Publish context-conditioned molecule transfer v10_2 Bioavailability_Ma

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
+  - split: test_ranking
+    path: test_ranking/data.parquet
+---
+# Bioavailability_Ma context-conditioned molecule transfer V10.2
+
+This release preserves its direct panels and appends training-only, individual-record continuous assay-evidence transfer pairs. Query values remain hidden from prompts.
+
+- Train rows: 93,984
+- Validation rows: 22,682
+- Test rows: 23,369

manifest.json

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+{
+  "arrow_schema": "prompt: string\ncompletion: string\nsplit: string\npair_id: string\nranking_query_id: string\nranking_member_index: int64\nranking_candidate_row_count: int64\nranking_candidate_parent_count: int64\nretrieval_parent_rank: int64\nretrieval_parent_context_index: int64\nretrieval_parent_context_count: int64\ntask_id: string\nsource_id: string\nretrieval_strategy: string\nquery_record_id: string\nretrieval_record_id: string\nquery_benchmark_row_id: string\nretrieval_benchmark_row_id: string\nquery_molecule_identity_key: string\nretrieval_molecule_identity_key: string\nquery_smiles: string\nretrieval_smiles: string\nquery_condition_group: string\nretrieval_condition_group: string\nquery_condition_scope: string\nretrieval_condition_scope: string\nquery_condition_atoms: list<element: string>\n  child 0, element: string\nretrieval_condition_atoms: list<element: string>\n  child 0, element: string\ncandidate_context_relation: string\nquery_source_record_count: int64\nretrieval_source_record_count: int64\nquery_agreement_fraction: double\nretrieval_agreement_fraction: double\nquery_gold_Y: int64\nretrieval_gold_Y: int64\nranking_balance_label: string\nquery_geometry_value: double\nretrieval_geometry_value: double\nabsolute_geometry_difference: double\ncalibration_sample_standard_deviation: double\ntarget_distribution: struct<nontransfer: double, transfer: double>\n  child 0, nontransfer: double\n  child 1, transfer: double\ncanonical_endpoint_key: string\nassay_concept: string\nmeasurement_kind: string\nmetadata: struct<calibration_sha256: string, groups: struct<assay_concept: string, measurement_kind: string, q (... 339 chars omitted)\n  child 0, calibration_sha256: string\n  child 1, groups: struct<assay_concept: string, measurement_kind: string, query_condition_group: string, query_conditi (... 190 chars omitted)\n      child 0, assay_concept: string\n      child 1, measurement_kind: string\n      child 2, query_condition_group: string\n      child 3, query_condition_scope: string\n      child 4, retrieval_strategy: string\n      child 5, source_id: string\n      child 6, task_id: string\n      child 7, evaluation_regime: string\n      child 8, evaluation_regime_source: string\n      child 9, level: string\n      child 10, evaluation_regime_level: string\n  child 2, soft_targets: struct<(A): double, (B): double>\n      child 0, (A): double\n      child 1, (B): double\n  child 3, source_snapshot_sha256: string\n  child 4, target_contract: string\nabsolute_canonical_value_difference: double\nstandardized_canonical_value_difference: double\nsd_logistic_similarity: double\ntarget_train_sample_standard_deviation: double\ntarget_a: double\ntarget_b: double\nlabel_mode: string\nbinary_label: int64\nis_decisive: bool\nmorgan_tanimoto_similarity: double\ngraph_a_position: int64\ngraph_b_position: int64\ngraph_offset: int64\nrepresentation: string\npair_bucket_key: string\nquery_parent_id: string\nretrieval_parent_id: string\nquery_scaffold: string\nretrieval_scaffold: string\nquery_evidence: struct<aggregation_method: string, display_measurement_text: string, display_unit_text: string, disp (... 