Publish verified oral V25 L5: degree 6, full validation/test universe holdout

README.md

@@ -0,0 +1,35 @@
+---
+configs:
+- config_name: default
+  data_files:
+  - split: train
+    path: train/data.parquet
+  - split: validation_ranking
+    path: validation_ranking/data.parquet
+  - split: test_ranking
+    path: test_ranking/data.parquet
+---
+# Oral bioavailability V25
+
+Independent L2-L6 releases derived from the frozen consolidated oral V24.1 splits.
+Record degree is six separately for query and reference roles. Parent molecule
+budgets remain 4096 per role, level, and binary/nonbinary family. Minority-first
+sampling, compatible-endpoint repair, and final binary 75/25 trimming are retained.
+Low degree and binary trimming can leave records unused; see record_coverage.json.
+
+The entire official validation and test connected scaffold universes are excluded
+from training across all levels, including records not selected as evaluation
+queries. Evaluation membership and reference ordering match oral V24.1: 500 total
+queries per level per split, Morgan top-50 ID references, and complete OOD pools.
+
+Conflict exclusions, support thresholds, reviewed identity/log10 geometry, and
+the ratio gate <=0.5 (undefined rejected) are preserved. Test measurements only
+participate in the inherited eligibility gate, not training target fitting.
+Numeric targets retain center 0.4 SD and temperature 0.1. Binary soft targets are
+refitted globally within each level from the final numeric training pairs, and
+all training, validation, and test rows are rendered using those updated targets.
+Internal v24.2 sampler/schema names identify reused algorithms, not the release.
+
+Level: L5
+
+Pair rows: {'train': 6892, 'validation_ranking': 23836, 'test_ranking': 22957}

