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.gitattributes

@@ -57,3 +57,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+replogle_concat.h5ad filter=lfs diff=lfs merge=lfs -text

all.toml

@@ -0,0 +1,16 @@
+[datasets]
+replogle = "/data/replogle_nogwps_v2" # ADDS ALL h5 or h5ad files in this folder to training
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+replogle = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]
+[fewshot."replogle.hepg2"]
+val = []
+test = []

hepg2.toml

@@ -0,0 +1,16 @@
+[datasets]
+replogle = "/data/replogle_nogwps_v2" # ADDS ALL h5 or h5ad files in this folder to training
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+replogle = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]
+[fewshot."replogle.hepg2"]
+test = ['GPS1', 'MRPL4', 'LONP1', 'CCT2', 'MVK', 'GSK3B', 'H3F3A', 'GART', 'RMI1', 'RPL6', 'MRPL34', 'WDHD1', 'UBE3C', 'HUWE1', 'NOP16', 'RABGGTA', 'HNRNPDL', 'SSU72', 'MED21', 'MRPS17', 'LYRM4', 'NSUN4', 'MALSU1', 'RAD51', 'MRPL38', 'RPL37A', 'DAP3', 'THOC1', 'PHB2', 'TXNL4B', 'NOL11', 'IARS2', 'GLE1', 'SNRNP27', 'CCNB1', 'SRBD1', 'TSEN54', 'NHP2', 'DDX6', 'UTP15', 'HNRNPH1', 'SMC1A', 'RNF14', 'ANAPC13', 'RPS3A', 'YARS', 'RRS1', 'STIL', 'EIF5A', 'EXOC1', 'EXOSC7', 'FKBP9', 'GPN3', 'MPHOSPH6', 'RAD51C', 'UTP20', 'SLC1A5', 'GTF2H4', 'POGZ', 'RPL23', 'GAR1', 'WDR18', 'NDUFAF3', 'ELP5', 'IPO11', 'GNL3L', 'KAT7', 'NFYB', 'MIPEP', 'XRCC6', 'PDAP1', 'UBR5', 'PITRM1', 'SRP14', 'WARS', 'STRIP1', 'ANAPC1', 'DDX5', 'CDC6', 'OIP5', 'NDUFS3', 'SUPT20H', 'HMGB3', 'TBCB', 'DARS', 'PRPF4', 'UBE2L3', 'TRMT6', 'KIAA0586', 'HNRNPK', 'NDUFA3', 'GABPB1', 'MRPS25', 'OSTC', 'USP14', 'POLR2I', 'NOC3L', 'MIS18BP1', 'RCL1', 'C12orf45', 'NLE1', 'LETM1', 'ZNF720', 'PPA2', 'TTC1', 'EIF2S3', 'GNPNAT1', 'RAMAC', 'MED8', 'RPL4', 'AAR2', 'DRAP1', 'DNTTIP2', 'PMF1', 'MRPL54', 'SF3B5', 'TFAM', 'SNRNP40', 'SRSF6', 'RPS19BP1', 'PRELID3B', 'RPF1', 'DDX21', 'CHERP', 'SNRPB', 'LRR1', 'PRKCA', 'RBM48', 'WDR12', 'RPL30', 'NUP54', 'RARS2', 'ATP6V1A', 'COX10', 'MRPL41', 'CEP68', 'MRPL3', 'RPS4X', 'PLK1', 'COPS4', 'CCAR1', 'SHQ1', 'SYS1', 'MRPL39', 'CCDC6', 'SRSF7', 'VPS29', 'PSMB5', 'CCDC115', 'TRAPPC11', 'CUL1', 'TMX2', 'RPL35A', 'TNPO3', 'DNAJA1', 'DHX36', 'ARGLU1', 'CBX1', 'TRNT1', 'THOC2', 'GTF3A', 'CS', 'SCAF1', 'ZDHHC7', 'ELP6', 'MRPL49', 'TMED10', 'SNRPD3', 'ZCCHC9', 'WDR33', 'POP7', 'COPS2', 'XPO1', 'BANP', 'GSPT1', 'TAZ', 'RPUSD4', 'XPO5', 'PMPCA', 'URB2', 'CSE1L', 'YARS2', 'PELP1', 'PPP2R3C', 'ATP6V1G1', 'ETF1', 'COG2', 'RNPC3', 'TM7SF2', 'BUB1', 'PPP2CA', 'AURKAIP1', 'MRPS33', 'GINS1', 'RPS27', 'LSM5', 'LSM10', 'PRPF4B', 'PFDN2', 'RPL18A', 'CHCHD2', 'KIF18B', 'TIMM10', 'RPP40', 'NAA50', 'PSMG2', 'CCDC59', 'PNO1', 'TP53RK', 'ATP2A2', 'USP10', 'PCBP1', 'SCAP', 'MRPS30', 'ICE1', 'SKP1', 'WDR1', 'TAF2', 'C1orf131', 'CSTF3', 'TAF1C', 'RPS7', 'PRPF3', 'GRPEL1', 'RAB4B', 'RUVBL2', 'MED26', 'PSMD4', 'GRSF1', 'JMJD6', 'BTAF1', 'PSMD14', 'CFL1', 'TRA2B', 'POLR3E', 'SNRPC', 'SEPHS2', 'CMTR1', 'MPHOSPH10', 'NFATC2IP', 'RPS12', 'ACTR1B', 'BTF3L4', 'BRCA1', 'MCMBP', 'MSRB1', 'POLD1', 'RPL23A', 'INO80', 'ATP5ME', 'CHCHD4', 'SBNO1', 'RFC3', 'MARS', 'TARS2', 'TARS', 'MTOR', 'TAF1B', 'GFER', 'MRPS7', 'PGS1', 'EXOC4', 'TOPBP1', 'TEAD3', 'CNOT1', 'MCM3AP', 'MCM7', 'CCDC86', 'MMS22L', 'GABPA', 'RAE1', 'PSME2', 'FAM32A', 'NFS1', 'EXOC7', 'TMSB10', 'COTL1', 'RAB6A', 'ENO1', 'SHC1', 'ELAC2', 'AURKA', 'VPS54', 'SRRM2', 'PTGR2', 'AARS', 'GTF3C1', 'NOL7', 'PTPMT1', 'TOP3A', 'SF3B4', 'ARL4D', 'PSMB2', 'DDX19A', 'COX7C', 'RPL32', 'DHX16', 'NVL', 'SRF', 'SUGT1', 'DCTN2', 'CTU2', 'TTC4', 'UHRF1', 'GTPBP4', 'HIPK1', 'PPP6C', 'ELOB', 'ASF1B', 'URM1', 'MED17', 'WDFY3', 'MRPS10', 'CCDC174', 'COPS5', 'TAF12', 'DENR', 'HDAC7', 'GTF2E1', 'OSGEP', 'EIF3L', 'BAG6', 'RBM28', 'TRAPPC4', 'PGPEP1', 'IMP4', 'RAB4A', 'MED11', 'CIAPIN1', 'H2AFZ', 'LSM6', 'POLR2G', 'TPX2', 'INTS11', 'DYNC1I2', 'EIF2S1', 'GYG1', 'EMC1', 'COASY', 'SP1', 'F8A1', 'NOL10', 'NAA20', 'CENPJ', 'THOC7', 'ANAPC10', 'RTTN', 'MED4', 'RBM17', 'NOLC1', 'PALB2', 'KRR1', 'HDAC3', 'TOMM40', 'POP1', 'RPS13', 'RPS27A', 'STXBP4', 'WDR5', 'CENPW', 'HGS', 'GTF2E2', 'XRN2', 'NUBP2', 'MBD3', 'TRAPPC5', 'MCM3', 'INTS1', 'DDX27', 'RIOK1', 'RPP14', 'RPL18', 'NCAPH2', 'TMEM127', 'EXOC3', 'LTV1', 'SKA3', 'BCR', 'NAA30', 'PI4KA', 'DCTN6', 'ZBTB17', 'TFRC', 'ATP6V1B2', 'TCOF1', 'FNBP4', 'HSD17B10', 'SPCS3', 'IWS1', 'PDCD6', 'TADA2B', 'NDUFA6', 'COQ4', 'IMPA2', 'MASTL', 'SMC6', 'RAD9A', 'POLL', 'INTS9', 'PABPC4', 'DDX52', 'ALG2', 'TSR2', 'PAF1', 'UFM1', 'INTS4', 'METAP2', 'CCNC', 'CCT4', 'GTF3C2', 'WDR83OS', 'SEPSECS', 'RFC5', 'SRRM1', 'MEX3A', 'RPA2', 'EIF4H', 'LSG1', 'KTI12', 'EIF4B', 'POP4', 'DLD', 'ARMC7', 'TUBGCP4', 'NMD3', 'MED30', 'ABCB7', 'AKIRIN2', 'E4F1', 'WBP1', 'MRPL32', 'EIF1AX', 'SEH1L', 'SMC5', 