184 chars omitted)\n  child 0, aggregation_method: string\n  child 1, display_measurement_text: string\n  child 2, display_unit_text: string\n  child 3, display_transform_id: string\n  child 4, source_record_count: int64\n  child 5, deduplicated_source_record_count: int64\n  child 6, aggregate_min: double\n  child 7, aggregate_max: double\n  child 8, aggregate_q1: double\n  child 9, aggregate_q3: double\nretrieval_evidence: struct<aggregation_method: string, display_measurement_text: string, display_unit_text: string, disp (... 184 chars omitted)\n  child 0, aggregation_method: string\n  child 1, display_measurement_text: string\n  child 2, display_unit_text: string\n  child 3, display_transform_id: string\n  child 4, source_record_count: int64\n  child 5, deduplicated_source_record_count: int64\n  child 6, aggregate_min: double\n  child 7, aggregate_max: double\n  child 8, aggregate_q1: double\n  child 9, aggregate_q3: double\nbucket_total_record_count: int64\nbucket_train_record_count: int64\nbucket_train_parent_count: int64\nevaluation_regime: string\ncalibration_scope: string\nlogit_geometry_transform: string\nquery_source_payload_json: string\nretrieval_source_payload_json: string\nlevel: string\nlevel_family: string\nquery_source_row_uid: string\nretrieval_source_row_uid: string\nupstream_pair_bucket_key: string",
+  "artifacts": {
+    "README.md": "f087f65430e6ffa724100db2518f05d60441b624feaba4a89d4c3afaeab00241",
+    "calibration.json": "801070b703c7e508540d517011b046ccca0d2cca82529baa3c8f07168464ea9a",
+    "test_ranking/data.parquet": "825a0d6d08eb99ca1284c33a1f1159323493c974c1a639d6f26f441124eb201c",
+    "train/data.parquet": "6bac1f9f795d731fc56b07b67440614e08e727b7f1a8f40eea8b1324c48ba735",
+    "validation_ranking/data.parquet": "fadac42908119b2289493ef38692edbbdff8b483328e78132502fa8202d76eb1"
+  },
+  "build": {
+    "degree_cap": 48,
+    "implementation_sha256": {
+      "assay_transfer/context_conditioned/__init__.py": "97ee26d7f7bf2e4f69e8ecd936a9d728770bb18642511bb2d177ae40ba2975f9",
+      "assay_transfer/context_conditioned/baselines.py": "e6cb7999d98273dc87c0236d94b344b247b2994d508c09e436811f30fb6cc15d",
+      "assay_transfer/context_conditioned/build.py": "43af4fa0e1a3acda199e7c331371eb350f1d664aab05728c325705848b9c6e0d",
+      "assay_transfer/context_conditioned/continuous_source.py": "080f68763e13a257b2980ab45ded6a806b7041077645853963ce257179f73098",
+      "assay_transfer/context_conditioned/dataset.py": "b1cbcd4c371d679315b75fe7130bdd2d52f7174b2a8900d7d8ec834548ef29ca",
+      "assay_transfer/context_conditioned/hf.py": "ac5298a42670c4f6b3878dbeeb30f83580fa340ca2f13d222ae01f295afb9b78",
+      "assay_transfer/context_conditioned/pairs.py": "2ec358955502e2dc63911107b99f66e75714fca44244b91959d4c468decc507f",
+      "assay_transfer/context_conditioned/publish.py": "4d7486c7c23beb3e5b8f857f0072757aa0897f2e0a463dd9768b09ea3d94582a",
+      "assay_transfer/context_conditioned/record_voter_binary.py": "0bf0a38f3bd1ec6bdbbf57da6a40d069d8a0b399fd40d176f2e9b18c166f22a2",
+      "assay_transfer/context_conditioned/splits.py": "4850692808b5a4523d604d649b043f1fa6ddd34ee260a21796a15fce94a3e37f",
+      "assay_transfer/context_conditioned/templates/BBB_Martins.jinja": "5829c615e0235ba26dfee96e922d496f32579ed472a9a67cc64c96e29b5e10b0",
+      "assay_transfer/context_conditioned/templates/Bioavailability_Ma.jinja": "ad3d8734bed1a0402f072b0e044be966a1a704062e14f064f424332aa2f090b5",
