| input_dim: 2001 |
| hidden_dim: 336 |
| output_dim: 2001 |
| pert_dim: 12731 |
| batch_dim: 4 |
| dropout: 0.1 |
| lr: 0.001 |
| loss_fn: mse |
| control_pert: NTC |
| embed_key: X_hvg |
| output_space: gene |
| gene_names: |
| - PuroR |
| - CYP51A1 |
| - CD99 |
| - CFLAR |
| - POLDIP2 |
| - CD38 |
| - FKBP4 |
| - NDUFAB1 |
| - TSPOAP1 |
| - WDR54 |
| - KMT2E |
| - ITGAL |
| - KDM7A |
| - AGK |
| - PHTF2 |
| - IFRD1 |
| - PRSS21 |
| - CCDC124 |
| - BLTP2 |
| - TSR3 |
| - JARID2 |
| - ST3GAL1 |
| - MMP25 |
| - IL32 |
| - UBE3C |
| - TRAF3IP3 |
| - CD9 |
| - NCAPD2 |
| - CD4 |
| - FYN |
| - ZBTB32 |
| - KDM5D |
| - PSMC4 |
| - SLC25A39 |
| - CLK1 |
| - CD6 |
| - TACC3 |
| - SLC30A9 |
| - CCDC88C |
| - XYLT2 |
| - SLC38A5 |
| - TTC27 |
| - CD74 |
| - RUNX3 |
| - SERPINB1 |
| - NLRP2 |
| - GRAMD1B |
| - BIRC3 |
| - STRAP |
| - PLEKHO1 |
| - GCLM |
| - DEPDC1 |
| - TYMP |
| - TOMM34 |
| - VIM |
| - FAS |
| - CD44 |
| - SLAMF7 |
| - SH2D2A |
| - TNFRSF1B |
| - BMAL2 |
| - PNPLA6 |
| - ABCF2 |
| - FUT8 |
| - GAB2 |
| - SLC4A7 |
| - TMSB10 |
| - RNF19A |
| - FAM136A |
| - DEPDC1B |
| - STAP1 |
| - RFC1 |
| - NSUN2 |
| - STAU2 |
| - INPP4A |
| - PSMA4 |
| - CAPG |
| - LCP2 |
| - CTNNA1 |
| - HSPA5 |
| - ATOSA |
| - WWC3 |
| - NOP16 |
| - UTS2 |
| - TNFRSF9 |
| - RCN1 |
| - CLPTM1L |
| - FOXP3 |
| - LIMA1 |
| - HERPUD1 |
| - CYBA |
| - HEBP2 |
| - MPHOSPH9 |
| - MSMO1 |
| - MRTO4 |
| - PHPT1 |
| - KIF1B |
| - SYNE2 |
| - ATP9A |
| - EIF2AK2 |
| - TRAF1 |
| - IL17RB |
| - SOAT1 |
| - PRDM1 |
| - SEC61A1 |
| - ATP2B4 |
| - NDC1 |
| - PARP12 |
| - ALDH18A1 |
| - TARBP1 |
| - SLC2A3 |
| - CTDP1 |
| - YBX3 |
| - GNA15 |
| - SNRNP40 |
| - BCAT1 |
| - HDAC7 |
| - VMP1 |
| - CASP8 |
| - INTS13 |
| - TM7SF3 |
| - HIPK2 |
| - CNN2 |
| - WDR3 |
| - WDR18 |
| - MCM10 |
| - DGKA |
| - ZC3H15 |
| - FAM107B |
| - MTHFD2 |
| - PDE4A |
| - SMARCD1 |
| - ASPM |
| - DDX3Y |
| - PFKP |
| - IDI1 |
| - KLF6 |
| - PLPP1 |
| - TRAM1 |
| - PKM |
| - RASSF1 |
| - IFI35 |
| - ACSL4 |
| - PRR11 |
| - POLR1A |
| - KIF2A |
| - ERLEC1 |
| - MAST4 |
| - BCL3 |
| - CLEC2D |
| - RORA |
| - TGFBR3 |
| - MAPK6 |
| - RAB27A |
| - NUCB2 |
| - DAPP1 |
| - WIPI1 |
| - AP3M2 |
