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topu-lbvs-mini/README.md

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+# TopU-LBVS-mini
+
+Compact 7-target protocol with a paired random-decoy control. One
+representative target per protein class, each containing both Setting 1 (TopU
+hard-decoy test) and Setting 3 (random ChEMBL* decoy control test) data with
+matched train/validation pools, identical test active counts, and identical
+1:40 active-to-decoy ratios. The paired (S1, S3) test sets isolate the effect
+of decoy construction.
+
+## Mini target panel (one per protein class)
+
+| Target | Class            | ChEMBL ID  |
+|--------|------------------|------------|
+| cp3a4  | Cytochrome P450  | CHEMBL340  |
+| aa2ar  | GPCR             | CHEMBL251  |
+| kcnh2  | Ion Channel      | CHEMBL240  |
+| egfr   | Kinase           | CHEMBL203  |
+| esr1   | Nuclear Receptor | CHEMBL206  |
+| aces   | Misc Enzymes     | CHEMBL220  |
+| thrb   | Protease         | CHEMBL204  |
+
+(Verify against `targets.csv` for the canonical list and per-target counts.)
+
+## Per-target file layout
+
+```
+<target>/
+├── s1/                                    # Setting 1: TopU hard-decoy test
+│   ├── <CHEMBL_ID>_final.csv              # train pool (SMILES + id + label)
+│   ├── <CHEMBL_ID>_final_ecfp4.npz        # train pool (ECFP4)
+│   ├── <CHEMBL_ID>_topUnbiased.csv        # full TopU library (test set)
+│   ├── <CHEMBL_ID>_topUnbiased_ecfp4.npz  # full TopU library (test set), ECFP4
+│   └── splits/
+│       ├── seed_2026/{train_idx.npy, val_idx.npy, split_info.json}
+│       ├── seed_2027/{...}
+│       └── seed_2028/{...}
+└── s3/                                    # Setting 3: random ChEMBL* decoy test
+    ├── <CHEMBL_ID>_train_s3_seed2026_ecfp4.npz
+    ├── <CHEMBL_ID>_train_s3_seed2027_ecfp4.npz
+    ├── <CHEMBL_ID>_train_s3_seed2028_ecfp4.npz
+    ├── <CHEMBL_ID>_val_s3_seed2026_ecfp4.npz
+    ├── <CHEMBL_ID>_val_s3_seed2027_ecfp4.npz
+    ├── <CHEMBL_ID>_val_s3_seed2028_ecfp4.npz
+    ├── <CHEMBL_ID>_test_s3_seed2026_ecfp4.npz
+    ├── <CHEMBL_ID>_test_s3_seed2027_ecfp4.npz
+    └── <CHEMBL_ID>_test_s3_seed2028_ecfp4.npz
+```
+
+## NPZ schema
+
+Each `*_ecfp4.npz` file contains:
+- `X`      : (n, 2048) uint8 — Morgan fingerprints (radius 2, 2048 bits)
+- `y`      : (n,) int — binary activity label (1=active, 0=inactive)
+- `smiles` : (n,) object — canonical SMILES
+- `ids`    : (n,) object — ChEMBL compound IDs
+
+## Protocol summary
+
+| Aspect                | Setting 1 (s1)                | Setting 3 (s3)                   |
+|-----------------------|-------------------------------|----------------------------------|
+| Training source       | ChEMBL* (TopU removed, 1:10)  | ChEMBL* + TopU pool (1:10)       |
+| Test source           | full TopU library             | random ChEMBL*+TopU pool         |
+| Train/val split       | 85% / 15% (PR-AUC selection)  | 85% / 15% (PR-AUC selection)     |
+| Test active count     | matches TopU library          | matches TopU library (paired)    |
+| Test ratio            | 1:40                          | 1:40                             |
+| Primary metric        | EF@1%                         | EF@1%                            |
+
+The (S1, S3) test sets share the same active count per target, so the EF@1%
+gap measures only the effect of decoy construction.
+
+## Seeds
+
+2026, 2027, 2028.
+
+## Targets
+
+See `targets.csv` for the full per-target metadata.