'ZC3H4', 'SNAPC2', 'PYURF', 'DNM1L', 'DHPS', 'EIF2B4', 'TIMM9', 'TRAPPC8', 'TAF7', 'CENPN', 'MTHFD1', 'DDX23', 'TINF2', 'FDXR', 'PSMC1', 'CENPK', 'EMC4', 'XRCC2', 'FASN', 'TFB1M', 'NAA15', 'ZNHIT1', 'EIF2B3', 'SHOC2', 'NKAP', 'ITGB1BP1', 'UFL1', 'PCNX3', 'RAD51D', 'GUK1', 'GMPPB', 'COQ5', 'SOD2', 'CCNH', 'TSFM', 'CDC45', 'ELL', 'BOD1L1', 'DDX17', 'RPP30', 'SUDS3', 'EIF2B2', 'COMTD1', 'IPO7', 'TIMM23B', 'E2F6', 'DAXX', 'SETD5', 'SYMPK', 'CCT8', 'POLR3F', 'INTS3', 'INTS13', 'DDX56', 'SRA1', 'ARL2', 'TAMM41', 'MAX', 'EBNA1BP2', 'MRPL16', 'CYREN', 'TPRKB', 'ANAPC11', 'COG1', 'MRPL51', 'ATP11B', 'AAAS', 'DPH3', 'non-targeting', 'MIOS', 'IARS', 'LPIN1', 'SEC61G', 'UBQLN4', 'THOC5', 'DDX1', 'UCHL5', 'MSL1', 'SLC39A9', 'TUBA1B', 'PRRC2A', 'ILF3', 'FCF1', 'PTEN', 'PGD', 'RBM4', 'RAC1', 'CALR', 'CTNNBL1', 'SCD', 'EIF4G2', 'DTL', 'SPATA5L1', 'BRF2', 'PXN', 'ANKLE2', 'RSL24D1', 'RPS2', 'CNOT9', 'GFOD2', 'ORC6', 'SLC39A7', 'GLRX5', 'ABHD11', 'PEX19', 'POLR3B', 'LSM4', 'RPL9', 'C19orf53', 'RPL28', 'ZNF787', 'CCT3', 'CTDP1', 'NACA', 'ERCC3', 'TNRC6A', 'METTL14', 'ELP3', 'PPIA', 'PET117', 'DCTN1', 'SDHAF2', 'PPME1', 'SURF6', 'SNAPC5', 'PPP1R15B', 'IMPDH2', 'UXT', 'BCLAF1', 'GTF2A1', 'URI1', 'PFN1', 'POLA1', 'ATP5MF', 'UTP11', 'MYBL2', 'SNRPD1', 'ACTR6', 'DNAJA3', 'UBAP1', 'MED14', 'GLRX3', 'NAA25', 'NUDT15', 'RNASEH2C', 'RPS3', 'CD3EAP', 'SDAD1', 'ZNHIT6', 'NSA2', 'SART3', 'HERC1', 'NUP133', 'MDN1', 'MRPS16', 'PYROXD1', 'PRPF31', 'CHCHD1', 'RPUSD3', 'POLG2', 'PPIL2', 'FAU', 'VPS35', 'UMPS', 'MED16', 'SNRNP35', 'C9orf78', 'NDUFB4', 'EIF4E', 'EXOSC2', 'MAK16', 'NARS2', 'ANKRD11', 'BMS1', 'NOB1', 'CCT7', 'PRPF8', 'RPL26', 'CHD4', 'PPP2R1A', 'TADA3', 'HAUS8', 'TP53I13', 'DRG1', 'C7orf26', 'RBM33', 'CHTOP', 'RPL10A', 'NAA10', 'ATF5', 'MYCBP', 'UBE2I', 'EXOSC3', 'ZFC3H1', 'BRF1', 'RTRAF', 'MRPS5', 'RPLP0', 'VARS', 'USP9X', 'ADRM1', 'RTCB', 'EIF4A1', 'PTCD3', 'LIMS1', 'GINS2', 'TUBG1', 'MLLT6', 'ATR', 'CUL2', 'RPS18', 'NUFIP1', 'TMEM242', 'C19orf25', 'NUP43', 'RPL10', 'DYNLL2', 'ISCA2', 'LSM3', 'NDUFB8', 'LAS1L', 'GNL2', 'DHX15', 'RPS6', 'SNAPC3', 'MBTPS1', 'NSMCE2', 'RPL24', 'ELOVL1', 'CD2BP2', 'SNRNP200', 'HSPA9', 'NOP9', 'FBXO42', 'HSD17B12', 'ATRIP', 'ANKRD39', 'KEAP1', 'HUS1', 'NPLOC4', 'TRAIP', 'RFC2', 'TUBD1', 'MCM6', 'THAP11', 'ALG13', 'RUVBL1', 'RFC4', 'CPSF4', 'WDR70', 'MRPL10', 'MRPL36', 'CENPT', 'RPL41', 'RBMXL1', 'MRPS23', 'COPS8', 'AHCTF1', 'XRCC5', 'AIFM1', 'LAMTOR1', 'PPP1R37', 'CPSF6', 'RBM10', 'SMNDC1', 'RABGGTB', 'NOM1', 'INPPL1', 'EIF2S2', 'YEATS2', 'DDX41', 'PRPF39', 'NCKAP1', 'SPTSSA', 'MBTPS2', 'ANKS6', 'CHMP7', 'ACTR8', 'PHF12', 'PSME1', 'VARS2', 'RPIA', 'MANF', 'TAF10', 'TBPL1', 'PFDN6', 'BET1', 'HS6ST1', 'INTS14', 'EHMT2', 'EIF3A', 'CENPC', 'THRAP3', 'ANAPC5', 'GEMIN5', 'RPAP2', 'GPN1', 'PPAN', 'EXOC2', 'PDCD11', 'RNF113A', 'RBBP8', 'RBM15', 'INO80B', 'NDC1', 'TRIAP1', 'UXS1', 'PSMB3', 'AP2M1', 'SMG5', 'ERCC2', 'YTHDC1', 'NOL8', 'AGBL5', 'COX5A', 'INTS6', 'UQCC2', 'ZNF236', 'CCT6A', 'UPF2', 'TAF8', 'DPH2', 'GPS2', 'NOL6', 'TIMM8A', 'POGLUT3', 'MNAT1', 'OGFOD1', 'RBM19', 'NPM1', 'CSNK2B', 'MRPL24', 'SLC2A8', 'SPG7', 'ATP6V0C', 'DIMT1', 'NAA35', 'NDUFAB1', 'RRP9', 'TERF2', 'WDR46', 'C17orf58', 'RPAP3', 'NCAPD2', 'TCERG1', 'TACC3', 'LDB1', 'PSMC5', 'MRPS26', 'RPL17', 'PDHA1', 'DCAF6', 'C9orf16', 'SPRTN', 'MYC', 'GEMIN4', 'EXOSC4', 'FDPS', 'DCTN4', 'RTEL1', 'VPS41', 'CCT5', 'PES1', 'PLEKHN1', 'SRP68', 'RAC3', 'SETD1A', 'PNKP', 'TUBE1', 'PABPN1', 'SLC7A6OS', 'NFYC', 'NARS', 'DOLK', 'CHEK1', 'SUPT16H', 'WTAP', 'SSBP3', 'PNN', 'EIF2B1', 'TEX10', 'TAF6', 'STX5', 'HSCB', 'WDR26', 'PAXBP1', 'WDR43', 'SART1', 'INTS8', 'SDC1', 'TAF5', 'EIF1', 'WDR75', 'NRBP1', 'INTS5', 'INTS10', 'SETDB1', 'CEP85', 'CDT1', 'KIN', 'BRD2', 'RBX1', 'RPL27A', 'BORA', 'QRSL1', 'CSTF1', 'NOL12', 'MRPS21', 'NDUFAF7', 'TBCA', 'THAP1', 'RRP12', 'OPA1', 'HJURP', 'BTF3', 'EXOSC5', 'IST1', 'CNN2', 'HSP90B1', 'HARS', 'FAM207A', 'PPA1', 'MRPL20', 'TTI1', 'LSM7', 'CIAO1', 'FNTA', 'SASS6', 'TFDP1', 'NELFA', 'MBNL1', 'POLR3K', 'PTPN11', 'PGAM1', 'STRAP', 'TIMM13', 'EIF3I', 'MRPL9', 'INTS12', 'PRELID1', 'PDRG1', 'MMS19', 'EIF1AD', 'MRPS35', 'PRDM4', 'NHLRC2', 'FARSA', 'BRCA2', 'THOC6', 'RRP7A', 'NUP153', 'UTP18', 'SARS2', 'CHORDC1', 'CDC42', 'MRPL27', 'NUP160', 'UTP23', 'RPS21', 'DDX20', 'CLPB', 'EDC4', 'NELFE', 'NAF1', 'COPS3', 'IPO9', 'CPSF3', 'BPTF', 'RPA1', 'EPRS', 'SRPRB', 'SNRNP48', 'NUB1', 'KRI1', 'AFG3L2', 'DBR1', 'GFM1', 'NAGLU', 'RPL7', 'PPRC1', 'DHX29', 'DERL2', 'CCP110', 'NUP85', 'NUDC', 'TUBB', 'SRP9', 'TBP', 'WDR77', 'DNAJC17', 'PRORP', 'PAM16', 'USP8', 'RPS28', 'DSTYK', 'NUP35', 'TRAPPC3', 'GINS4', 'BARD1', 'THOC3', 'PSMA3', 'GTF3C6', 'SLBP', 'MAT2A', 'PRPF19', 'SRSF1', 'EFTUD2', 'CDC16', 'HNRNPA1', 'PDCD6IP', 'TADA1', 'RARS']
+# train gets all other perturbations automatically