| - EIF2B3 |
| - TCOF1 |
| - MAP4K4 |
| - MGAT4A |
| - BUD23 |
| - TRIP13 |
| - FAM50A |
| - ACTN1 |
| - TFRC |
| - SREBF1 |
| - SMC1A |
| - HSD17B10 |
| - HMMR |
| - P4HA2 |
| - NFATC3 |
| - ACADVL |
| - STK10 |
| - ACAP1 |
| - NDE1 |
| - MCM2 |
| - GSDMB |
| - PTGS2 |
| - MAP3K13 |
| - ST6GAL1 |
| - TBX21 |
| - PICALM |
| - EED |
| - ATP2A3 |
| - BCS1L |
| - LMAN1 |
| - ENO1 |
| - MYDGF |
| - TUBE1 |
| - ACAT1 |
| - FNDC3B |
| - FOSL2 |
| - RAB7A |
| - ARHGAP15 |
| - MCM6 |
| - SPAG5 |
| - TRAF4 |
| - PAG1 |
| - ICAM3 |
| - UBE2T |
| - FGFR1 |
| - CST7 |
| - TIGAR |
| - P2RY10 |
| - ITM2A |
| - SP140 |
| - FDFT1 |
| - KIF22 |
| - PGM1 |
| - DDX1 |
| - EPB41L2 |
| - SMARCA2 |
| - SESN1 |
| - CPOX |
| - CLDND1 |
| - HSP90AA1 |
| - DLGAP4 |
| - IGSF9B |
| - NDC80 |
| - ARG2 |
| - PTPRC |
| - STK17B |
| - CDC14B |
| - AACS |
| - IL12RB2 |
| - FYB1 |
| - ME2 |
| - NFE2L1 |
| - P2RX5 |
| - OXCT1 |
| - CYLD |
| - SMAP2 |
| - GSTP1 |
| - HADHA |
| - CD59 |
| - CD82 |
| - AK6 |
| - SEH1L |
| - MTIF2 |
| - MGST2 |
| - DNAJA1 |
| - B4GALT1 |
| - CHMP5 |
| - DIMT1 |
| - IPO11 |
| - SNX10 |
| - LAT2 |
| - HUWE1 |
| - PPP1R15A |
| - FTL |
| - SRRT |
| - BAX |
| - OGFOD1 |
| - NOP14 |
| - RTRAF |
| - AURKA |
| - PIR |
| - DDX18 |
| - KHSRP |
| - TPX2 |
| - DOCK9 |
| - ANKRD10 |
| - SMOX |
| - TESC |
| - SNX5 |
| - OAS1 |
| - PEBP1 |
| - ERP29 |
| - FXYD5 |
| - BIRC5 |
| - LAG3 |
| - ZBTB25 |
| - RGS1 |
| - YPEL3 |
| - NUDC |
| - ICAM1 |
| - DNAJB11 |
| - PUS7 |
| - CMTM6 |
| - FH |
| - SEL1L3 |
| - NLRP1 |
| - CD200 |
| - PSME1 |
| - WDR76 |
| - PHGDH |
| - CLSPN |
| - RFFL |
| - DPYSL2 |
| - ADA2 |
| - CDC6 |
| - UPRT |
| - SH2D3C |
| - CREM |
| - FKBP5 |
| - SRPK1 |
| - HSP90AB1 |
| - HNRNPH3 |
| - JAK2 |
| - SCD |
| - ABLIM1 |
| - HNRNPM |
| - TIMM13 |
| - MKNK2 |
| - OSM |
| - PES1 |
| - MAPK1 |
| - CYTH4 |
| - MFNG |
| - GRK3 |
| - LGALS1 |
| - EIF3L |
| - SNU13 |
| - DDX17 |
| - TOMM22 |
| - XBP1 |
| - RTCB |
| - SUN2 |
| - MCM5 |
| - APOBEC3H |
| - TTLL12 |
| - GRAP2 |
| - NCF4 |
| - CSF2RB |
| - IL2RB |
| - RANGAP1 |
| - PHF5A |
| - POLR3H |
| - DESI1 |
| - GZMB |
| - GNPNAT1 |
| - DDHD1 |
| - PSMA3 |
| - AHSA1 |
| - RIN3 |
| - LGMN |