manifest.json

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+{
+  "artifacts": {
+    "README.md": "bbff05e6ce27ce31c5503d57ef81dceafdef8fea37fcceb18a0377dd75de1895",
+    "calibration.json": "b0911153c12072bc869aa71243a25cea2f35551590d6fb305dcfdf78a547a782",
+    "record_coverage.json": "156cbb624f668767c671641896c6f94af4823be509713475f45040b20191ed57",
+    "test_ranking/data.parquet": "2c531077c83ec21c8f108f3baa31b6616126f24ccb810a41dd3ff10f62744ad5",
+    "train/data.parquet": "9f05b4255f279e703d1367912c6e6362efd88eb33fc3bade636c5d12ade4ee92",
+    "validation_ranking/data.parquet": "ca349a68706c7d79f2154bbbfde5aede4e6e642e16b9c3b27a621d836d00574f"
+  },
+  "binary_limit": "75/25",
+  "binary_target_fit_train_sha256": "03ca24437409a387bbb0f26f7313ac6dcaff28fcf2946c77d03eb8c3cb0c5232",
+  "binary_target_group_by": "level",
+  "continuous_limit": "soft",
+  "degree_cap": 6,
+  "full_universe_audit": {
+    "test_gate_only": {
+      "parent_id_count": 454,
+      "parent_id_training_overlap": 0,
+      "record_id_count": 17401,
+      "record_id_training_overlap": 0,
+      "records": 17401,
+      "scaffold_count": 133,
+      "scaffold_training_overlap": 0
+    },
+    "validation": {
+      "parent_id_count": 382,
+      "parent_id_training_overlap": 0,
+      "record_id_count": 13984,
+      "record_id_training_overlap": 0,
+      "records": 13984,
+      "scaffold_count": 157,
+      "scaffold_training_overlap": 0
+    }
+  },
+  "implementation_sha256": {
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+    "/vast/projects/myatskar/design-documents/joseph/starling_assay_transfer/assay_transfer/record_level/oral_v24_2/build.py": "30bf7a7d5f454104dbb7c18881a35fcc32f2061796e7e77008587046cf0060f5",
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+    "/vast/projects/myatskar/design-documents/joseph/starling_assay_transfer/assay_transfer/record_level/oral_v24_2/repair.py": "2f019086f032e3c31dc52c75c3919f8a014553ab978ad5c6fd17fbf0a08f94aa",
+    "/vast/projects/myatskar/design-documents/joseph/starling_assay_transfer/assay_transfer/record_level/oral_v24_2/report.py": "f6090892136be1333e624d2fee728989a7c72415274131f5fabf68d154786428",
+    "/vast/projects/myatskar/design-documents/joseph/starling_assay_transfer/assay_transfer/record_level/oral_v24_2/sampling.py": "9e2b8171246b07aa6c57b6824a48ec240512773d2f1c95054ffdffc5d0ca534f",
+    "/vast/projects/myatskar/design-documents/joseph/starling_assay_transfer/assay_transfer/record_level/oral_v24_2/splits.py": "ac982cb9e20dc35c9ef043d0d421c08a1b470129e80ecf472aa6c19aa5720a3c",
+    "/vast/projects/myatskar/design-documents/joseph/starling_assay_transfer/assay_transfer/record_level/oral_v24_2/verify.py": "6ec4f8913d2861639a77ef1f906219a0fd8258eb35c8b61405b5658cd3137f49",
+    "/vast/projects/myatskar/design-documents/joseph/starling_assay_transfer/assay_transfer/record_level/oral_v25.py": "70e935aeb35ab21ec5754391eadab8cdf65a86a5c7cb0ecb086df6b3eb13798e"
+  },
+  "independent_test_evaluation": true,
+  "level": "L5",
+  "pair_manifest_sha256": "fdd8417fdb76bb1ec67150d3665c162d76412307f4b50c6ecb00338533aad222",
+  "parent_cap_per_role_within_level": 4096,
+  "parent_cap_scope": "within_level_and_budget_family",
+  "ranking_id_max_references": 50,
+  "release_id": "oral_v25",
+  "rows": {
+    "test_ranking": 22957,
+    "train": 6892,
+    "validation_ranking": 23836
+  },
+  "selection": {
+    "test": {
+      "bucket_parents": 206,
+      "composition": {
+        "id/binary": 429,
+        "id/continuous": 71
+      },
+      "distinct_parents": 81,
+      "eligible_buckets": 35,
+      "eligible_records": 513,
+      "queries": 500,
+      "queries_per_bucket": {
+        "[\"fg\",\"bidirectional_permeability\",\"10^-5 cm/s\",\"__unknown__\",\"__unknown__\",\"caco_2\",\"__unknown__\",\"L5\"]": 3,
+        "[\"fg\",\"bidirectional_permeability\",\"10^-5 cm/s\",\"__unknown__\",\"__unknown__\",\"intestinal perfusion\",\"rat\",\"L5\"]": 5,
+        "[\"fg\",\"bidirectional_permeability\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"ABCB1\",\"caco_2\",\"__unknown__\",\"L5\"]": 27,
+        "[\"fg\",\"bidirectional_permeability\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"ABCB1\",\"mdck\",\"__unknown__\",\"L5\"]": 5,
+        "[\"fg\",\"bidirectional_permeability\",\"nm/s\",\"__unknown__\",\"__unknown__\",\"caco_2\",\"__unknown__\",\"L5\"]": 3,
+        "[\"fg\",\"bidirectional_permeability\",\"ratio\",\"__unknown__\",\"__unknown__\",\"caco_2\",\"__unknown__\",\"L5\"]": 14,
+        "[\"fg\",\"bidirectional_permeability\",\"ratio\",\"__unknown__\",\"__unknown__\",\"mdck\",\"__unknown__\",\"L5\"]": 4,
+        "[\"fg\",\"efflux_or_secretory_transport\",\"%\",\"__unknown__\",\"__unknown__\",\"caco_2\",\"__unknown__\",\"L5\"]": 1,
+        "[\"fg\",\"efflux_or_secretory_transport\",\"10^-6 cm/s\",\"__unknown__\",\"__unknown__\",\"caco_2\",\"__unknown__\",\"L5\"]": 1,
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+        "[\"fg\",\"efflux_or_secretory_transport\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"ABCB1\",\"cell assay\",\"__unknown__\",\"L5\"]": 2,