hepg2_zeroshot.toml

@@ -0,0 +1,14 @@
+[datasets]
+replogle = "/data/replogle_nogwps_v2" # ADDS ALL h5 or h5ad files in this folder to training
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+replogle = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+"replogle.hepg2" = "test"
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]

jurkat.toml

@@ -0,0 +1,16 @@
+[datasets]
+replogle = "/data/replogle_nogwps_v2" # ADDS ALL h5 or h5ad files in this folder to training
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+replogle = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]
+[fewshot."replogle.jurkat"]
+test = ['TAF10', 'GTF2E1', 'RPP14', 'SCD', 'RPUSD3', 'NEDD8', 'LSM3', 'SEC61B', 'GEMIN5', 'BRIP1', 'COX15', 'PPAN', 'PSMB5', 'SUGT1', 'CPNE1', 'NOL9', 'CABIN1', 'TRAPPC3', 'LAMTOR1', 'CWC25', 'COG6', 'DBF4', 'ATP2A2', 'KAT7', 'ZNF720', 'GFER', 'NOP9', 'CHMP7', 'STT3B', 'DHDDS', 'CRCP', 'SEH1L', 'TUBB2A', 'C19orf25', 'UBE2H', 'RPL36', 'RPAP3', 'ISG20L2', 'SET', 'NUDC', 'NIFK', 'EIF6', 'ATP5MF', 'PEX19', 'PDPK1', 'ANAPC11', 'RPL41', 'ZNF236', 'UXS1', 'PPIH', 'LSM12', 'AGBL5', 'FCF1', 'RBBP5', 'non-targeting', 'UQCRQ', 'DNAJC9', 'CTU2', 'LRP5', 'TPRKB', 'PKMYT1', 'UTP11', 'DPY19L4', 'MCM2', 'TAF6L', 'ARGLU1', 'PRELID3B', 'VEZT', 'PTK2', 'GTF2F1', 'CCNC', 'UBA5', 'MNAT1', 'WDR3', 'DRG1', 'LETM1', 'CCNH', 'POP1', 'MVD', 'CALR', 'ADAM10', 'TUFM', 'NDUFB3', 'AARS', 'PYURF', 'MRPL15', 'MIS18A', 'KATNB1', 'ERCC3', 'MRPL50', 'EXOC5', 'LENG8', 'MRPS10', 'ZNF24', 'EIF3D', 'MED19', 'MRPS28', 'MRPS22', 'GYG1', 'XPO5', 'ZFR', 'EHMT2', 'TNRC6A', 'PRPF40A', 'C9orf16', 'AAR2', 'RPN1', 'ZRSR2', 'ATRIP', 'HECTD1', 'WAC', 'RPTOR', 'OSTC', 'MRPL51', 'UROD', 'VPS72', 'AASDHPPT', 'SNX15', 'ELL', 'GNB1L', 'TIMELESS', 'NOC4L', 'MIS18BP1', 'BANF1', 'SPOUT1', 'CHERP', 'IWS1', 'STXBP4', 'RPS26', 'DNTTIP2', 'PSMD13', 'GPN3', 'HSPA9', 'TOPBP1', 'HDAC3', 'MLST8', 'UQCRC2', 'COX17', 'KLC2', 'BDP1', 'WDR43', 'EXOSC9', 'PRORP', 'PGD', 'MTOR', 'GTF3A', 'EXOC1', 'VPS18', 'H2AFZ', 'MEN1', 'RRP15', 'HAUS4', 'URM1', 'LYRM4', 'PTPN11', 'RPS13', 'GTF2H3', 'SPCS3', 'ORC3', 'NOB1', 'GINS2', 'TSEN2', 'RPL8', 'NAA35', 'DGCR8', 'MRPL43', 'PGS1', 'ZFC3H1', 'TMX2', 'RFC3', 'HSCB', 'BCL2L1', 'NDC1', 'BANP', 'FARS2', 'MPHOSPH6', 'WDR25', 'MED21', 'NUDCD3', 'REXO2', 'METTL14', 'EXOC7', 'UBA2', 'NFRKB', 'NCBP1', 'SLC25A3', 'ARF4', 'SNAPC2', 'MCM4', 'THOC7', 'RMI1', 'EXOSC3', 'HSD17B12', 'MOB4', 'SP1', 'MMGT1', 'RPL39', 'MRPL36', 'H2AFX', 'EEF1G', 'EIF4H', 'MRPS11', 'PITRM1', 'TFAM', 'SLU7', 'ALG1', 'THAP11', 'USP9X', 'PPRC1', 'RNF14', 'DIS3', 'CMTR1', 'CENPW', 'SRP72', 'C17orf58', 'TWF1', 'RPS3A', 'RPS7', 'ANAPC13', 'MRPL24', 'TRAPPC1', 'NEPRO', 'PFDN1', 'NPM1', 'NCBP2', 'PSMD4', 'UFL1', 'COPS2', 'TP53RK', 'HMGA1', 'MRPL39', 'BRD2', 'CDC123', 'CAP1', 'ZC3H4', 'KDM1A', 'RCOR1', 'BAG6', 'MRPS21', 'TIMM9', 'ATXN10', 'NDUFA11', 'HBS1L', 'NLE1', 'USF2', 'UQCRH', 'SMARCE1', 'MRPS18A', 'EXOSC10', 'RIOK1', 'NELFB', 'DYNLL2', 'DHX9', 'CCNB1', 'UBA3', 'MRPL35', 'DCTN4', 'DAXX', 'METAP2', 'FAM207A', 'PPARGC1B', 'ELAC2', 'MRPL23', 'MT2A', 'TEX10', 'XRCC2', 'ZMYM4', 'GPN1', 'NCAPH2', 'SRF', 'DNMT1', 'RPS19BP1', 'DPH3', 'CCDC6', 'MSL1', 'RPS2', 'NRBP1', 'DHX29', 'POLG2', 'PREB', 'COA5', 'N6AMT1', 'BUD13', 'FBXW7', 'PDRG1', 'RFC5', 'PUM1', 'SETDB1', 'GINS4', 'PET117', 'NOLC1', 'VHL', 'PDAP1', 'PPP2CB', 'EFR3A', 'RPL37', 'LSG1', 'C1D', 'MEX3A', 'LSM10', 'RAD51C', 'KARS', 'SRA1', 'MRPL20', 'PHB2', 'PTGR2', 'CENPJ', 'MANF', 'NELFA', 'MRPS25', 'SMUG1', 'BRK1', 'KEAP1', 'MALSU1', 'HS6ST1', 'TRMT10C', 'PPP6C', 'RFC4', 'VPS25', 'TRRAP', 'SLC35G2', 'METTL16', 'RPP40', 'DHX16', 'MRPL14', 'MVK', 'RBBP8', 'CEP85', 'PDCD6', 'NIP7', 'PRMT1', 'MRPS18C', 'ATP6V1B2', 'PNPT1', 'CEBPZ', 'CNN2', 'RFT1', 'DCTN2', 'MAT2A', 'TAF8', 'MIS12', 'GMPPB', 'INTS11', 'PPIA', 'SCNM1', 'PIGH', 'C18orf21', 'DDX27', 'KIAA0586', 'INTS14', 'SRP19', 'PYROXD1', 'GPKOW', 'NSMCE1', 'TIPIN', 'POP5', 'COPS5', 'OSGEP', 'CSNK1A1', 'SRFBP1', 'HSP90B1', 'RAD51D', 'MRPS17', 'SNUPN', 'GLB1', 'COX7B', 'PPP1R8', 'TIMM44', 'GEMIN4', 'POLR3H', 'USP10', 'TRAPPC8', 'RABGGTB', 'RPL26', 'WBP1', 'CLASRP', 'UBR4', 'EXOC4', 'VARS2', 'MBTPS1', 'RPS20', 'PIK3C3', 'EIF4E', 'POGZ', 'PTPMT1', 'TIMM8A', 'YEATS4', 'NKAPD1', 'DCTN3', 'IARS', 'PWP1', 'NOL11', 'DDX56', 'TERF1', 'ACD', 'INO80', 'RPL26L1', 'STRAP', 'VPS33A', 'TAZ', 'ACTB', 'RPE', 'PPIL4', 'TADA2B', 'SAMD4B', 'GRWD1', 'TBP', 'WDR54', 'MAK16', 'ISCA2', 'TSEN34', 'QRSL1', 'UFM1', 'BOD1L1', 'EPB41L2', 'DHX33', 'NHP2', 'SKP2', 'NVL', 'HMGN2', 'ATR', 'WDR82', 'ELP2', 'MRPS34', 'TTI1', 'PALB2', 'PARN', 'NOM1', 'SETD5', 'WDR26', 'UPF3A', 'MED14', 'DCUN1D5', 'GTF2A1', 'HUWE1', 'ENO1', 'COPS4', 'PRKRA', 'DNM1L', 'GTF2H1', 'CDC7', 'C7orf26', 'RPUSD4', 'CHMP6', 'ADSL', 'DHX15', 'DPM2', 'CTDP1', 'PDCD6IP', 'MRPL3', 'CMPK1', 'EIF2B5', 'TUBGCP5', 'MRPL4', 'SHC1', 'ORC5', 'THG1L', 'RBMXL1', 'INTS10', 'DUT', 'RPAP1', 'ZNHIT1', 'MRPL44', 'CXXC1', 'PSMG2', 'ACTR10', 'LEO1', 'FAF2', 'COG2', 'TMEM199', 'SRRT', 'SKA1', 'STARD7', 'RAB4B', 'TNPO3', 'KTI12', 'UCHL5', 'RPS15A', 'DDX10', 'NDUFV2', 'GUK1', 'EGLN2', 'SUPT20H', 'RPL17', 'NOL10', 'URI1', 'WDR83OS', 'VPS35', 'NAA25', 'SPATA5', 'SLC39A10', 'KRR1', 'KIN', 'MED29', 'PFDN5', 'SUGP1', 'ANKRD49', 'ZC3H13', 'TOR2A', 'NDUFA6', 'DDX20', 'CD2BP2', 'TOMM20', 'WDR75', 'SURF6', 'MRPL27', 'MAGOH', 'CHCHD3', 'OPA1', 'TRA2B', 