| # Arc State Norman fine-tuning split. | |
| # Explicit train/test perturbation lists for the GEARS simulation | |
| # split (seed=1): 139 train + 107 test, zero overlap. | |
| [datasets] | |
| norman = "data/processed/norman_state.h5ad" # adjust to your local path | |
| [training] | |
| norman = "train" | |
| [zeroshot] | |
| [fewshot."norman.A549"] | |
| train = [ | |
| "TSC22D1+ctrl", | |
| "ctrl", | |
| "CEBPE+RUNX1T1", | |
| "MAML2+ctrl", | |
| "ctrl+CEBPE", | |
| "SGK1+TBX3", | |
| "ctrl+FOXA1", | |
| "FOXA3+FOXA1", | |
| "ETS2+IGDCC3", | |
| "GLB1L2+ctrl", | |
| "MAP2K6+IKZF3", | |
| "BAK1+ctrl", | |
| "FEV+ctrl", | |
| "MAP2K3+SLC38A2", | |
| "ctrl+ETS2", | |
| "ctrl+FEV", | |
| "ctrl+SET", | |
| "TBX3+ctrl", | |
| "LHX1+ctrl", | |
| "RREB1+ctrl", | |
| "ZNF318+ctrl", | |
| "ctrl+ZBTB25", | |
| "MAP4K5+ctrl", | |
| "UBASH3B+ctrl", | |
| "SLC6A9+ctrl", | |
| "MIDN+ctrl", | |
| "DLX2+ctrl", | |
| "CBFA2T3+ctrl", | |
| "HES7+ctrl", | |
| "SET+CEBPE", | |
| "IGDCC3+ZBTB25", | |
| "AHR+ctrl", | |
| "FOXO4+ctrl", | |
| "ctrl+CBFA2T3", | |
| "ctrl+RUNX1T1", | |
| "POU3F2+ctrl", | |
| "ctrl+CNN1", | |
| "IGDCC3+MAPK1", | |
| "MAP2K3+ctrl", | |
| "MAP4K3+ctrl", | |
| "ZBTB25+ctrl", | |
| "ZC3HAV1+CEBPE", | |
| "UBASH3B+UBASH3A", | |
| "MAP2K3+MAP2K6", | |
| "PTPN1+ctrl", | |
| "RUNX1T1+ctrl", | |
| "PTPN12+ctrl", | |
| "TP73+ctrl", | |
| "ctrl+MAP7D1", | |
| "FOSB+ctrl", | |
| "MAPK1+ctrl", | |
| "IRF1+ctrl", | |
| "TMSB4X+BAK1", | |
| "BPGM+SAMD1", | |
| "IKZF3+ctrl", | |
| "HOXB9+ctrl", | |
| "ctrl+HOXC13", | |
| "MAPK1+IKZF3", | |
| "ctrl+UBASH3B", | |
| "ctrl+HOXB9", | |
| "ETS2+ctrl", | |
| "CLDN6+ctrl", | |
| "FOXA3+ctrl", | |
| "CEBPE+ctrl", | |
| "KIF18B+KIF2C", | |
| "ctrl+SAMD1", | |
| "COL1A1+ctrl", | |
| "PTPN12+UBASH3A", | |
| "FOXF1+ctrl", | |
| "FEV+MAP7D1", | |
| "PLK4+ctrl", | |
| "BPGM+ctrl", | |
| "LYL1+ctrl", | |
| "ctrl+MAP2K6", | |
| "SGK1+ctrl", | |
| "MAPK1+TGFBR2", | |
| "ctrl+DLX2", | |
| "MAP2K6+ctrl", | |
| "ctrl+TBX3", | |
| "CNN1+ctrl", | |
| "ctrl+CEBPA", | |
| "HNF4A+ctrl", | |
| "MAP7D1+ctrl", | |
| "PTPN12+SNAI1", | |
| "KMT2A+ctrl", | |
| "CNN1+UBASH3A", | |
| "IGDCC3+ctrl", | |
| "ISL2+ctrl", | |
| "TGFBR2+IGDCC3", | |
| "TMSB4X+ctrl", | |
| "KIF2C+ctrl", | |
| "ctrl+CLDN6", | |
| "ctrl+KIF2C", | |
| "IRF1+SET", | |
| "CSRNP1+ctrl", | |
| "CEBPE+CEBPA", | |
| "ctrl+UBASH3A", | |
| "NCL+ctrl", | |
| "ctrl+BAK1", | |
| "ctrl+IKZF3", | |
| "FOXF1+HOXB9", | |
| "UBASH3B+CNN1", | |
| "ZC3HAV1+ctrl", | |
| "SET+ctrl", | |
| "FOSB+UBASH3B", | |
| "SNAI1+UBASH3B", | |
| "ctrl+STIL", | |
| "HOXC13+ctrl", | |
| "ATL1+ctrl", | |
| "CEBPE+PTPN12", | |
| "CEBPA+ctrl", | |
| "NIT1+ctrl", | |
| "SAMD1+UBASH3B", | |
| "TGFBR2+ctrl", | |
| "SAMD1+TGFBR2", | |
