Publish BBB V23.2 L5 degree96 release

README.md

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+---
+configs:
+- config_name: default
+  data_files:
+  - split: train
+    path: train/data.parquet
+  - split: validation_ranking
+    path: validation_ranking/data.parquet
+---
+# BBB assay transfer V23.2: UID level datasets
+
+Five separate, noncumulative datasets use BBB evidence library V10 and the pinned
+upstream acquisition UID mapping. L1 = direct brain exposure; L2 = central functional
+access proxy; L3 = passive permeability; L4 = efflux transport; L5 = influx transport.
+Both the query and reference belong to the dataset's level. Source identity is
+preserved independently. The mapping is joined on `source_row_uid`, never on
+SMILES, source IDs, or upstream canonical IDs. Missing UIDs are excluded with an
+identity audit; they are not assigned an inferred level.
+
+V23.2 rebuilds from V10. It is not a filter of the published V23/V9 pairs.
+Each exact V10 assay bucket is intersected with level before calibration, split
+support gates, pair sampling, and ranking selection. `upstream_pair_bucket_key`
+preserves the original bucket; `pair_bucket_key` appends the level to its JSON key.
+Both acquisition UIDs and immutable canonical record IDs are retained in release rows.
+
+V23's relaxed initial calibration gate (10 records, no initial molecule minimum)
+is reconstructed using the V10 calibration implementation. Subsequent training
+requires 12 training records and 6 distinct training parents per level-bucket.
+Whole level-buckets with 10–11 records and at least 6 parents form OOD validation.
+ID holds out the gold-validation scaffold components across all levels together.
+OOD is bucket OOD; parent overlap with other buckets is possible.
+
+Continuous targets retain V23's reviewed geometry, with recalculated sample SD
+(ddof=1) on train plus validation within the level-bucket, or the whole OOD bucket.
+Original assay keys select reviewed log transforms. Unreviewed tail alerts and
+invalid transformations are excluded and audited. Binary calibration requires
+both categories with at least three records each. Empirical binary targets retain
+V23's source-native estimator, fitted only on retained training pairs.
+
+The nonmixed build gives every level-bucket a record-role degree cap of 96,
+including L1. It exports five separate L1-L5 datasets. The mixed build pools
+all levels in one dataset and uses degree 48 for buckets with at least the
+configured number of training records, and degree 96 for smaller buckets.
+By default the cutoff is the smallest integer above the geometric mean of
+training level-bucket sizes: 33 records for this pinned split (355 of 944
+training buckets). Override with `--big-bucket-min-records` when building pairs.
+Neither variant applies an L1-specific cap or share ceiling. Both retain the
+global parent-role cap of 576 across levels. Degree is a cap, not a guarantee:
+limited eligible partners and parent caps can reduce the realized degree.
+The two variants are sampled separately and have separately fitted empirical
+binary targets. Mixing datasets does not permit cross-level pairs.
+
+Validation bucket quotas are computed across levels separately for each regime
+and measurement family, using V23's second-smallest positive count rule. Up to
+three heldout queries are selected per bucket. ID uses 19–20 nearest training
+records; OOD uses the other 9–10 records. Ranking groups are complete and stay
+within one level. Sparse level panels retain their actual support. There is no
+test split. `assay_concept` and the metadata level group identify the level;
+`source_id` continues to identify scientific source provenance.
+
+Prompt rendering and masking reuse V23. Level and UID fields are provenance,
+not extra prompt evidence. Each dataset carries the complete calibration artifact
+because rows refer to its SHA-256. Input hashes are pinned in `inputs.json`.
+
+Use the project `openrlhf_tfv4` Python environment:
+
+```bash
+python -m assay_transfer.record_level.v23_2.build all --variant all
+python -m assay_transfer.record_level.v23_2.build verify
+```
+
+Outputs: `assay_transfer/record_level/artifacts/v23_2/degree96/hf/bbb_martins/by_level/L1`
+through `L5`, plus `degree96/hf/bbb_martins/mixed`. The verified V10 splits and UID audit are shared with the original build.
+`all` rebuilds pairs and exports; `splits` is a separate explicit reconstruction.
+Use `--variant nonmixed` or `--variant mixed` for one variant. Existing outputs
+require explicit `--overwrite`. The original lower-degree artifacts are retained.
+
+Dataset: L5
+
+Rows: {'train': 9723, 'validation_ranking': 270}