'GTF2F2', 'MICOS10', 'SFSWAP', 'SEC63', 'RRP1', 'NELFCD', 'TBCA', 'RNF168', 'MASTL', 'TIMM10', 'CSTF3', 'RPL10', 'PNO1', 'PSME1', 'MED8', 'ILF3', 'PPP1R11', 'NHLRC2', 'MMS19', 'BRCA2', 'RINT1', 'UQCRB', 'DNAJC19', 'YEATS2', 'SRRM1', 'RPL36A', 'LSM4', 'DDX5', 'POLRMT', 'RNF8', 'POP4', 'IMPA2', 'CD3EAP', 'WDR92', 'MARS', 'HPS5', 'TMEM127', 'ELOVL1', 'ADRM1', 'ALG13', 'DYNLL1', 'CBLL1', 'HIST1H2BC', 'LRR1', 'METTL23', 'TSG101', 'TRAPPC5', 'MRPL34', 'TWISTNB', 'MED10', 'RARS', 'COMTD1', 'LARS2', 'ANKRD11', 'RPP38', 'POLR3D', 'PNN', 'MTPAP', 'FARSA', 'DPH6', 'DDOST', 'GINS3', 'ERCC2', 'F8A1', 'VBP1', 'THOC3', 'RSL24D1', 'HEATR1', 'MON1A', 'CPSF4', 'CUL2', 'RPP30', 'SPG7', 'IPO7', 'MSRB1', 'FAM136A', 'NCAPD2', 'CNOT3', 'NOP14', 'RPS27', 'MED26', 'CNOT2', 'UMPS', 'EDC4', 'SPCS2', 'SHOC2', 'AKIRIN2', 'RBMX2', 'PMPCA', 'RBX1', 'TRMT6', 'POLG', 'IPO13', 'LONP1', 'EIF3A', 'SUPT16H', 'RPS24', 'AAMP', 'PTBP1', 'MED17', 'UTP20', 'NPLOC4', 'ATP5PD', 'CLOCK', 'GTF3C4', 'CYFIP1', 'ADAT2', 'UBE3C', 'SMG9', 'RIOK2', 'SNRNP40', 'UHRF1', 'NOL6', 'CDK12', 'LSM7', 'NOL7', 'SSBP3', 'USP37', 'SRSF6', 'PDCD5', 'BNIP1', 'SLBP', 'MRPS31', 'SEPHS2', 'TTC1', 'EIF2B1', 'MRGBP', 'SUMO2', 'PDCD2', 'NDUFB4', 'MRPL16', 'IGBP1', 'CCDC86', 'TEFM', 'SUPV3L1', 'ARIH1', 'SNAPC1', 'SLC7A5', 'RPP21', 'EXOSC8', 'DOHH', 'BCR', 'EIF2B2', 'DDX51', 'MED22', 'PABPC4', 'DDX6', 'RPL36AL', 'BTF3', 'TUBE1', 'DDX11', 'EIF2B3', 'FNBP4', 'CLPB', 'RPS18', 'CNOT10', 'CSTF1', 'ATP6V1G1', 'CHTOP', 'MRPS5', 'XRCC1', 'POLR3B', 'UBR5', 'NAA30', 'SYS1', 'CDK9', 'GFM1', 'ACTR8', 'VPS13D', 'PPME1', 'TIMM13', 'C1orf131', 'MTG2', 'ZNHIT3', 'SUPT5H', 'NUP35', 'SMAGP', 'DIMT1', 'TSPYL5', 'ANAPC10', 'TBCB', 'SOD2', 'RPL23A', 'MRPS24', 'SEPSECS', 'CNOT11', 'PSMD9', 'LTV1', 'HMGCS1', 'RAC1', 'SNF8', 'VPS37A', 'SMC6', 'RPS12', 'COPS3', 'CIAPIN1', 'EIF3L', 'DMAP1', 'URB2', 'HSPA14', 'SRP14', 'WDR77', 'CHCHD4', 'PMF1', 'SDHA', 'NDUFAB1', 'RAMAC', 'TXN', 'PRRC2A', 'TPI1', 'NSF', 'NOL8', 'TMED10', 'MRPS26', 'MRPS6', 'NCOA4', 'PHF12', 'RPS14', 'TSFM', 'SNRPA', 'KIF20A', 'DDX21', 'NOC3L', 'MFN2', 'WTAP', 'AC118549.1', 'TOMM22', 'TRMT5', 'TAF3', 'NISCH', 'MCM3', 'ZNF143', 'ELP3', 'SDR39U1', 'GABPB1', 'CS', 'YARS2', 'TMEM214', 'EXOSC1', 'EIF1AD', 'POLR1D', 'NBAS', 'PPP1CB', 'GRPEL1', 'ARL2', 'DDX24', 'DNAJC8', 'IMP4', 'DAP3', 'DHX37', 'ANKS6', 'EIF4G1', 'MCM6', 'TAF6', 'MTHFD1', 'MRPL55', 'SMC5', 'METAP1', 'RPL5', 'EP400', 'TMEM161B', 'RBM10', 'PSMG3', 'CLK2', 'KCTD10', 'FUNDC2', 'ATP5PO', 'COX6C', 'SBNO1', 'IST1', 'ABT1', 'NOP16', 'TOP1', 'PTCD3', 'CINP', 'SRP9', 'GLRX5', 'FEN1', 'NDUFA3', 'MAX', 'MRPS9', 'COX10', 'IARS2', 'BAP1', 'LSM6', 'MBNL1', 'WARS', 'HNRNPA1', 'RABGGTA', 'MED24', 'INF2', 'CCDC59', 'MRPL54', 'UTP23', 'MED30', 'TSR2', 'MRPL22', 'UTP15', 'SEM1', 'GPS2', 'CRKL', 'OIP5', 'TARS2', 'PPP2CA', 'FAM50A', 'PAXBP1', 'LDB1', 'AARS2', 'ABHD11', 'GTF3C3', 'CEP97', 'METTL21A', 'THOC6', 'SNIP1', 'MRPL19', 'MYC', 'SERBP1', 'XRN2', 'FASTKD5', 'COQ4', 'TLN1', 'HDAC7', 'RBM28', 'UBE2L3', 'SETX', 'TBL3', 'TFB2M', 'NASP', 'FYN', 'ACTR6', 'GEMIN6', 'COX5A', 'HSD17B10', 'TRNT1', 'CLCC1', 'EIF3M', 'ELP6', 'FGFR1OP', 'UBE2Z', 'EXOSC2', 'ASCC3', 'INTS4', 'MRPS12', 'ZDHHC7', 'YRDC', 'TPT1', 'ATF4', 'OXA1L', 'COPS8', 'DR1', 'STAT5B', 'TARS', 'FAU', 'ABHD17A', 'GNL2', 'SBDS', 'AHCY', 'IMPDH2', 'RRP7A', 'RCL1', 'MYBBP1A', 'BYSL', 'KXD1', 'ATP5F1B', 'TIGD1', 'MLLT6', 'SUDS3', 'COPS6', 'PLK4', 'SMG7', 'SYMPK', 'INO80C', 'TAF7', 'SLC7A6OS', 'SLC35B1', 'RPL10A', 'ATP1A1', 'CHTF18', 'RPS23', 'UTP18', 'ATP11B', 'CEP68', 'DESI1', 'WDR46', 'NAPG', 'BTAF1', 'CHD4', 'PELP1', 'SACM1L', 'GSPT1', 'KIF4A', 'SNRNP27', 'DCTN5', 'WDR36', 'ARPC4', 'LST1', 'PGK1', 'WDHD1', 'MIPEP', 'CHORDC1', 'SCAP', 'NUP133', 'TAF2', 'CUL3', 'SAE1', 'UTP6', 'CHMP5', 'CENPE', 'ATP5ME', 'ORC4', 'MIOS', 'VPS29', 'TRAPPC11', 'AIFM1', 'CPSF3', 'SASS6', 'CCAR1', 'TAF1D', 'RPS6', 'COQ2', 'POLD3', 'SENP6', 'SPTSSA', 'POLR3C', 'RPL7L1', 'WNK1', 'CLNS1A', 'CNIH4', 'DHODH', 'CPSF1', 'COG1', 'MRPL13', 'SMG8', 'RPL37A', 'CCDC84', 'AFG3L2', 'SPEN', 'THAP1', 'CPSF6', 'CSDE1', 'ANKRD39', 'RPL29', 'FXN', 'WDR5', 'SNRNP48', 'ING3', 'ALDOA', 'USP14', 'TMEM258', 'DCAF6', 'PI4KA', 'C5orf30', 'MED20', 'XRCC5', 'WDR55', 'SRPRB', 'HERC1', 'GINS1', 'NDUFAF7', 'INTS6', 'NPM3', 'WDR70', 'NAA20', 'EIF3B', 'NOL12', 'TCOF1', 'GTPBP4', 'PMPCB', 'MBIP', 'RRN3', 'TOX4', 'TADA1', 'GFOD2', 'NAE1', 'TAF11', 'HNRNPU', 'TOP3A', 'NSUN4', 'TAMM41', 'CUL1', 'GTF2A2', 'TEN1', 'DCTN6', 'PPP4C', 'ACTR1B', 'MED12', 'EIF4G2', 'UBE2M', 'NAA50', 'BRD8', 'PRELID1', 'PTMA', 'DDX59', 'EIF2B4', 'ZCRB1', 'CAMLG', 'DDX52', 'EXOSC4', 'MPHOSPH10', 'BRF2', 'GABPA', 'CASC3', 'TAF12', 'ARMC6', 'ASF1B', 'NKAP', 'HMBOX1', 'RAC3', 'UBAP1', 'PHB', 'WDR4', 'MRPS27', 'MRPS30', 'SPTLC1', 'SRRM2', 'KIF18B', 'TERF2', 'MCMBP', 'DARS', 'SETD1A', 'RBBP4', 'SERF2', 'SNAPC5', 'YARS', 'UQCRFS1', 'LARS', 'RPL28', 'GEMIN7', 'CRLS1', 'SRSF10', 'GRSF1', 'LAMTOR2', 'SEC61G', 'CHCHD1', 'BRCA1', 'MRPS2', 'PPA1', 'ILF2', 'SNTB2', 'RHOQ', 'SLC1A5', 'CENPH', 'HNRNPR', 'TYK2', 'MDN1', 'INTS9', 'LRPPRC', 'WDR18', 'NSMCE2', 'E2F6', 'CENPN', 'ATP6V0D1', 'TRMT112', 'MRTO4', 'RSRC2', 'CYC1', 'DENR', 'PPIE', 'INTS12', 'RNGTT', 'HLA-C', 'TAF1C', 'PRXL2A', 'INO80B', 'COG4', 'HAUS8', 'COX7C', 'HNRNPDL', 'DDX1', 'NAA10', 'HMGB3', 'ABCB7', 'CCNL1', 'EPRS', 'VPS54']
+# train gets all other perturbations automatically