topu-lbvs-mini/aa2ar/s1/splits/seed_2026/split_info.json

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+{
+  "target": "aa2ar",
+  "seed": 2026,
+  "created_at": "2026-03-09T00:05:39.680424",
+  "n_actives_total": 5032,
+  "n_inactives_raw": 50320,
+  "n_inactives_working": 50320,
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+  "train_inactives": 42770,
+  "train_total": 47047,
+  "train_ratio": 10.0,
+  "train_pct_of_actives": 0.849960254372019,
+  "val_actives": 755,
+  "val_inactives": 7550,
+  "val_total": 8305,
+  "val_ratio": 10.0,
+  "val_pct_of_actives": 0.15003974562798092,
+  "warnings": [],
+  "n_warnings": 0,
+  "test_actives": 127,
+  "test_inactives": 5080,
+  "test_total": 5207,
+  "test_ratio": 40.0,
+  "final_npz": "CHEMBL251_final_ecfp4.npz",
+  "topu_npz": "CHEMBL251_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
+  "verify_errors": []
+}

topu-lbvs-mini/aa2ar/s1/splits/seed_2027/split_info.json

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+  "topu_npz": "CHEMBL251_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
+  "verify_errors": []
+}

topu-lbvs-mini/aa2ar/s1/splits/seed_2028/split_info.json

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+  "final_npz": "CHEMBL251_final_ecfp4.npz",
+  "topu_npz": "CHEMBL251_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
+  "verify_errors": []
+}

topu-lbvs-mini/aces/s1/splits/seed_2026/split_info.json

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+  "topu_npz": "CHEMBL220_topUnbiased_ecfp4.npz",
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+}

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+  "topu_npz": "CHEMBL220_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
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+}

topu-lbvs-mini/aces/s1/splits/seed_2028/split_info.json

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+  "topu_npz": "CHEMBL220_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
+  "verify_errors": []
+}

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+  "topu_npz": "CHEMBL203_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
+  "verify_errors": []
+}

topu-lbvs-mini/esr1/s1/splits/seed_2026/split_info.json

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+{
+  "target": "esr1",
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+  "created_at": "2026-03-09T00:05:41.706682",
+  "n_actives_total": 3114,
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+  "final_npz": "CHEMBL206_final_ecfp4.npz",
+  "topu_npz": "CHEMBL206_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
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+}

topu-lbvs-mini/esr1/s1/splits/seed_2027/split_info.json

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+{
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+  "final_npz": "CHEMBL206_final_ecfp4.npz",
+  "topu_npz": "CHEMBL206_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
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+}

topu-lbvs-mini/esr1/s1/splits/seed_2028/split_info.json

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+{
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+  "final_npz": "CHEMBL206_final_ecfp4.npz",
+  "topu_npz": "CHEMBL206_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
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+}

topu-lbvs-mini/kcnh2/s1/splits/seed_2026/split_info.json

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+{
+  "target": "kcnh2",
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+  "final_npz": "CHEMBL240_final_ecfp4.npz",
+  "topu_npz": "CHEMBL240_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
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+}

topu-lbvs-mini/kcnh2/s1/splits/seed_2027/split_info.json

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+{
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+  "final_npz": "CHEMBL240_final_ecfp4.npz",
+  "topu_npz": "CHEMBL240_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
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+}

topu-lbvs-mini/kcnh2/s1/splits/seed_2028/split_info.json

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+{
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+  "final_npz": "CHEMBL240_final_ecfp4.npz",
+  "topu_npz": "CHEMBL240_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
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+}

topu-lbvs-mini/targets.csv

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+target,name,chembl_id,class,pdb_code,raw_active_count,raw_inactive_count,cleaned_active_count,cleaned_inactive_count,topu_active_count,topu_inactive_count
+cp3a4,Cytochrome P450 3A4,CHEMBL340,Cytochrome P450,3nxu,3702,30526,3686,30235,154,6160
+aa2ar,Adenosine A2a receptor,CHEMBL251,GPCR,3eml,5194,6237,5159,6212,127,5080
+kcnh2,HERG,CHEMBL240,Ion channel,8zyq,7110,16267,7067,16086,352,14080
+egfr,Epidermal growth factor receptor erbB1,CHEMBL203,Kinase,2rgp,7575,7645,7509,7582,153,6120
+esr1,Estrogen receptor alpha,CHEMBL206,Nuclear Receptor,1sj0,3268,5813,3226,5614,112,4480
+aces,Acetylcholinesterase,CHEMBL220,Other Enzymes,1e66,4701,5907,4575,5797,117,4680
+thrb,Thrombin,CHEMBL204,Protease,1ype,4661,5339,4434,5256,104,4160

topu-lbvs-mini/thrb/s1/CHEMBL204_topUnbiased_ecfp4.npz

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+version https://git-lfs.github.com/spec/v1
+oid sha256:3f4d03186b6e6328347cf655e337de0bb4d4c3c948a1448c437800eee36a8238
+size 365959

topu-lbvs-mini/thrb/s1/splits/seed_2026/split_info.json

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+{
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+  "final_npz": "CHEMBL204_final_ecfp4.npz",
+  "topu_npz": "CHEMBL204_topUnbiased_ecfp4.npz",
+  "verify_status": "PASS",
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+}

topu-lbvs-mini/thrb/s1/splits/seed_2027/split_info.json

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+{
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+}

topu-lbvs-mini/thrb/s1/splits/seed_2028/split_info.json

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+  "verify_status": "PASS",
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+}