| - EIF5 |
| - MTHFD1 |
| - PSMB5 |
| - CCNB1IP1 |
| - APEX1 |
| - DHRS2 |
| - PCK2 |
| - NFKBIA |
| - MYBL2 |
| - NFATC2 |
| - PFDN4 |
| - DOK5 |
| - TPD52L2 |
| - NELFCD |
| - PRELID3B |
| - PSMA7 |
| - CDC25B |
| - TRIB3 |
| - RASSF2 |
| - SAMHD1 |
| - NOP56 |
| - E2F1 |
| - AHCY |
| - PPP1R16B |
| - USP14 |
| - LPIN2 |
| - MYL12A |
| - RNF125 |
| - MIB1 |
| - RIOK3 |
| - PGRMC1 |
| - ALG13 |
| - PLS3 |
| - NAA10 |
| - PIM2 |
| - PGK1 |
| - SMS |
| - PHEX |
| - CD40LG |
| - TIMP1 |
| - MAGED2 |
| - RBM3 |
| - NDFIP2 |
| - ACP5 |
| - DNAJC3 |
| - PARP4 |
| - KPNA3 |
| - FLT1 |
| - RGCC |
| - HSF4 |
| - LYRM1 |
| - NUTF2 |
| - NUP93 |
| - PSMD7 |
| - COTL1 |
| - NME4 |
| - SLC7A5 |
| - DNAJA3 |
| - RBL2 |
| - PYCARD |
| - BCKDK |
| - IL21R |
| - CCP110 |
| - VPS35L |
| - CTSH |
| - FAH |
| - HOMER2 |
| - EHD4 |
| - ATP8B4 |
| - GABPB1 |
| - EIF3J |
| - MYEF2 |
| - BPNT2 |
| - LAPTM4B |
| - IKBKB |
| - NCALD |
| - UBR5 |
| - GSDMD |
| - GFUS |
| - ERI1 |
| - SLC39A14 |
| - GSR |
| - MCM4 |
| - BNIP3L |
| - KCNN4 |
| - NUCB1 |
| - GYS1 |
| - ECH1 |
| - DOT1L |
| - CD37 |
| - IL4I1 |
| - TIMM44 |
| - ASF1B |
| - RASAL3 |
| - TIMM50 |
| - FBL |
| - GPI |
| - EBI3 |
| - SLC1A5 |
| - FZR1 |
| - BBC3 |
| - DENND3 |
| - PLIN3 |
| - NOP53 |
| - NKG7 |
| - ETFB |
| - RABAC1 |
| - GRWD1 |
| - PRPF31 |
| - KXD1 |
| - ETHE1 |
| - CDK6 |
| - NAMPT |
| - PIK3CG |
| - HBP1 |
| - ZC3HAV1 |
| - TAX1BP1 |
| - GARS1 |
| - HSPB1 |
| - BUD31 |
| - EIF3B |
| - AIMP2 |
| - EZH2 |
| - AHR |
| - CHCHD3 |
| - GIMAP2 |
| - SPIN1 |
| - NMRK1 |
| - TRIM14 |
| - TGFBR1 |
| - SEC61B |
| - AKNA |
| - KDM4C |
| - DOCK8 |
| - BAG1 |
| - NPDC1 |
| - ABCA2 |
| - GATA3 |
| - MAPK8 |
| - VSIR |
| - SPOCK2 |
| - SFXN3 |
| - NPM3 |
| - GTPBP4 |
| - BCCIP |
| - SH3PXD2A |
| - PITRM1 |
| - MAP3K8 |
| - GLRX3 |
| - TFAM |
| - CCDC6 |
| - UBE2S |
| - DNAJC12 |
| - PPIF |
| - PSMD3 |
| - DHX40 |
| - KPNB1 |
| - C1QBP |
| - CCDC47 |
| - SYNGR2 |
| - UTP6 |
| - CYTH1 |
| - PSMD11 |
| - CCL1 |
| - DHX58 |
| - PPP1R9B |
| - LRRC59 |
| - EFTUD2 |
| - HLF |
| - YWHAE |
| - MMD |
| - WSB1 |
| - ALDOC |
| - RAB34 |
| - TMEM33 |
| - CHIC2 |
| - ZNF330 |
| - KLHL2 |
| - IL2 |
| - GRPEL1 |