jurkat_zeroshot.toml

@@ -0,0 +1,14 @@
+[datasets]
+replogle = "/data/replogle_nogwps_v2" # ADDS ALL h5 or h5ad files in this folder to training
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+replogle = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+"replogle.jurkat" = "test"
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]

k562.toml

@@ -0,0 +1,16 @@
+[datasets]
+replogle = "/data/replogle_nogwps_v2" # ADDS ALL h5 or h5ad files in this folder to training
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+replogle = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]
+[fewshot."replogle.k562"]
+test = ['RPS4X', 'DSN1', 'CPOX', 'ERCC2', 'NOC4L', 'MCM4', 'ALDOA', 'AAMP', 'INTS4', 'UBE2L3', 'TSEN54', 'SRFBP1', 'GNL3', 'UQCRC2', 'RARS', 'SLC7A6OS', 'MAX', 'GUK1', 'AURKA', 'IPO11', 'N6AMT1', 'MRPL50', 'TSPYL5', 'RPL28', 'NOL12', 'GPKOW', 'TAF1B', 'SAE1', 'ANAPC13', 'TPRKB', 'ACTR2', 'SEM1', 'ORC5', 'DBR1', 'DYNLL1', 'RBMXL1', 'EIF4A1', 'BUB1B', 'TSFM', 'UTP6', 'TXN', 'NAA15', 'COPS2', 'CENPK', 'INTS8', 'NIFK', 'KANSL3', 'BDP1', 'MRPL9', 'HMGA1', 'NCAPG2', 'SSU72', 'WDR83OS', 'RPS13', 'MCM2', 'PDAP1', 'GTF3C3', 'AASDHPPT', 'RSRC2', 'BRF1', 'NOP16', 'SOD2', 'NAF1', 'MED30', 'WDR75', 'LAMTOR2', 'ELOVL1', 'WDR3', 'PPME1', 'TIMM13', 'TIMM44', 'DAP3', 'TMX2', 'RPL35', 'PPARGC1B', 'RPL17', 'RRP12', 'SKA3', 'MRPS10', 'NEDD8', 'GEMIN4', 'PAXBP1', 'TCERG1', 'FAM32A', 'MCM7', 'PRPF4B', 'COQ4', 'SS18L2', 'SUPT5H', 'SRBD1', 'SDE2', 'CLASRP', 'CCDC86', 'PELP1', 'TWISTNB', 'TOP3A', 'CCDC84', 'MRPS9', 'TEX10', 'MED17', 'ATP6AP1', 'NAGLU', 'GINS3', 'RNF123', 'PABPN1', 'KTI12', 'MRPS12', 'MICOS10', 'NDUFA8', 'GNL2', 'WDR77', 'PET117', 'LETM1', 'MRPL17', 'GTF3C2', 'DDX51', 'RPL7', 'TTC27', 'NOL7', 'AAAS', 'GPS1', 'NFRKB', 'PSMD13', 'SLC1A5', 'MCM5', 'SNRNP48', 'EMC1', 'DDX56', 'DPH3', 'RFC5', 'ATP6V0C', 'CENPE', 'DRAP1', 'EIF4E', 'RBM42', 'HMGCS1', 'IMP4', 'GNL3L', 'TINF2', 'PGD', 'MRPL55', 'CENPT', 'CPSF4', 'NDUFB3', 'MRPL39', 'RPP38', 'BTF3', 'PSME2', 'NDUFB10', 'MED29', 'MRPL1', 'NEMF', 'CSE1L', 'CWF19L2', 'FGFR1OP', 'NEPRO', 'CDC16', 'TRMT6', 'TADA3', 'EIF1AD', 'LRR1', 'FAM207A', 'SAMM50', 'LAMTOR3', 'POLR3H', 'MRPL44', 'POLD3', 'ATRIP', 'GEMIN5', 'non-targeting', 'DAD1', 'MED10', 'HDAC3', 'MIOS', 'HYOU1', 'NLE1', 'TELO2', 'ALG13', 'DR1', 'COX11', 'SLC25A3', 'SNAPC1', 'EIF4G1', 'MRPL22', 'SRP72', 'TOPBP1', 'CUL1', 'CHCHD4', 'ILF2', 'RPUSD3', 'MARS', 'PRPF18', 'MRGBP', 'RTCB', 'MRPL27', 'PRPF4', 'XRCC3', 'TIMM22', 'BYSL', 'NUP214', 'CS', 'CDK9', 'VPS13D', 'PIK3R4', 'ALG14', 'INTS9', 'SRP14', 'EP400', 'VARS2', 'MED11', 'UQCC2', 'LTV1', 'NUFIP1', 'LSM2', 'TFDP1', 'SAP18', 'POLR3E', 'ACD', 'SBNO1', 'NMD3', 'NFATC2IP', 'NCAPH', 'H2AFX', 'SCAF1', 'RBM19', 'NELFCD', 'CCAR1', 'QRSL1', 'CSNK1A1', 'PFDN1', 'ZNHIT6', 'MRPL45', 'NDUFA6', 'SUPT6H', 'NBAS', 'DDX20', 'THAP1', 'DNAJC19', 'POLR3B', 'COX5B', 'UXS1', 'SPCS3', 'TRPM7', 'CCNH', 'MRPL15', 'INO80B', 'RFC4', 'RPL24', 'EXOSC10', 'NDUFB6', 'YEATS2', 'GTF3C6', 'RBBP8', 'RPL39', 'OGFOD1', 'NOM1', 'ISCA2', 'CHAF1B', 'NUP54', 'CHMP3', 'POLE', 'FCF1', 'MARS2', 'MRPL28', 'NDUFAF3', 'RPL36A', 'TP53RK', 'TARS2', 'CD2BP2', 'DDX49', 'LARS2', 'DHX16', 'PTPMT1', 'DARS', 'UBA2', 'RARS2', 'HSCB', 'SETD2', 'MRPS2', 'MRPL54', 'RAC3', 'RNASEH2C', 'MRPL10', 'RRS1', 'RRP1', 'COPS3', 'NUP88', 'CPNE7', 'PSMD9', 'POLR1B', 'RPL30', 'TAMM41', 'PPIE', 'CRKL', 'ZNHIT2', 'SEPHS2', 'HECTD1', 'ATP6V1H', 'GTF2H2', 'EXOSC8', 'PDPK1', 'GPN1', 'SNRNP35', 'THOC2', 'SYMPK', 'PRPF19', 'FBL', 'TLN1', 'RNF20', 'YARS2', 'TRAPPC11', 'MYBL2', 'MRPL16', 'ATP6V1C1', 'DDX27', 'MEX3A', 'NCAPD3', 'CENPH', 'PGAM1', 'RPTOR', 'MRPS23', 'ELP5', 'DHPS', 'SENP6', 'PDCD2', 'SDHAF2', 'TXNL4B', 'WDR61', 'RBM48', 'POGZ', 'URI1', 'COPS5', 'SACM1L', 'RPS18', 'RAB18', 'UBE2Z', 'HINFP', 'PTMA', 'PRKRA', 'COX6C', 'RPS11', 'PXN', 'ZRANB2', 'RPAP2', 'DNAJC17', 'TUBGCP5', 'USP37', 'DMAP1', 'RPS26', 'POP1', 'FNTA', 'SNUPN', 'XRCC2', 'CYCS', 'POLD1', 'SRRM2', 'UQCRFS1', 'POLD2', 'VPS41', 'EIF2B3', 'SYS1', 'RPL41', 'CEP68', 'SRP9', 'TM7SF2', 'ISG20L2', 'UROD', 'CCP110', 'SYF2', 'RPL23', 'PNN', 'HSD17B12', 'GNB1L', 'THOC3', 'TAF2', 'DCTN3', 'ADAT2', 'MCM3AP', 'RPL26', 'EIF6', 'FAM136A', 'POLR1E', 'SMC5', 'MRPL2', 'MRPL3', 'RANGAP1', 'SDAD1', 'COPS4', 'NSL1', 'ZCCHC9', 'CCT8', 'HAUS8', 'NHLRC2', 'UTP18', 'DHDDS', 'CCT7', 'FARSB', 'COX10', 'PRORP', 'U2SURP', 'TUBE1', 'SOD1', 'NCAPD2', 'UPF3A', 'DIMT1', 'BRIX1', 'CENPC', 'UQCRH', 'PARN', 'HSPA9', 'RPF1', 'GTF2E1', 'RPP21', 'FARSA', 'RPL36AL', 'CHCHD2', 'ZFC3H1', 'RPS23', 'PTK2', 'TTI1', 'PPP4R2', 'C9orf78', 'SDHC', 'POLR1A', 'GEMIN8', 'EXOC1', 'VPS28', 'MRPL43', 'SMC6', 'THG1L', 'UFL1', 'ABHD11', 'KIAA1143', 'SPRTN', 'INO80', 'SRSF1', 'SSBP1', 'CPSF1', 'EIF2B5', 'TAF12', 'MRPL13', 'DCTN4', 'ADSL', 'MIS18BP1', 'NOB1', 'DDX6', 'CDK2', 'RPS27', 'MED7', 