manifest.json

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+    "calibration.json": "34587e1aadc37eb132a6634351c4b2520917c52a90de81d11e2e1e55f9e51fa9",
+    "train/data.parquet": "4c93579f97bbc6b999f83d2fab09e8726d6b74d821363414539f2fd912332df9",
+    "validation_ranking/data.parquet": "0b518461f4517a007b54974d4604682ad29f17bd2c9a8660e353761e59b7dbdb"
+  },
+  "big_bucket_min_records": 33,
+  "calibration_sha256": "34587e1aadc37eb132a6634351c4b2520917c52a90de81d11e2e1e55f9e51fa9",
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+  "rows": {
+    "train": 9723,
+    "validation_ranking": 270
+  },
+  "source_snapshot": {
+    "gold_validation": {
+      "path": "/vast/projects/myatskar/design-documents/joseph/TxAgent/data/gold_labels/BBB_Martins/v1/scaffold/valid_molecule_condition_labels.jsonl",
+      "sha256": "8477a2bf858d8e7a6cd4cd7ae9cd686e4c975a5df50f35a35c5a192de8a486d1"
+    },
+    "manifest": {
+      "path": "/vast/projects/myatskar/design-documents/joseph/TxAgent/data/evidence_libraries/bbb_martins/v10/manifest.json",
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+    "pair_buckets": {
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+      "sha256": "479d3c4c2f5d905409d86531be0deb9104c6c3f5da53705e10aeb00776f20763"
+    },
+    "record_pruning": {
+      "path": "/vast/projects/myatskar/design-documents/joseph/TxAgent/data/evidence_libraries/bbb_martins/v10/reviews/assay_transfer_record_pruning_v3/manifest.json",
+      "sha256": "c7434dee98f74c46819f4ec2dd28d12afaa47e36971a5ec77bba253d6543477e"
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+    "records": {
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+      "sha256": "82208d3d8d1de42ac9731cb6a02be37b4ddb5f8a729f889b471dbf798581f662"
+    },
+    "source_contract": {
+      "path": "/vast/projects/myatskar/design-documents/joseph/TxAgent/data/evidence_libraries/bbb_martins/v10/02_canonicalized/source_contract.json",
+      "sha256": "dca8064421dd5223403e3ac6b32c45967a28052c40ab0cb4813a1647c1351960"
+    },
+    "stage2_manifest": {
+      "path": "/vast/projects/myatskar/design-documents/joseph/TxAgent/data/evidence_libraries/bbb_martins/v10/02_canonicalized/manifest.json",
+      "sha256": "ca01a7cf34446d0fa09be20af863256c56d655fe5bfd72cb298f95c8e49da2b0"
+    },
+    "stage3_manifest": {
+      "path": "/vast/projects/myatskar/design-documents/joseph/TxAgent/data/evidence_libraries/bbb_martins/v10/03_pair_buckets/manifest.json",
+      "sha256": "cb2618fc7335f8761b2d01c11fb6e7b8a075eb1da86cb00fc2393eef8740431c"
+    },
+    "uid_levels": {
+      "path": "/vast/projects/myatskar/design-documents/joseph/TxAgent/data/artifacts/starling/source_uid_levels/bbb_martins.parquet",
+      "sha256": "d30ac0c3d335e213812fc684dd8c1154eacd5edb78c0f9d09629994c93852159"
+    },
+    "uid_manifest": {
+      "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/v23_2/upstream_calibration/pair_bucket_distance_calibration.json.gz",
+      "sha256": "58011f38c38e8150d523673561dcabeb65218b6d2e93cc5dfa668d9bb00bcdeb"
+    }
+  },
+  "split_manifest_sha256": "50d298aa7ad116261c1a7306ebaa3c865a5267668bd4d76c1492b827ca201a2e",
+  "training_policy": "degree96_all_buckets",
+  "variant": "nonmixed",
+  "version": "v23.2"
+}

train/data.parquet

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+size 2296430

validation_ranking/data.parquet

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