| - GAR1 |
| - MFSD10 |
| - KLHL5 |
| - NCAPG |
| - UGDH |
| - HTATIP2 |
| - CTSC |
| - ZBTB16 |
| - HSPA8 |
| - LPXN |
| - PRPF19 |
| - TMEM109 |
| - CHORDC1 |
| - IL10RA |
| - CD5 |
| - AIP |
| - POU2AF1 |
| - PPFIBP1 |
| - CD69 |
| - CLEC2B |
| - SELPLG |
| - BIN2 |
| - IL23A |
| - ATP5F1B |
| - METAP2 |
| - LTA4H |
| - GPN3 |
| - DUSP16 |
| - CDKN1B |
| - CDK2AP1 |
| - OAS3 |
| - OAS2 |
| - GTF2H3 |
| - VDR |
| - STX2 |
| - IL26 |
| - IFNG |
| - MDM1 |
| - KRR1 |
| - NOP2 |
| - CDCA3 |
| - CHPT1 |
| - GNPTAB |
| - ENO2 |
| - ATN1 |
| - C12orf57 |
| - PTPN6 |
| - GOLT1B |
| - TMEM14C |
| - PAK1IP1 |
| - ADTRP |
| - ASF1A |
| - HDDC2 |
| - RIPOR2 |
| - SRSF3 |
| - MCM3 |
| - BAG2 |
| - CRYBG1 |
| - SMAP1 |
| - GMNN |
| - TRIM38 |
| - PERP |
| - HECA |
| - CUTA |
| - CCND3 |
| - BYSL |
| - VEGFA |
| - HMGCS1 |
| - KIF20A |
| - HSPA9 |
| - HBEGF |
| - HMGCR |
| - ITK |
| - ARSB |
| - CCNG1 |
| - ARRDC3 |
| - LNPEP |
| - PDE4D |
| - BRIX1 |
| - SLC12A7 |
| - IL4 |
| - RAD50 |
| - IL5 |
| - ST8SIA4 |
| - GNPDA1 |
| - NR3C1 |
| - SEC24A |
| - TXNDC15 |
| - ATP6V0E1 |
| - STC2 |
| - HRH2 |
| - SELENOK |
| - TIMMDC1 |
| - BCL6 |
| - FAM162A |
| - PCCB |
| - XRN1 |
| - KAT2B |
| - PDCD10 |
| - PFKFB4 |
| - ECT2 |
| - C3orf14 |
| - CBLB |
| - IFT57 |
| - GNB4 |
| - GBE1 |
| - FRMD4B |
| - CISH |
| - RRP9 |
| - SSR3 |
| - FOXP1 |
| - EIF4G1 |
| - IL1A |
| - PIKFYVE |
| - NCL |
| - ACTR1B |
| - CENPA |
| - CYTIP |
| - ITGA4 |
| - PPM1G |
| - IFIH1 |
| - WDR75 |
| - STAT1 |
| - CCT4 |
| - GNLY |
| - ST3GAL5 |
| - HSPE1 |
| - KDM3A |
| - IL18R1 |
| - UXS1 |
| - ABCB6 |
| - ID2 |
| - ODC1 |
| - CEBPZ |
| - DARS1 |
| - SLC1A4 |
| - SOS1 |
| - WIPF1 |
| - PNO1 |
| - AAK1 |
| - EPAS1 |
| - MSH6 |
| - FARSB |
| - DHCR24 |
| - ICMT |
| - WDR77 |
| - RAP1A |
| - RNF19B |
| - SFPQ |
| - SRM |
| - C1orf21 |
| - IVNS1ABP |
| - MIIP |
| - PLA2G4A |
| - GADD45A |
| - UCHL5 |
| - CTH |
| - CRYZ |
| - ZBTB17 |
| - CD58 |
| - CD2 |
| - KIF21B |
| - LGALS8 |
| - SLAMF1 |
| - CD48 |
| - SDHB |
| - KDM5B |
| - UAP1 |
| - CTBS |
| - GBP3 |
| - GBP1 |
| - ECE1 |
| - HMGCL |
| - SLC2A1 |
| - EBNA1BP2 |
| - CDC20 |
| - ATP6V0B |
| - PRDX1 |
| - VAMP4 |