'MCMBP', 'KLC2', 'PLK4', 'MRPS34', 'DOLK', 'POP5', 'ZNF24', 'ORC4', 'ANKS6', 'ING3', 'ROMO1', 'FAM50A', 'CAPZB', 'NELFE', 'SPTSSA', 'POLR2G', 'ANKLE2', 'SART3', 'RTF1', 'TNPO3', 'IPO13', 'CHTOP', 'JMJD6', 'NKAP', 'SMC1A', 'GLE1', 'HIST1H2BN', 'LARS', 'NDUFB7', 'EXOSC7', 'E2F6', 'ELAC2', 'ANKRD11', 'CIAO1', 'CDIPT', 'UFM1', 'REXO2', 'RNPC3', 'RAD51', 'PFDN6', 'NAA25', 'TRAPPC4', 'OPA1', 'NAPG', 'NSMCE1', 'MCM6', 'GTF2H1', 'MED12', 'METAP2', 'EIF3M', 'ACTR1B', 'NARS', 'URB1', 'EXOSC4', 'MAK16', 'CNN2', 'ANAPC11', 'ELP6', 'TRA2B', 'CCNB1', 'CXXC1', 'WDR36', 'MSRB1', 'COX7B', 'DDX18', 'DNM1L', 'DDX59', 'DDX5', 'SFSWAP', 'PRIM1', 'GPN2', 'KIF14', 'TGS1', 'YKT6', 'MRPS6', 'PFDN2', 'MRPL33', 'EXOSC1', 'ARL4D', 'DCAF6', 'MIS12', 'WDR4', 'NOC3L', 'MIS18A', 'TUBA1B', 'COPS6', 'HNRNPC', 'COA5', 'MRTO4', 'BET1', 'RPS7', 'NUP85', 'NRBP1', 'TBCA', 'RNGTT', 'MRPS16', 'KCTD10', 'CCT2', 'CENPN', 'ASF1B', 'OXA1L', 'ALG1', 'CLCC1', 'FNBP4', 'IARS', 'RPS27A', 'NASP', 'RBM17', 'MMS19', 'DDX52', 'MRPS31', 'PMF1', 'CHD4', 'RPS21', 'SARS2', 'GTF2E2', 'GTF2A2', 'RAD17', 'METTL3', 'CIAPIN1', 'URB2', 'ABT1', 'NSMCE2', 'RCL1', 'GLRX5', 'CLK2', 'SRRT', 'HARS', 'EIF2B2', 'MT2A', 'MPHOSPH10', 'RPA2', 'LENG8', 'CHMP6', 'CNOT1', 'EDC4', 'TIMM8A', 'PPP4C', 'GINS4', 'PNPT1', 'KARS', 'MTPAP', 'DDX55', 'RAD9A', 'VHL', 'NUP35', 'UTP20', 'NCBP1', 'SRP54', 'RAD51C', 'SKP2', 'SKP1', 'C1D', 'USP10', 'COX5A', 'NIP7', 'ANAPC5', 'HGS', 'GTF3A', 'NUDC', 'MFAP1', 'ATP6V0D1', 'PSMB2', 'NDUFB8', 'IFITM2', 'NCKAP1', 'WNK1', 'SMC2', 'NCAPH2', 'EEF1G', 'GEMIN7', 'SRP68', 'VPS72', 'RBM25', 'PDCD6', 'INTS1', 'MBTPS2', 'COX15', 'SNRNP27', 'POP7', 'GFER', 'KRR1', 'BRK1', 'NDUFB4', 'MRPS18A', 'RINT1', 'COPS8', 'CEP152', 'MTOR', 'CHMP4B', 'DDX10', 'PFDN4', 'CLNS1A', 'ATR', 'SF3B5', 'EXOSC2', 'SPC25', 'MOB4', 'EXOSC5', 'ARGLU1', 'PGK1', 'MAD2L2', 'RPA3', 'AP2S1', 'DBF4', 'MRPL41', 'NPLOC4', 'RRP7A', 'GAR1', 'RIOK1', 'LSM3', 'GFM1', 'PSMG3', 'MED8', 'COPE', 'SDHA', 'CDC7', 'PAF1', 'GSPT1', 'TMEM199', 'MRPL36', 'EIF4B', 'COG4', 'UNC50', 'MYBBP1A', 'MRPS25', 'PDCD11', 'DICER1', 'YEATS4', 'GTF2B', 'SUPT16H', 'CRLS1', 'KIF18B', 'RPN2', 'PKMYT1', 'GINS1', 'TRAPPC3', 'ZMAT5', 'TAF10', 'GTF2F1', 'COQ2', 'DNAJC11', 'YPEL5', 'SPATA5L1', 'MANF', 'RFC2', 'DHX36', 'GNPNAT1', 'RAB4A', 'MMS22L', 'CDC123', 'INTS5', 'RPUSD4', 'PPP6C', 'TTC1', 'ERAL1', 'DPAGT1', 'LST1', 'URM1', 'OSTC', 'FEN1', 'RRP9', 'EPRS', 'DDX21', 'C9orf16', 'TAF7', 'RPN1', 'RPLP2', 'ATP6V1D', 'WDR82', 'BARD1', 'LONP1', 'ENO1', 'ATL2', 'SLU7', 'GRPEL1', 'FDXR', 'PPIH', 'METTL16', 'MRPL38', 'TIMM10', 'MYCBP', 'RFC3', 'PRELID1', 'DCTN5', 'DCTN6', 'CYFIP1', 'DKC1', 'DNAJA3', 'SRF', 'TBL3', 'MRPS7', 'NELFA', 'WDR12', 'NOLC1', 'PPA2', 'DCTN1', 'PPP1R2', 'ZNF100', 'EXOC2', 'MRPL49', 'UBA3', 'DHX37', 'HIST1H2BC', 'RFT1', 'COX17', 'GTF2F2', 'GTF2H3', 'PTPN23', 'PPAN', 'NUDCD3', 'WDHD1', 'RPS5', 'AARS', 'ALG2', 'RPL31', 'UPF2', 'HAUS1', 'TSR2', 'ACTR6', 'FAF2', 'CHMP7', 'SLC39A7', 'ATP6V0B', 'TRIAP1', 'SNRPC', 'SLC39A9', 'MRPL18', 'RRN3', 'DYNC1H1', 'CMPK1', 'RAB6A', 'GTF3C1', 'C19orf25', 'LSM7', 'SRP19', 'TBCB', 'MRPS27', 'GOLT1B', 'FXN', 'WDR54', 'TRNT1', 'PHB2', 'SEPSECS', 'CD3EAP', 'KRI1', 'AARS2', 'NOP14', 'TCOF1', 'PES1', 'PRMT1', 'THAP11', 'NISCH', 'TMEM258', 'HJURP', 'TPX2', 'LSG1', 'GMPS', 'VPS37A', 'DDX41', 'EIF2S3', 'PAM16', 'VPS25', 'WDR55', 'NCBP2', 'WARS', 'ANKRD49', 'TTK', 'CCT3', 'RPL14', 'TPR', 'PIK3C3', 'METTL1', 'SERBP1', 'PNKP', 'STRIP1', 'MED20', 'UBL5', 'BUB1', 'TSEN2', 'CNIH4', 'DERL2', 'ABCE1', 'SPCS2', 'GTF2H2C', 'MRPL19', 'GMPPB', 'TFAM', 'AKIRIN2', 'RPL6', 'VPS51', 'ARMC6', 'RPP30', 'CEP85', 'AATF', 'BCLAF1', 'POLR3K', 'CHMP5', 'BRIP1', 'EXOSC3', 'NAE1', 'CCT5', 'EBNA1BP2', 'SHQ1', 'PMPCA', 'FASTKD5', 'COASY', 'ECD', 'NPM3', 'MVK', 'DLD', 'ABCB7', 'TRAPPC8', 'CHORDC1', 'USPL1', 'MIPEP', 'TARDBP', 'MNAT1', 'OSGEP', 'EXOC7', 'AHCY', 'PRELID3B', 'H2AFZ', 'KPNA6', 'TAF8', 'INTS2', 'GRWD1', 'TSG101', 'SPC24', 'POLR2H', 'ATP1A1', 'DHX33', 'RBMX2', 'GTF3C5', 'SP2', 'PCNA', 'EIF2S1', 'ACTR8', 'RPS12', 'HAUS6', 'ZMAT2', 'MRPS14', 'HAUS4', 'NDUFS3', 'SEH1L', 'SNRPD1', 'NVL', 'PMPCB', 'CTU2', 'TRAPPC5', 'TUBGCP3', 'ELL', 'PFN1', 'CNOT3', 'MAU2', 'PPRC1', 'ABHD17A', 'NUP62', 'SRSF7', 'PPP2CA', 'UBR5', 'CLTC', 'RPL27A', 'EARS2', 'RPS6', 'UBE2H', 'TTC4', 'RNF8', 'SNRPG', 'IPO7', 'ANLN', 'METAP1', 'ATP6AP2', 'DDX11', 'NSUN4', 'MRPS11', 'UBE2D3', 'QARS', 'ZW10', 'C17orf58', 'EIF3D', 'VBP1', 'MED28', 'GTF2A1', 'PPIA', 'MAT2A', 'SRRM1', 'DCTN2', 'BCS1L', 'EIF2B1', 'BTF3L4', 'NELFB', 'TMEM127', 'UXT', 'DCUN1D5', 'NOP10', 'RABGGTB', 'ATF5', 'DDOST', 'NOL8', 'GLRX3', 'GINS2', 'MRPL51', 'KIF4A', 'UQCRQ', 'NACA', 'ZNHIT3', 'KIF20A', 'DRG1', 'BNIP1', 'PCBP1', 'PGS1', 'RAD51D', 'CDC42', 'PFDN5', 'PPIL2', 'RPL29', 'VARS', 'CUL2', 'VPS33A']
+# train gets all other perturbations automatically