+      "assay_transfer/context_conditioned/templates/Skin_Reaction.jinja": "cca2084355bc79720a7799ef9af84fe2c8f81e6f318d621151ba52c0c1032cd7",
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+      "assay_transfer/context_conditioned/templates/prompt_v5.jinja": "5206a666dcc04b20eb2969c30574282580a28d52ced1c425555892b554035e2d",
+      "assay_transfer/context_conditioned/test_dataset.py": "e2dc39004cae616e3bc92b8acd496f5e3eca12c86e2bc430348af9e7561e79a2",
+      "assay_transfer/context_conditioned/v10.py": "71353232c65de6b98045bc62950df7c35448aa8f12195ff4e5669c6acf63eff6",
+      "assay_transfer/context_conditioned/v10_oral.py": "403ec722f575e8c8c74ba1b18b38468b9cb3b271181d20c792066011bb7a6cb4",
+      "assay_transfer/context_conditioned/v6.py": "2e420033d9041acf54258e732844ec326f860de0edf3f186abb695f302eb2e98",
+      "assay_transfer/context_conditioned/v7_continuous.py": "a625885ac040bbd0a7f017899e3e50f2167c19b5242ae01140363f0d6819910d",
+      "assay_transfer/context_conditioned/v8.py": "e63bbe7c45c43d119e9f6739acbeac5b0c02ea55baad7e9f41c5a244e16c7f61",
+      "assay_transfer/context_conditioned/v9.py": "77e2c02b2572eeed251439a5bc933da18f3ac7f1ecdd91c1622874fa59612e02",
+      "assay_transfer/context_conditioned/v9_official.py": "4f9e96bfb25d03dcdd294766656adee1e504daa63c2c51f63f21a07288e03a3b",
+      "assay_transfer/shared/artifacts.py": "9a7233e7b5ffd04481466c32f7687a05b1d1f5308a2594bf53abe90341cc6427",
+      "assay_transfer/shared/pairs.py": "a0ab429dcd342c98f42bc98da4da39c0b732b7212c040cc6df9dfde3462fb898",
+      "assay_transfer/shared/rendering.py": "367445b3dab67752f81ee703848b222654fa0111c06ad5fb1552272495ae107f",
+      "assay_transfer/shared/tasks.py": "70f920db036385ec2f408b783db154938c4a2e7ec0a357a5a52504e754b0b7c2",
+      "assay_transfer/shared/v3_validation.py": "dea8142e2398decfbd4ac0859dc8921d73a70851b80a85e46ff2ecf299b0aa83",
+      "requirements-data-pipeline.txt": "f0aa5dfea67de8b2f32bce91cbb0fd078c5925b8d014c1fb406ba8806985e1a7"
+    },
+    "packages": {
+      "jinja2": "3.1.6",
+      "pyarrow": "23.0.0",
+      "rdkit_core": "2025.09.4",
+      "rdkit_distribution": "2025.9.4"
+    },
+    "python_version": "3.11.14",
+    "repository": {
+      "commit": "7ae235a1573a01dc281266ff781bda01e80d8ae0",
+      "dirty": true
+    },
+    "seed": 20260818
+  },
+  "calibration_scope": "official_train_plus_validation",
+  "direct_rows": {
+    "test_ranking": 23369,
+    "train": 46992,
+    "validation_ranking": 22682
+  },
+  "generation": "v10",
+  "hub_dataset_id": "jiosephlee/context-conditioned-molecule-transfer-v10.2-bioavailability-ma-mixed-continuous-intern",
+  "indirect_train_rows": 46992,
+  "indirect_train_rows_by_source": {
+    "fa": 7719,
+    "fg": 609,
+    "fh": 7836,
+    "oral_exposure": 30828
+  },
+  "label_mode": "mixed_continuous",
+  "membership": {
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+    "train": "51f6a60362ecacff975e3b237808404d65afa0dfa0e797aa723f49179db86d94",
+    "validation_ranking": "b162dba94feee948456643c74b7055f28423a2f62b199f08f89f837d66ec3976"
+  },
+  "morgan_similarity": {
+    "combined": {
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+        "rows": 46769
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+      "transfer": {
+        "mean": 0.18163652441863504,
+        "rows": 47215
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+        "rows": 23496
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+  },