+        "[\"fg\",\"efflux_or_secretory_transport\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"ABCB1\",\"intestinal perfusion\",\"rat\",\"L5\"]": 18,
+        "[\"fg\",\"efflux_or_secretory_transport\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"ABCB1\",\"literature report\",\"__unknown__\",\"L5\"]": 72,
+        "[\"fg\",\"efflux_or_secretory_transport\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"ABCB1\",\"llc-pk1\",\"__unknown__\",\"L5\"]": 2,
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+        "[\"fg\",\"efflux_or_secretory_transport\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"ABCC2\",\"intestinal perfusion\",\"rat\",\"L5\"]": 1,
+        "[\"fg\",\"efflux_or_secretory_transport\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"ABCC2\",\"mdck\",\"__unknown__\",\"L5\"]": 5,
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+        "[\"fg\",\"efflux_or_secretory_transport\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"ABCG2\",\"mdck\",\"__unknown__\",\"L5\"]": 14,
+        "[\"fg\",\"efflux_or_secretory_transport\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"source_token:mrp\",\"caco_2\",\"__unknown__\",\"L5\"]": 2,
+        "[\"fg\",\"intestinal_metabolism\",\"%\",\"__unknown__\",\"__unknown__\",\"caco_2\",\"__unknown__\",\"L5\"]": 10,
+        "[\"fg\",\"intestinal_metabolism\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"UGT\",\"intestinal microsomes\",\"human\",\"L5\"]": 2,
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+      },
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+        "median": 5,
+        "min": 1
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+      "shortfall": 0
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+      "composition": {
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+        "ood/continuous": 4
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+        "[\"fg\",\"bidirectional_permeability\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"ABCB1\",\"caco_2\",\"__unknown__\",\"L5\"]": 34,
+        "[\"fg\",\"bidirectional_permeability\",\"binary_outcome_class\",\"fg_substrate_status_binary.v1\",\"ABCB1\",\"mdck\",\"__unknown__\",\"L5\"]": 9,
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+  "source_snapshot": {
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+      "sha256": "01a01901f2b96ed6897fd08cbd84e4affc3cd8725e7dcf68377eca7db9bacb67"
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+      "sha256": "3e0b83798135f8d26f13b650a97238c966ff219bf329e39d595cbd2d79f7f52e"
+    },
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+      "path": "/vast/projects/myatskar/design-documents/joseph/TxAgent/data/gold_labels/Bioavailability_Ma/v1/scaffold/valid_molecule_condition_labels.jsonl",
+      "sha256": "a04cf813c136b2b7d4363d7651738fee73a01def93c95f93ac059bc94383ea7d"
+    },
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+      "sha256": "84bc63c623a76029253e1b4d606b274199d16c38ede574bb6be75e998ff8dd28"
+    },
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+      "sha256": "3d5d50e58096f7073d0ccedb03ef564998fd113b52ffbe6d17c3d9c6061f0fb0"
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+      "sha256": "57402e107be2cd8e39ba9e7d4795500a88a8b2daba0c695409e133ec851d9798"
+    },
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+      "sha256": "96755c3962ccbf98daa29f80cbf07ec32777ceab3b02375834f1108a279bd2da"
+    },
+    "source_contract": {
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+      "sha256": "d3a3e235a9505618c71d50b2d6524a8f912e0a829d9aa0ce2f35dd57d273a098"
+    },
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+      "sha256": "ae408740ec5e78368d9a4f8702782794e93e78ad6ce90dde050bc69b127a3343"
+    },
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+      "sha256": "4888127944cb6b7aac2e8c1c02a0e12feebdcce6faaca81529a840270f8ee2cf"
+    },
+    "uid_levels": {
+      "path": "/vast/projects/myatskar/design-documents/joseph/TxAgent/data/artifacts/starling/source_uid_levels/bioavailability_ma.parquet",
+      "sha256": "c1d8b8f137303f9c222e2e4a0509fbcd4e48390e91459c6c757b945707731fd6"
+    },
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+      "path": "/vast/projects/myatskar/design-documents/joseph/TxAgent/data/artifacts/starling/source_uid_levels/manifest.json",
+      "sha256": "0a5146a7c6ff49e8cf0f4cc78bae7228aad67fbda6c552d246a91cf9ffa8d57c"
+    },
+    "upstream_calibration": {
+      "path": "/vast/projects/myatskar/design-documents/joseph/starling_assay_transfer/assay_transfer/record_level/artifacts/v24/upstream_calibration/bioavailability_ma/pair_bucket_distance_calibration.json.gz",
+      "sha256": "47b82b1060b9efacb090ab1633d48d57e5bc54d4e17c80d595e66aeaf36a8d2c"
+    }
+  },
+  "split_manifest_sha256": "86efb4b17034b77886f21e2ec84da3aacbb877f8744f8e4fd725f0601457b3ec",
+  "task_id": "bioavailability_ma",
+  "validation_test_copy_ids": [],
+  "variant": "nonmixed",
+  "version": "v25"
+}

record_coverage.json

@@ -0,0 +1,26 @@
+{
+  "query": {
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