| - DPH5 |
| - FASLG |
| - STMN1 |
| - NEK2 |
| - CENPF |
| - ESYT2 |
| - CTSD |
| - KIF14 |
| - FASTKD2 |
| - NRP2 |
| - IRAG2 |
| - HMGN3 |
| - TNFAIP3 |
| - MYB |
| - SGK1 |
| - CCNI |
| - CCND2 |
| - ELL2 |
| - ITGB1BP1 |
| - HEATR1 |
| - CTNNAL1 |
| - SET |
| - NEK6 |
| - NR4A3 |
| - KDSR |
| - IFI27L2 |
| - SLIRP |
| - YPEL5 |
| - FAM98A |
| - IFIT3 |
| - IFIT2 |
| - MXI1 |
| - HELLS |
| - DENND10 |
| - GOT1 |
| - MTHFD1L |
| - ACAT2 |
| - TCP1 |
| - NUDCD1 |
| - MASTL |
| - DNAJC15 |
| - UFM1 |
| - ELF1 |
| - HSPH1 |
| - EXOSC8 |
| - EGR1 |
| - SERP1 |
| - SOCS2 |
| - WASHC3 |
| - DUSP4 |
| - TNFRSF10B |
| - PTK2B |
| - TNFRSF8 |
| - RDH10 |
| - TRIM25 |
| - SCPEP1 |
| - SLC35B1 |
| - CD80 |
| - CCR2 |
| - TNFSF10 |
| - GPSM2 |
| - CXCR4 |
| - GTF3A |
| - ANXA11 |
| - HYCC1 |
| - CALD1 |
| - SRGN |
| - CISD1 |
| - EGR2 |
| - P4HA1 |
| - ZWINT |
| - CIT |
| - DDX54 |
| - CDKN2C |
| - PRDX4 |
| - DDX39A |
| - ADGRE5 |
| - NLN |
| - OPTN |
| - NR4A1 |
| - PDE1B |
| - TUBA1B |
| - HJURP |
| - AMD1 |
| - NDUFAF4 |
| - NMI |
| - BATF3 |
| - G0S2 |
| - RAB38 |
| - AGO2 |
| - CKS2 |
| - DNPEP |
| - SDC4 |
| - NCOA3 |
| - PLCG1 |
| - CSE1L |
| - PTGIS |
| - IL9R |
| - STAMBP |
| - RRP36 |
| - SNRPC |
| - SERPINB6 |
| - XPO5 |
| - H1-3 |
| - H1-1 |
| - CDKN1A |
| - GLO1 |
| - RIOK1 |
| - NRN1 |
| - EEF1E1 |
| - RUNX2 |
| - LRRFIP1 |
| - AHNAK |
| - MT2A |
| - GOT2 |
| - TM9SF2 |
| - SEPTIN6 |
| - PTGER2 |
| - HS3ST3B1 |
| - MBOAT7 |
| - PPDPF |
| - INSIG2 |
| - POLR1B |
| - PSD4 |
| - CD70 |
| - TNFSF14 |
| - SNRPD2 |
| - VASP |
| - PSMF1 |
| - DSTN |
| - NCLN |
| - ERGIC3 |
| - PLAGL2 |
| - KDM5C |
| - PSMB2 |
| - IGFLR1 |
| - CCR7 |
| - PRMT1 |
| - TRAP1 |
| - IFI6 |
| - EMG1 |
| - DLGAP5 |
| - ZBTB1 |
| - EVI2A |
| - CANX |
| - HIVEP3 |
| - HELB |
| - IL22 |
| - KLF2 |
| - KDM4B |
| - TUBA4A |
| - SRD5A3 |
| - PAICS |
| - SDF2L1 |
| - ATF4 |
| - LIF |
| - DNAJB9 |
| - MYO1B |
| - MTX2 |
| - TWSG1 |
| - EIF2AK4 |
| - KNSTRN |
| - DUT |
| - CHAC1 |
| - CLN6 |
| - PALLD |
| - DCTD |
| - CD68 |
| - TXNDC17 |
| - SLC44A2 |
| - CDKN2D |
| - EGLN3 |
| - MIS18BP1 |
| - REEP5 |
| - SEC14L1 |
| - ARHGEF6 |
| - CRACR2A |
| - SAT1 |
| - TOMM40 |
