": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 923757
},
"chain_uid": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 921450
},
"sequence_clusters_30": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 41718
},
"sequence_hashes": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 166930
},
"sequences": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 166930
},
"split_components": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 6019
},
"structure_clusters": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 44485
}
},
"row_counts": {
"test": 301,
"train": 344140,
"valid": 304
}
},
"component_stats": {
"split_component_count": 6033,
"test_component_count": 302,
"train_component_count": 5429,
"valid_component_count": 302
},
"cpu_count": 32,
"dropped_complex_membership_keys": 18838,
"elapsed_seconds": 77.882,
"exclude_sequences_with_x": true,
"filtered_chain_rows": 32222,
"filtered_complex_rows": 18838,
"foldseek_path": "",
"include_source_split_component_edges": true,
"max_rows_per_shard": 50000,
"min_sequence_length": 10,
"mmseqs_path": "",
"nvidia-smi_path": "C:\\Windows\\system32\\nvidia-smi.EXE",
"nvidia-smi_version": "Mon Jul 6 14:22:11 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 / 123W | 866MiB / 8188MiB | 26% 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 6516 C+G ...p\\app-3.6.2\\GitHubDesktop.exe N/A |\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 21252 C+G ...__2p2nqsd0c76g0\\app\\Codex.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 196292 C+G ...Chrome\\Application\\chrome.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",
"quality_filter": {
"drop_complexes_with_filtered_members": true,
"exclude_sequences_with_x": true,
"min_sequence_length": 10
},
"retained_chain_rows": 1037226,
"retained_complex_rows": 344745,
"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
{
"chains": {
"fields": {
"chain_uid": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 1037226
},
"seqs": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 175111
},
"sequence_cluster_30": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 43208
},
"sequence_hash": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 175111
},
"split_component": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 6033
},
"structure_cluster": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 47196
}
},
"post_write": {
"fields": {
"chain_uid": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 1037226
},
"seqs": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 175111
},
"sequence_cluster_30": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 43208
},
"sequence_hash": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 175111
},
"split_component": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 6033
},
"structure_cluster": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 47196
}
},
"rows": 1037226,
"split_counts": {
"test": 302,
"train": 1036622,
"valid": 302
}
},
"rows": 1037226,
"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": 302,
"train": 1036622,
"valid": 302
}
},
"complexes": {
"member_chain_rows": 987199,
"member_fields": {
"asymmetric_unit_chain_uids": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 923757
},
"chain_uid": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 921450
},
"sequence_clusters_30": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 41718
},
"sequence_hashes": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 166930
},
"sequences": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 166930
},
"split_components": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 6019
},
"structure_clusters": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 44485
}
},
"member_split_consistency": "passed",
"payload_columns_regenerated_from_chains": true,
"post_write": {
"asymmetric_unit_chain_rows": 1541919,
"member_chain_rows": 987199,
"member_fields": {
"asymmetric_unit_chain_uids": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 923757
},
"chain_uid": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 921450
},
"sequence_clusters_30": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 41718
},
"sequence_hashes": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 166930
},
"sequences": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 166930
},
"split_components": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 6019
},
"structure_clusters": {
"crossing_values": 0,
"max_pairwise_overlap": 0,
"unique_values": 44485
}
},
"payload_columns_match_chain_rows": true,
"rows": 344745,
"shard_split_routing": "passed",
"split_counts": {
"test": 301,
"train": 344140,
"valid": 304
}
},
"rows": 344745,
"split_counts": {
"test": 301,
"train": 344140,
"valid": 304
}
}
}