k562_zeroshot.toml

@@ -0,0 +1,14 @@
+[datasets]
+replogle = "/data/replogle_nogwps_v2" # ADDS ALL h5 or h5ad files in this folder to training
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+replogle = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+"replogle.k562" = "test"
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]

replogle_concat.h5ad

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a7992a6109d589f2d49c2eaccff45a9f860418af23125d41b80d8e3929a33d56
+size 30010775846

rpe1.toml

@@ -0,0 +1,16 @@
+[datasets]
+replogle = "/data/replogle_nogwps_v2" # ADDS ALL h5 or h5ad files in this folder to training
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+replogle = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]
+[fewshot."replogle.rpe1"]
+test = ['RPA3', 'POLR1E', 'TMEM258', 'PPIH', 'SMC2', 'NUBP2', 'RNF8', 'ATF4', 'USPL1', 'SDHA', 'RFT1', 'IPO7', 'PSMG2', 'SRSF10', 'MRPL23', 'ZC3H4', 'STRAP', 'SBDS', 'COPS8', 'LSM12', 'GTF2F1', 'PPP2R3C', 'VPS29', 'USP9X', 'TRAPPC8', 'PFDN4', 'METTL17', 'CNOT9', 'VPS35', 'FNBP4', 'XRCC1', 'CEBPZ', 'ATP5F1B', 'MAX', 'POLA1', 'CYREN', 'REXO2', 'PSMA4', 'CSTF1', 'MRPS17', 'RPL36A', 'MRPL55', 'ZNF143', 'CEP152', 'SSU72', 'MRPL45', 'CDT1', 'SRF', 'RPL23A', 'RBX1', 'SLU7', 'WDR12', 'NAGLU', 'LSM5', 'EFTUD2', 'PALB2', 'BCR', 'NUP88', 'MIPEP', 'UTP23', 'NUP107', 'DYNC1H1', 'DYNLL2', 'POLR3C', 'KDM1A', 'TNRC6A', 'NMD3', 'RFC4', 'SMG5', 'PSMD14', 'NUP160', 'POLR2I', 'HMGN2', 'RPL17', 'SLBP', 'IARS2', 'VBP1', 'ZRANB2', 'GPS2', 'DAXX', 'CDK9', 'ELP3', 'NSL1', 'MANF', 'TBPL1', 'UBE2H', 'TIMM8A', 'POP5', 'PDCD7', 'RAB4B', 'NARS', 'TMEM214', 'TUBB2A', 'ANAPC13', 'SBNO1', 'RMI1', 'ALG2', 'NDUFB3', 'GEMIN6', 'MTHFD1', 'RFC2', 'DDOST', 'SCNM1', 'WDR1', 'PPP1R15B', 'CHTOP', 'MRPS31', 'COQ4', 'SP2', 'TOP1', 'CLPB', 'ATP6V1A', 'ORC1', 'GFM1', 'NDC1', 'GABPB1', 'HTATSF1', 'LSM10', 'TADA3', 'SPEN', 'PYROXD1', 'SF3B5', 'ESYT2', 'RPAP1', 'PSMA3', 'RPL30', 'CNOT11', 'TIMM44', 'MRPL44', 'NELFA', 'ENY2', 'LETM1', 'CNOT3', 'OXA1L', 'CCDC59', 'MMS19', 'NKAP', 'BANP', 'KCTD10', 'CMTR1', 'SMAGP', 'RAD17', 'URM1', 'GFER', 'PAF1', 'PARN', 'EIF2B2', 'NSMCE2', 'GPN3', 'DHDDS', 'SETD5', 'BCL2L1', 'ALG1', 'ANAPC11', 'GLE1', 'NCKAP1', 'XRCC2', 'DCTN6', 'LSG1', 'ATP6V1G1', 'C1D', 'TRNT1', 'TRAPPC5', 'FAF2', 'POLR2B', 'NEMF', 'PRELID1', 'E2F6', 'AP2S1', 'RPN1', 'CAMLG', 'NOC3L', 'BAP1', 'CWC25', 'PHB', 'HNRNPK', 'SDHAF2', 'SNTB2', 'PRPF19', 'TUBGCP3', 'GPS1', 'ZCRB1', 'NUP54', 'KTI12', 'EXOSC3', 'TERF1', 'KATNB1', 'MRPS6', 'SNRPD3', 'CDC16', 'ILF2', 'TBP', 'COX6C', 'ZRSR2', 'ANKRD39', 'MRPL27', 'ATP6V1D', 'RPL6', 'ELOB', 'INO80C', 'TUBGCP5', 'MRPL39', 'TADA2B', 'YTHDC1', 'TCERG1', 'THAP1', 'ACTR6', 'RPIA', 'SGPP1', 'MRPL36', 'MRPL4', 'SPATA5', 'MPG', 'CCDC115', 'GEMIN5', 'PNN', 'MRPS33', 'UPF1', 'BAG6', 'ORC6', 'BET1', 'BRK1', 'TRMT10C', 'GTF3A', 'SRSF6', 'MARS', 'BTF3', 'TAF6', 'TARS2', 'KXD1', 'FAM32A', 'NAE1', 'MAD2L2', 'NCBP2', 'NUBP1', 'PABPN1', 'KIF4A', 'LRP5', 'ABCE1', 'TSR2', 'CNOT2', 'CENPH', 'INTS1', 'THAP11', 'MSRB1', 'MRPS35', 'MRPL17', 'JMJD6', 'MRPS10', 'WDR54', 'YEATS2', 'PSMD13', 'POP4', 'SYF2', 'HUS1', 'DPM2', 'SNRPC', 'USP10', 'CSE1L', 'ERAL1', 'TBCD', 'RPL8', 'SNRPD1', 'GCLC', 'PRMT1', 'DAP3', 'KRI1', 'NELFB', 'MRPL41', 'MRPL46', 'GTF3C2', 'GEMIN8', 'SHQ1', 'PFN1', 'FAU', 'MRPS16', 'DBR1', 'HLA-C', 'CNN2', 'TAF3', 'INTS2', 'ELP2', 'COPS6', 'NAF1', 'BCLAF1', 'LSM2', 'PGAM5', 'SPCS3', 'METAP1', 'MAD2L1', 'TOMM40', 'ABHD11', 'PGAM1', 'TMEM161B', 'WTAP', 'CRLS1', 'DCTN1', 'H2AFZ', 'EHMT2', 'RPL28', 'MCM6', 'HSPA9', 'ATP11B', 'ILF3', 'RRS1', 'CARS', 'SMC1A', 'CHMP5', 'PHF10', 'MRPS11', 'MMGT1', 'PTPN23', 'NAA30', 'TRAPPC11', 'TP53RK', 'ZDHHC7', 'CD2BP2', 'NDUFAF3', 'COQ2', 'NCOA4', 'TEN1', 'SNRPE', 'GTF3C4', 'HYOU1', 'SHC1', 'PKMYT1', 'HSP90B1', 'POGLUT3', 'KPNA6', 'C5orf30', 'RPP21', 'COX5A', 'NIFK', 'UBR5', 'CCND3', 'DAD1', 'MRPS18A', 'MNAT1', 'NUP133', 'KLC2', 'GSPT1', 'EXOC5', 'TPR', 'PLK4', 'DDX11', 'DTL', 'MRPL38', 'MRPS18C', 'PSMC1', 'ELOF1', 'KIAA0586', 'DNAJC11', 'ATP6AP1', 'CPNE1', 'DDX52', 'DDX20', 'GRWD1', 'PSMB5', 'DDX27', 'TEFM', 'CSDE1', 'CXXC1', 'HAUS1', 'TAF1D', 'RARS2', 'NCAPH2', 'ATP6AP2', 'TRPM7', 'ATXN10', 'SLC7A6OS', 'TOE1', 'NRBP1', 'EXOC3', 'GTF2H4', 'TRA2B', 'UPF2', 'ANAPC5', 'GUK1', 'RCOR1', 'PRPF8', 'LAMTOR4', 'RAB6A', 'EIF2B5', 'TTF2', 'KIN', 'RBBP4', 'VEZT', 'PPP1R37', 'PPP6C', 'SARNP', 'ARPC4', 'GEMIN4', 'RPLP0', 'TSG101', 'TAF2', 'EXOSC7', 'EIF3J', 'MBTPS1', 'EIF4B', 'SKA3', 'ARGLU1', 'GFOD2', 'TIPIN', 'PSAT1', 'FEN1', 'STX5', 'TUBGCP2', 'RPL14', 'CCNB1', 'DHX16', 'WDR77', 'KDM5C', 'GTF3C3', 'VHL', 'WDR43', 'RANGAP1', 'ALG13', 'ZNHIT2', 'NCAPH', 'TUBB', 'TACC3', 'TFAM', 'SDC1', 'VPS13D', 'EIF2B4', 'UXS1', 'BRCA2', 'SKP2', 'PABPC4', 'COX17', 'EEF1B2', 'PRKRA', 'BTF3L4', 'PRPF40A', 'SEC61B', 'RBMXL1', 'CDIPT', 'RPLP2', 'RPN2', 'SETDB1', 'COG4', 'EDC4', 'SNRPA', 'RABGGTA', 'CDK2', 'ATP5PO', 'SP1', 'GLRX5', 'MRPL35', 'MRPS24', 'FAM207A', 'METTL16', 'EIF1AX', 'NARS2', 'MRPS9', 'SRP68', 'ADSL', 'MCMBP', 'SEM1', 'TARDBP', 'DDX19A', 'ASF1B', 'RPE', 'TOMM22', 'HDAC7', 'SAMM50', 'MBTPS2', 'TSEN54', 'EIF3D', 'MRPS25', 'NSA2', 'PIGH', 'RNASEH2C', 'CNOT10', 'ATL2', 'SF3B3', 'WAC', 'SCFD1', 'OGFOD1', 'RPL13', 'SHOC2', 'EXOC1', 'HAUS8', 'KIF14', 'ACTR8', 'TPT1', 'PPP1R12A', 'RUVBL1', 'DDX23', 'SMNDC1', 'MRPL11', 'IMPDH2', 'CSTF3', 'LRR1', 'POLG', 'RTTN', 'IGBP1', 'RPA2', 'RPL29', 'COX10', 'RPS13', 'RPUSD3', 'NFYC', 'DDX41', 'PMPCA', 'ZFR', 'ATP6V1F', 'MRPL24', 'RSRC2', 