+  "official_split_policy": "official_gold_train_valid_test.train_plus_valid_calibration.v1",
+  "prompt_contract": {
+    "direct": "context_conditioned_A_value_only.v10",
+    "indirect": "source_native_query_safe_record_prompt.v25"
+  },
+  "ranking_reference_scope": "official_train_only",
+  "realized_indirect_to_direct_ratio": 1.0,
+  "rows": {
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+    "train": 93984,
+    "validation_ranking": 22682
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+  "schema_version": "context_conditioned_molecule_transfer.v11",
+  "source": {
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+      "eligible_records": 67482,
+      "manifest_sha256": "54569cbc2c61756a64f2534cb6bb3a914ce51125997d8ba127e6447ffad08367",
+      "release": "/vast/projects/myatskar/design-documents/joseph/starling_assay_transfer/assay_transfer/record_level/artifacts/oral_v25",
+      "split_manifest_sha256": "86efb4b17034b77886f21e2ec84da3aacbb877f8744f8e4fd725f0601457b3ec",
+      "unit": "individual_v25_continuous_indirect_record"
+    },
+    "snapshot_manifest_sha256": "5b94e7ed0581d8b2766bae7d1a8902d880ec19738376a85309b63a270860490c",
+    "snapshot_root": "/vast/projects/myatskar/design-documents/joseph/starling_assay_transfer/assay_transfer/context_conditioned/artifacts/v9_official/sources/Bioavailability_Ma"
+  },
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+    "train": 1958,
+    "validation_ranking": 262
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+  "target_contract": "sd_sigmoid_center_0.4_temperature_0.1_unclipped.v10.2",
+  "target_policy": {
+    "center_sd": 0.4,
+    "tau_sd": 0.1
+  },
+  "task_id": "Bioavailability_Ma",
+  "training": {
+    "candidate_policy": "official_train_unique_parent_0.4sd_balanced",
+    "direction": "one_reference_A_to_query_B",
+    "graph": {
+      "balance_boundary_sd": 0.4,
+      "degree_cap": 48,
+      "method": "top_morgan_0.4sd_balanced_no_reverse.v1",
+      "query_order": "ascending_preconstraint_sparse_class_size_then_record_id",
+      "query_order_sha256": "c206af13da09e6427769f8758c77218eef29731bf60597b58010f7390d9d574d",
+      "realized_near_count": {
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+          "12": 1958
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+        "sparse_query_count": 0,
+        "sparse_query_sha256": "4f53cda18c2baa0c0354bb5f9a3ecbe5ed12ab4d8e11ba873c2f11161202b945"
+      },
+      "reference_parent_per_query": "unique",
+      "reverse_parent_pairs": "forbidden",
+      "selection": "scarce_class_first_then_descending_morgan_parent_record",
+      "similarity": {
+        "max": 1.0,
+        "mean": 0.2214192774993604,
+        "min": 0.0
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+      "target_near_far": {
+        "far": 12,
+        "near": 12
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+    },
+    "indirect_candidate_pair_count": 132783,
+    "indirect_record_degree_cap": 2,
+    "indirect_selected_pair_count": 46992,
+    "indirect_selected_unique_queries": 46992,
+    "indirect_selection": "bucket_round_robin_unique_query_v25_order",
+    "reference_count_per_query": 24,
+    "retrieval_parent_may_repeat_across_context_records": false,
+    "selection": "highest_available_morgan_with_no_reverse_parent_edges"
+  },
+  "version": "v10_2"
+}

test_ranking/data.parquet

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train/data.parquet

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validation_ranking/data.parquet

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