Build rigor split dataset from published benchmark artifacts

README.md

@@ -34,6 +34,11 @@ 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`.
@@ -52,92 +57,111 @@ verification edges when supplied.
 {
   "batch_size": 16384,
   "chain_scan": {
-    "assembly_membership_edges_seen": 1138910,
-    "asymmetric_unit_membership_edges_seen": 1069448,
+    "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": 22,
+      "train": 21,
       "valid": 1
     },
     "row_counts": {
-      "test": 334,
-      "train": 1068780,
-      "valid": 334
+      "test": 302,
+      "train": 1036622,
+      "valid": 302
     }
   },
   "complex_edge_scan": {
-    "complex_member_edges_seen": 775327,
-    "complexes_scanned_for_edges": 363583
+    "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": 8,
+      "train": 7,
       "valid": 1
     },
-    "member_chain_rows": 1138910,
+    "member_chain_rows": 987199,
     "member_fields": {
       "asymmetric_unit_chain_uids": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 1069448
+        "unique_values": 923757
       },
       "chain_uid": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 1069448
+        "unique_values": 921450
       },
       "sequence_clusters_30": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 48857
+        "unique_values": 41718
       },
       "sequence_hashes": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 183467
+        "unique_values": 166930
       },
       "sequences": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 183467
+        "unique_values": 166930
       },
       "split_components": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 6684
+        "unique_values": 6019
       },
       "structure_clusters": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 66989
+        "unique_values": 44485
       }
     },
     "row_counts": {
-      "test": 335,
-      "train": 362909,
-      "valid": 339
+      "test": 301,
+      "train": 344140,
+      "valid": 304
     }
   },
   "component_stats": {
-    "split_component_count": 6684,
-    "test_component_count": 334,
-    "train_component_count": 6016,
-    "valid_component_count": 334
+    "split_component_count": 6033,
+    "test_component_count": 302,
+    "train_component_count": 5429,
+    "valid_component_count": 302
   },
   "cpu_count": 32,
-  "elapsed_seconds": 75.866,
+  "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": "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+-----------------------------------------------------------------------------------------+",
+  "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,
@@ -159,32 +183,32 @@ verification edges when supplied.
       "chain_uid": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 1069448
+        "unique_values": 1037226
       },
       "seqs": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 183467
+        "unique_values": 175111
       },
       "sequence_cluster_30": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 48857
+        "unique_values": 43208
       },
       "sequence_hash": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 183467
+        "unique_values": 175111
       },
       "split_component": {
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         "max_pairwise_overlap": 0,
-        "unique_values": 6684
+        "unique_values": 6033
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         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 66989
+        "unique_values": 47196
       }
     },
     "post_write": {
@@ -192,42 +216,42 @@ verification edges when supplied.
         "chain_uid": {
           "crossing_values": 0,
           "max_pairwise_overlap": 0,
-          "unique_values": 1069448
+          "unique_values": 1037226
         },
         "seqs": {
           "crossing_values": 0,
           "max_pairwise_overlap": 0,
-          "unique_values": 183467
+          "unique_values": 175111
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         "sequence_cluster_30": {
           "crossing_values": 0,
           "max_pairwise_overlap": 0,
-          "unique_values": 48857
+          "unique_values": 43208
         },
         "sequence_hash": {
           "crossing_values": 0,
           "max_pairwise_overlap": 0,
-          "unique_values": 183467
+          "unique_values": 175111
         },
         "split_component": {
           "crossing_values": 0,
           "max_pairwise_overlap": 0,
-          "unique_values": 6684
+          "unique_values": 6033
         },
         "structure_cluster": {
           "crossing_values": 0,
           "max_pairwise_overlap": 0,
-          "unique_values": 66989
+          "unique_values": 47196
         }
       },
-      "rows": 1069448,
+      "rows": 1037226,
       "split_counts": {
-        "test": 334,
-        "train": 1068780,
-        "valid": 334
+        "test": 302,
+        "train": 1036622,
+        "valid": 302
       }
     },
-    "rows": 1069448,
+    "rows": 1037226,
     "sequence_verification_edges": {
       "checked_edges": 0,
       "cross_split_edges": 0,
@@ -237,106 +261,106 @@ verification edges when supplied.
       "total_edges": 0
     },
     "split_counts": {
-      "test": 334,
-      "train": 1068780,
-      "valid": 334
+      "test": 302,
+      "train": 1036622,
+      "valid": 302
     }
   },
   "complexes": {
-    "member_chain_rows": 1138910,
+    "member_chain_rows": 987199,
     "member_fields": {
       "asymmetric_unit_chain_uids": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 1069448
+        "unique_values": 923757
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       "chain_uid": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 1069448
+        "unique_values": 921450
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         "max_pairwise_overlap": 0,
-        "unique_values": 48857
+        "unique_values": 41718
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       }
     },
     "member_split_consistency": "passed",
     "payload_columns_regenerated_from_chains": true,
     "post_write": {
-      "asymmetric_unit_chain_rows": 1760175,
-      "member_chain_rows": 1138910,
+      "asymmetric_unit_chain_rows": 1541919,
+      "member_chain_rows": 987199,
       "member_fields": {
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           "max_pairwise_overlap": 0,
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       "payload_columns_match_chain_rows": true,
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       "shard_split_routing": "passed",
       "split_counts": {
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-      "valid": 339
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+      "train": 344140,
+      "valid": 304
     }
   }
 }

artifacts/chain_split_assignments.parquet

@@ -1,3 +1,3 @@
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-size 2768050
+oid sha256:4dfcb85273c7fdc06574645cda0cb555e9bfb48a4b3b11b6bf4dfc05e228135f
+size 2684850

artifacts/composite_clusters.parquet

@@ -1,3 +1,3 @@
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-oid sha256:83f0be4998ffb99327b988fc85d00f5f5ac58fce881265c747f77a6bb7ae53b5
-size 123818
+oid sha256:75015439a928dcbb5bd62d213e146150bb89faee5c6b3f22abb0b0a49194c330
+size 112540

artifacts/leakage_assertions.json

@@ -4,32 +4,32 @@
       "chain_uid": {
         "crossing_values": 0,
         "max_pairwise_overlap": 0,
-        "unique_values": 1069448
+        "unique_values": 1037226
       },
       "seqs": {
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+        "unique_values": 43208
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       "sequence_hash": {
         "crossing_values": 0,
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+        "unique_values": 175111
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       "split_component": {
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+        "unique_values": 6033
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         "max_pairwise_overlap": 0,
-        "unique_values": 66989
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     "post_write": {
@@ -37,42 +37,42 @@
         "chain_uid": {
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           "max_pairwise_overlap": 0,
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@@ -82,106 +82,106 @@
       "total_edges": 0
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