'AAAS', 'ATP6V0B', 'ATP6V1E1', 'SLC35G2', 'SS18L2', 'PSMC5', 'PCBP1', 'HSPA14', 'SRSF7', 'PSMB3', 'TIMM22', 'TFRC', 'HARS', 'REV3L', 'EIF2S3', 'HNRNPR', 'VPS54', 'CAP1', 'CENPW', 'DGCR8', 'PTPN11', 'VPS18', 'UQCRQ', 'DHPS', 'RBM33', 'KAT7', 'GTF3C5', 'MRPL51', 'CAPZB', 'EXOC2', 'CENPJ', 'INO80', 'PRRC2A', 'IARS', 'TAZ', 'TXNL4B', 'SLC35B1', 'UNC50', 'VARS', 'ZNF720', 'PRIM1', 'RBM10', 'MRPL42', 'SNRNP200', 'CHMP6', 'EIF5A', 'NASP', 'EIF3B', 'CNOT1', 'POGZ', 'MBD3', 'SPRTN', 'MIOS', 'GTF2H3', 'TAF11', 'CENPK', 'DRG1', 'IPO9', 'H2AFX', 'ACD', 'SRA1', 'NAA35', 'CHORDC1', 'PPRC1', 'EPRS', 'WDR18', 'PPP4R2', 'XRCC5', 'ENO1', 'TMEM242', 'HECTD1', 'PGD', 'PGS1', 'PNKP', 'MRPS30', 'ZFC3H1', 'ECD', 'EIF4G2', 'RPS8', 'EIF2B1', 'EIF2S1', 'NPLOC4', 'ATP6V0D1', 'MOB4', 'HNRNPC', 'HUWE1', 'NDUFA3', 'LRPPRC', 'NHLRC2', 'MRGBP', 'ATP1A1', 'BMS1', 'DRAP1', 'GRSF1', 'SUDS3', 'MTG2', 'MTPAP', 'PMF1', 'SEH1L', 'CASC3', 'HIPK1', 'CALR', 'PIAS1', 'ZNF292', 'ATR', 'RIOK1', 'THRAP3', 'CNIH4', 'UBR4', 'CHD4', 'THOC6', 'CTNNBL1', 'CSNK2B', 'MED14', 'PXN', 'CCNC', 'BANF1', 'SRP72', 'NUTF2', 'KIAA1143', 'WDHD1', 'NMT1', 'BRIP1', 'TFB1M', 'NOP14', 'MFN2', 'EXOSC2', 'LARS', 'SART1', 'DNAJA3', 'SMC6', 'SLC7A5', 'ORC5', 'RPS26', 'ATIC', 'MRPL18', 'CTR9', 'TEAD3', 'PRXL2A', 'HMGA1', 'LSM4', 'RBBP5', 'RPAP3', 'CHCHD3', 'EIF4G1', 'TELO2', 'LONP1', 'UBL5', 'GOLT1B', 'LIMS1', 'TEX10', 'GARS', 'GNL3', 'SLC25A3', 'RBM42', 'RPRD1B', 'CCT7', 'DENR', 'CYCS', 'ACTR1B', 'NLE1', 'ACTB', 'MRPL20', 'DCUN1D5', 'WARS', 'RTCB', 'TP53I13', 'BRF1', 'NAA25', 'RPL23', 'SUPT20H', 'UBA5', 'MCM3', 'NUP62', 'TSEN2', 'NDUFV2', 'UQCRH', 'SERBP1', 'EIF3A', 'ZMAT5', 'ATP6V1C1', 'AIFM1', 'PDCD11', 'TMED2', 'NSUN4', 'DUT', 'CRCP', 'MRPS23', 'CMPK1', 'SNAPC1', 'MIS18BP1', 'SPTLC1', 'RNF168', 'ZW10', 'ETF1', 'RPL26L1', 'IPO13', 'ARL2', 'RPL10A', 'DPH2', 'MRPL1', 'CENPN', 'TOP3A', 'DSN1', 'MCM4', 'VPS37A', 'TUFM', 'RCL1', 'STIL', 'RPL24', 'RBM25', 'GBF1', 'DNAJC17', 'NISCH', 'CLOCK', 'TUBA1B', 'GTF2H2', 'GRPEL1', 'PPIL1', 'SMG7', 'UBQLN4', 'RBM4', 'DBF4', 'PPP2CA', 'MIS18A', 'YKT6', 'SDHC', 'TWF1', 'TOX4', 'RPS27A', 'STRIP1', 'AURKA', 'DYNC1I2', 'SUPV3L1', 'EGLN2', 'OIP5', 'NAA20', 'CINP', 'POLD3', 'OSTC', 'ITGB1BP1', 'PPP2CB', 'BUB1', 'ZNHIT1', 'DIMT1', 'HEXIM1', 'TSFM', 'POLR2M', 'RPL35', 'RAD51D', 'HSPE1', 'COA5', 'CPNE7', 'FDXR', 'STXBP4', 'GINS4', 'PAM16', 'MCM2', 'FKBP9', 'GYG1', 'TTK', 'RPS27', 'ANKS6', 'PPIL2', 'TTC4', 'MRPL14', 'TMX2', 'LAMTOR1', 'RUVBL2', 'ALG14', 'KEAP1', 'CPOX', 'TOMM20', 'CCDC137', 'MRPS21', 'TUBA1C', 'TRMT5', 'CDC73', 'BUD13', 'DNAJA1', 'SMARCE1', 'DMAP1', 'SNUPN', 'NAPG', 'CENPE', 'INO80B', 'RTRAF', 'SUPT16H', 'CPSF3', 'CUL1', 'CUL3', 'CCNH', 'EIF4H', 'PPME1', 'ZNF787', 'RAC3', 'MSL1', 'ATP6V1B2', 'SPG7', 'DPY19L4', 'SPC24', 'OPA1', 'CABIN1', 'POLL', 'SNRPB', 'PRPF39', 'NSMCE1', 'RPS19', 'SLC39A10', 'TMEM199', 'YARS', 'EIF4E', 'CCT4', 'DYNLL1', 'SAE1', 'ANAPC1', 'MRPS34', 'HNRNPU', 'COX7C', 'NUP85', 'METTL1', 'UROD', 'SUMO2', 'WDR44', 'IMPA2', 'IST1', 'MRPL32', 'PEF1', 'RNF14', 'TTI1', 'EIF2S2', 'PPIL4', 'ZBTB17', 'RNPC3', 'TBCB', 'GPN2', 'VPS41', 'SRPRB', 'COQ5', 'POLD1', 'WDR33', 'UMPS', 'TUBG1', 'METTL23', 'CCP110', 'MRPL49', 'CDC6', 'ARL4D', 'CS', 'RPA1', 'HMGCS1', 'NUB1', 'GMPPB', 'SNRNP27', 'NCAPD2', 'CHCHD2', 'NFYB', 'RNF20', 'EIF1', 'PTK2', 'ZNF236', 'VPS28', 'TFDP1', 'C9orf16', 'PDCD6', 'GART', 'PSME1', 'YEATS4', 'U2SURP', 'TNPO3', 'CENPC', 'ERCC2', 'ATP5MF', 'POLD2', 'CLTC', 'EEF1G', 'ISCA2', 'RNMT', 'DNAJC19', 'NSF', 'CHMP7', 'DHX33', 'SARS2', 'DSTYK', 'DPAGT1', 'UBE2M', 'MRPL22', 'CENPT', 'NDUFA8', 'INTS13', 'UQCRC2', 'GPKOW', 'ATF5', 'BRIX1', 'SASS6', 'ACTR2', 'HAUS4', 'CTU2', 'POLRMT', 'MRPS7', 'MMS22L', 'EIF3L', 'WDR4', 'TMEM127', 'ELP6', 'RPL15', 'GSK3B', 'MYBL2', 'WBP1', 'MRPL37', 'GTF3C6', 'AP2M1', 'DDX17', 'SET', 'EIF3M', 'PRORP', 'RNGTT', 'MFAP1', 'HJURP', 'MRPS14', 'EPB41L2', 'WDR5', 'BUB1B', 'RPL32', 'TRIAP1', 'FASTKD5', 'CCDC84', 'COG1', 'FDPS', 'DNAJC8', 'FUNDC2', 'EXOC7', 'NUDCD3', 'XRN1', 'MBIP', 'YARS2', 'DDX55', 'URI1', 'NDUFB10', 'EIF3I', 'TUBGCP4', 'SLC2A8', 'TTC1', 'MPHOSPH6', 'UFM1', 'UBE2I', 'CBLL1', 'PITRM1', 'NUP153', 'VPS33A', 'MRPS26', 'EIF2B3', 'CYC1', 'CEP97', 'SEPHS2', 'PLEKHN1', 'EXOSC1', 'INTS14', 'MCM5', 'AGBL5', 'WDR83OS', 'ARMC6', 'AFG3L2', 'RHOQ', 'HBS1L', 'RPL35A', 'PDCD5', 'AASDHPPT', 'FAM136A', 'HPS5', 'HDAC3', 'YPEL5', 'RPS2', 'SEC63', 'NDUFA11', 'SRRT', 'ADAM10', 'GET3', 'TUBE1', 'EIF6', 'NUP214', 'NDUFB8', 'RPL5', 'PET117', 'NAA50', 'SPCS2', 'SNAPC3', 'ELL', 'PRIM2', 'MRPL34', 'TLCD1', 'CCT6A', 'TIMM10', 'RPL26', 'MVD', 'HMGB3', 'CIAO1', 'ADRM1', 'HNRNPA1', 'SNRNP25', 'FXN', 'MTOR', 'IWS1', 'SSBP3', 'BDP1', 'COMTD1', 'MICOS10', 'RPL39', 'HSD17B10', 'SMG8', 'DPH6', 'DCTN4', 'PTEN', 'PHB2', 'MED11', 'RAB18', 'PES1', 'NKAPD1', 'NUDC', 'RPS3', 'CDK1', 'COG6', 'EXOSC4', 'LAS1L', 'RPP14', 'EXOSC8', 'RPS6', 'NOM1', 'DDX1', 'FBXW7', 'KCMF1', 'PTPN1', 'TXN', 'RPL9', 'MRPL19', 'MRPL28', 'GNPNAT1', 'PPA2', 'PGK1', 'SNRPG', 'SAMD4B', 'NOLC1', 'EEFSEC', 'AHCTF1', 'CLNS1A', 'TAF8', 'DOHH', 'NUP35', 'RPUSD4', 'EP400', 'IFITM2', 'THOC7']
+# train gets all other perturbations automatically

rpe1_zeroshot.toml

@@ -0,0 +1,14 @@
+[datasets]
+replogle = "/data/replogle_nogwps_v2" # ADDS ALL h5 or h5ad files in this folder to training
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+replogle = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+"replogle.rpe1" = "test"
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]