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topu-lbvs-few-tier1/README.md

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+# TopU-LBVS-few-tier1
+
+Setting 2: Few-shot TopU → TopU evaluation, Tier 1 (46 targets with fewer than 50 TopU actives).
+
+## Protocol summary
+
+- **Source**: TopU library only (1:40 active:decoy throughout)
+- **Train/val/test active split**: 6:2:2 (Bemis–Murcko scaffold-based)
+- **Inactive assignment**: random, preserving the 1:40 ratio per split
+- **Train ratio**: 1:40 (act:dec)
+- **Validation ratio**: 1:40
+- **Test ratio**: 1:40
+- **Primary metric**: EF@10%  (validation: PR-AUC)
+- **Seeds**: 2026, 2027, 2028
+
+## Per-target file layout
+
+```
+<target>/
+├── <CHEMBL_ID>_train_s2_seed2026_ecfp4.npz
+├── <CHEMBL_ID>_train_s2_seed2027_ecfp4.npz
+├── <CHEMBL_ID>_train_s2_seed2028_ecfp4.npz
+├── <CHEMBL_ID>_val_s2_seed2026_ecfp4.npz
+├── <CHEMBL_ID>_val_s2_seed2027_ecfp4.npz
+├── <CHEMBL_ID>_val_s2_seed2028_ecfp4.npz
+├── <CHEMBL_ID>_test_s2_seed2026_ecfp4.npz
+├── <CHEMBL_ID>_test_s2_seed2027_ecfp4.npz
+└── <CHEMBL_ID>_test_s2_seed2028_ecfp4.npz
+```
+
+## NPZ schema
+
+Each NPZ 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
+
+## Tier rule
+
+A target belongs to Tier 1 if its TopU library has with fewer than 50 TopU actives.
+Tier assignment is computed from the master `targets_master.csv` at the dataset root.
+
+## Targets
+
+See `targets.csv` for the full list of 46 Tier 1 targets, with
+their UniProt / PDB / ChEMBL identifiers, protein class, and per-target counts.