| "FOXA1+ctrl", | |
| "SAMD1+ctrl", | |
| "ctrl+MAPK1", | |
| "UBASH3A+ctrl", | |
| "AHR+FEV", | |
| "ETS2+IKZF3", | |
| "ctrl+ISL2", | |
| "ctrl+SLC38A2", | |
| "PTPN12+ZBTB25", | |
| "ctrl+SNAI1", | |
| "HOXA13+ctrl", | |
| "ctrl+FOXF1", | |
| "ctrl+PTPN12", | |
| "SAMD1+PTPN12", | |
| "HK2+ctrl", | |
| "ctrl+IGDCC3", | |
| "ctrl+TGFBR2", | |
| "FOXA3+FOXF1", | |
| "ZC3HAV1+CEBPA", | |
| "KIF18B+ctrl", | |
| "SNAI1+ctrl", | |
| "FOXA1+FOXF1", | |
| "PLK4+STIL", | |
| "STIL+ctrl", | |
| ] | |
| test = [ | |
| "CBL+PTPN9", | |
| "DUSP9+ctrl", | |
| "MAP2K6+SPI1", | |
| "UBASH3B+PTPN12", | |
| "BCORL1+ctrl", | |
| "MEIS1+ctrl", | |
| "CBL+ctrl", | |
| "KLF1+FOXA1", | |
| "TBX3+TBX2", | |
| "SLC4A1+ctrl", | |
| "DUSP9+MAPK1", | |
| "COL2A1+ctrl", | |
| "CEBPE+KLF1", | |
| "UBASH3B+OSR2", | |
| "UBASH3B+ZBTB25", | |
| "DUSP9+ETS2", | |
| "ZNF318+FOXL2", | |
| "UBASH3B+PTPN9", | |
| "S1PR2+ctrl", | |
| "CELF2+ctrl", | |
| "JUN+CEBPA", | |
| "CDKN1A+ctrl", | |
| "ctrl+MEIS1", | |
| "MAPK1+PRTG", | |
| "MAP2K3+IKZF3", | |
| "KLF1+COL2A1", | |
| "PTPN12+OSR2", | |
| "ETS2+CEBPE", | |
| "POU3F2+FOXL2", | |
| "DUSP9+PRTG", | |
| "CKS1B+ctrl", | |
| "BCL2L11+TGFBR2", | |
| "AHR+KLF1", | |
| "CEBPB+CEBPA", | |
| "PRTG+ctrl", | |
| "ETS2+CNN1", | |
| "C3orf72+ctrl", | |
| "CNN1+MAPK1", | |
| "FOXL2+MEIS1", | |
| "FOXL2+ctrl", | |
| "FOSB+CEBPE", | |
| "PTPN12+PTPN9", | |
| "FOSB+CEBPB", | |
| "ctrl+CDKN1A", | |
| "BCL2L11+BAK1", | |
| "FOXA3+HOXB9", | |
| "ARID1A+ctrl", | |
| "ctrl+COL2A1", | |
| "CEBPE+CNN1", | |
| "ZC3HAV1+HOXC13", | |
| "CBL+CNN1", | |
| "ZBTB10+PTPN12", | |
| "CBL+UBASH3B", | |
| "CEBPB+PTPN12", | |
| "BCL2L11+ctrl", | |
| "OSR2+ctrl", | |
| "ctrl+SPI1", | |
| "CEBPB+MAPK1", | |
| "ETS2+MAPK1", | |
| "DUSP9+IGDCC3", | |
| "CEBPB+ctrl", | |
| "CBL+PTPN12", | |
| "CEBPB+OSR2", | |
| "ctrl+PRTG", | |
| "SGK1+S1PR2", | |
| "DUSP9+KLF1", | |
| "CDKN1B+ctrl", | |
| "FEV+ISL2", | |
| "JUN+ctrl", | |
| "POU3F2+CBFA2T3", | |
| "FOXA1+HOXB9", | |
| "ZBTB10+ctrl", | |
| "CEBPE+SPI1", | |
| "PTPN13+ctrl", | |
| "CBL+TGFBR2", | |
| "FOXA1+FOXL2", | |
| "FOXF1+FOXL2", | |
| "ETS2+PRTG", | |
| "PTPN9+ctrl", | |
| "LYL1+CEBPB", | |
| "DUSP9+SNAI1", | |
| "ctrl+CEBPB", | |
| "TGFBR2+PRTG", | |
| "PRDM1+ctrl", | |
| "FOSB+OSR2", | |
| "FOXL2+HOXB9", | |
| "ctrl+PTPN9", | |
| "ctrl+OSR2", | |
| "ZBTB10+ELMSAN1", | |
| "JUN+CEBPB", | |
| "ZBTB10+SNAI1", | |
| "ctrl+FOXL2", | |
| "CEBPE+CEBPB", | |
| "PRDM1+CBFA2T3", | |
| "FOXA3+FOXL2", | |
| "CDKN1C+CDKN1B", | |
| "CDKN1C+CDKN1A", | |
| "SPI1+ctrl", | |
| "EGR1+ctrl", | |
| "ZBTB10+DLX2", | |
| "CBL+UBASH3A", | |
| "SNAI1+DLX2", | |
| "IGDCC3+PRTG", | |
| "CDKN1C+ctrl", | |
| "ctrl+CDKN1B", | |
| "CDKN1B+CDKN1A", | |
| "C3orf72+FOXL2", | |
| ] | |