topu-lbvs-few-tier1/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
+5ht3a,Serotonin 3a (5-HT3a) receptor,CHEMBL1899,Ion channel,8bla,778,2307,772,2289,49,1960
+5ht6r,Serotonin 6 (5-HT6) receptor,CHEMBL3371,GPCR,8jlz,4168,2212,4131,2189,47,1880
+ace,Angiotensin-converting enzyme,CHEMBL1808,Protease,3bkl,581,529,578,529,10,400
+ada17,ADAM17,CHEMBL3706,Protease,2oi0,1728,877,1728,876,18,720
+akt2,Serine/threonine-protein kinase AKT2,CHEMBL2431,Kinase,3d0e,1021,2258,1016,2242,48,1920
+ampc,Beta-lactamase,CHEMBL2026,Other Enzymes,1l2s,170,61861,121,61814,12,480
+cac1h,Voltage-gated T-type calcium channel alpha-1H subunit,CHEMBL1859,Ion channel,9ayh,399,1421,398,1417,27,1080
+csf1r,Macrophage colony stimulating factor receptor,CHEMBL1844,Kinase,3krj,1884,2059,1867,2048,46,1840
+cxcr4,C-X-C chemokine receptor type 4,CHEMBL2107,GPCR,3odu,919,855,907,853,15,600
+dhi1,11-beta-hydroxysteroid dehydrogenase 1,CHEMBL4235,Other Enzymes,3frj,3295,675,3294,670,14,560
+dpp4,Dipeptidyl peptidase IV,CHEMBL284,Protease,2i78,4009,1483,3875,1437,31,1240
+dyr,Dihydrofolate reductase,CHEMBL202,Other Enzymes,3nxo,978,921,975,918,19,760
+fa10,Coagulation factor X,CHEMBL244,Protease,3kl6,5395,2188,5315,2126,43,1720
+fak1,Focal adhesion kinase 1,CHEMBL2695,Kinase,3bz3,1649,2123,1642,2099,44,1760
+fnta,Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit,CHEMBL2094108,Other Enzymes,3e37,1745,652,1745,651,12,480
+glcm,Beta-glucocerebrosidase,CHEMBL2179,Other Enzymes,2v3f,415,12008,410,11966,21,840
+hdac2,Histone deacetylase 2,CHEMBL1937,Other Enzymes,3max,1995,1767,1978,1758,28,1120
+hdac8,Histone deacetylase 8,CHEMBL3192,Other Enzymes,3f07,2129,1465,2123,1451,29,1160
+hivint,Human immunodeficiency virus type 1 integrase,CHEMBL3471,Other Enzymes,3nf7,2275,2462,2254,2447,48,1920
+hivpr,Human immunodeficiency virus type 1 protease,CHEMBL243,Protease,1xl2,4511,1556,4491,1550,25,1000
+hmdh,HMG-CoA reductase,CHEMBL402,Other Enzymes,3ccw,269,1064,261,1058,11,440
+hxk4,Hexokinase type IV,CHEMBL3820,Other Enzymes,3f9m,1041,463,1041,463,10,400
+inha,Enoyl-[acyl-carrier-protein] reductase,CHEMBL1849,Other Enzymes,4trj,267,671,261,671,14,560
+kpcb,Protein kinase C beta,CHEMBL3045,Kinase,2i0e,620,1252,616,1235,26,1040
+mcr,Mineralocorticoid receptor,CHEMBL1994,Nuclear Receptor,2aa2,944,490,943,489,10,400
+mk10,c-Jun N-terminal kinase 3,CHEMBL2637,Kinase,2zdt,1262,1653,1258,1648,37,1480
+mmp13,Matrix metalloproteinase 13,CHEMBL280,Protease,830c,2588,762,2585,763,17,680
+mp2k1,Dual specificity mitogen-activated protein kinase kinase 1,CHEMBL3587,Kinase,3eqh,889,2043,887,2021,44,1760
+nos1,"Nitric-oxide synthase, brain",CHEMBL3048,Other Enzymes,1qw6,567,1261,544,1246,19,760
+parp1,Poly [ADP-ribose] polymerase-1,CHEMBL3105,Other Enzymes,3l3m,3596,952,3589,947,20,800
+pde5a,Phosphodiesterase 5A,CHEMBL1827,Other Enzymes,1udt,1872,1649,1866,1641,34,1360
+pgh2,Cyclooxygenase-2,CHEMBL4321,Other Enzymes,3ln1,462,746,462,743,15,600
+ppara,Peroxisome proliferator-activated receptor alpha,CHEMBL239,Nuclear Receptor,2p54,2566,2365,2559,2341,40,1600
+ppard,Peroxisome proliferator-activated receptor delta,CHEMBL3979,Nuclear Receptor,2znp,1698,2055,1689,2038,35,1400
+pygm,Muscle glycogen phosphorylase,CHEMBL4696,Other Enzymes,1c8k,149,687,148,685,10,400
+pyrd,Dihydroorotate dehydrogenase,CHEMBL1966,Other Enzymes,1d3g,1093,1084,1089,1084,25,1000
+rock1,Rho-associated protein kinase 1,CHEMBL3231,Kinase,2etr,1667,2022,1649,2010,44,1760
+rxra,Retinoid X receptor alpha,CHEMBL2061,Nuclear Receptor,1mv9,610,1066,609,1063,20,800
+scn5a,Sodium channel protein type V alpha subunit,CHEMBL1980,Ion channel,6lqa,766,2065,764,2061,43,1720
+tgfr1,TGF-beta receptor type I,CHEMBL4439,Kinase,3hmm,1129,1030,1127,1028,22,880
+thb,Thyroid hormone receptor beta-1,CHEMBL1947,Nuclear Receptor,1q4x,574,5734,574,5709,20,800
+trpa1,Transient receptor potential cation channel subfamily A member 1,CHEMBL6007,Ion channel,6x2j,632,463,631,463,10,400
+try1,Trypsin I,CHEMBL209,Protease,2ayw,1223,817,1165,797,16,640
+tysy,Thymidylate synthase,CHEMBL1952,Other Enzymes,1syn,507,505,505,503,10,400
+urok,Urokinase-type plasminogen activator,CHEMBL3286,Protease,1sqt,856,868,840,848,17,680
+wee1,Serine/threonine-protein kinase WEE1,CHEMBL5491,Kinase,3biz,541,627,541,624,12,480

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