| - BST2 |
| - LSM7 |
| - SNX9 |
| - AFDN |
| - ARPC1B |
| - JUND |
| - LSP1 |
| - ADRM1 |
| - EIF2S3 |
| - ZC3H4 |
| - GMFG |
| - SESN2 |
| - PPAN |
| - DKC1 |
| - MPP1 |
| - NOL11 |
| - HABP4 |
| - RBM39 |
| - ACSS2 |
| - EMC8 |
| - GINS2 |
| - SH3BGRL |
| - PRR7 |
| - NFATC1 |
| - ABCB7 |
| - RFTN1 |
| - SLC6A6 |
| - KIF3A |
| - MGAT1 |
| - TUBG1 |
| - PSME3 |
| - NDFIP1 |
| - NINJ1 |
| - TOP2A |
| - RARA |
| - PDHA1 |
| - SELENOS |
| - CHSY1 |
| - LGALS3 |
| - PPARG |
| - TRIM22 |
| - IMMT |
| - SCLY |
| - XAF1 |
| - FLOT2 |
| - NIP7 |
| - PCNA |
| - SERINC3 |
| - PATJ |
| - POMP |
| - ALOX5AP |
| - MYH10 |
| - EPSTI1 |
| - CNDP2 |
| - WDR74 |
| - PLAAT4 |
| - CEP20 |
| - GIMAP4 |
| - BTG1 |
| - KRAS |
| - LARS1 |
| - CCDC59 |
| - AMPD3 |
| - MICAL2 |
| - RRAS2 |
| - TTC9 |
| - EIF2S1 |
| - CCNB1 |
| - CAMK1 |
| - BHLHE40 |
| - GSTM3 |
| - FKBP11 |
| - SLC38A2 |
| - RSAD2 |
| - CMPK2 |
| - IAH1 |
| - TIMM17A |
| - NARS1 |
| - RBM17 |
| - IL2RA |
| - EMP1 |
| - CDCA8 |
| - TPGS2 |
| - SLC43A3 |
| - TIMM10 |
| - FADS2 |
| - CARS2 |
| - ETS1 |
| - NREP |
| - WDR36 |
| - OSTF1 |
| - ANXA1 |
| - CEMIP2 |
| - PSAT1 |
| - ADAM19 |
| - HAVCR2 |
| - OASL |
| - P2RX4 |
| - BICDL1 |
| - TMEM243 |
| - HILPDA |
| - TES |
| - MDFIC |
| - MTO1 |
| - PRR5L |
| - CDK4 |
| - TROAP |
| - LTV1 |
| - AHI1 |
| - MICAL1 |
| - STX11 |
| - MDM2 |
| - KLHL36 |
| - EGLN1 |
| - NTPCR |
| - GLUL |
| - DHX9 |
| - NIBAN1 |
| - SP110 |
| - ITM2C |
| - DNAJB2 |
| - ISCU |
| - PWP1 |
| - SLC41A2 |
| - CKAP2 |
| - BORA |
| - RCBTB2 |
| - AOAH |
| - BZW2 |
| - TBRG4 |
| - DBNL |
| - MYO1G |
| - TM6SF1 |
| - CALCOCO2 |
| - ACTL6A |
| - TANK |
| - EPRS1 |
| - IL10 |
| - BIN1 |
| - IMP4 |
| - GYPC |
| - STAM |
| - NIBAN2 |
| - ARPC5L |
| - ENPP2 |
| - DSCC1 |
| - MYC |
| - SIT1 |
| - DENND4C |
| - PPIL1 |
| - PIM1 |
| - IRF4 |
| - TCF19 |
| - IER3 |
| - NUMA1 |
| - SYTL2 |
| - TGS1 |
| - SDCBP |
| - DDX60 |
| - SORL1 |
| - DCUN1D5 |
| - SQOR |
| - NUSAP1 |
| - KIF23 |
| - RSL24D1 |
| - GCHFR |
| - RABGGTB |
| - IFI44L |
| - IFI44 |
| - ADCY3 |
| - PNPT1 |
| - DYNC2LI1 |
| - CYP1B1 |
| - ACTR2 |
| - LRPPRC |
| - MYOF |
| - STAMBPL1 |
| - KIF11 |
| - DUSP5 |
| - CALHM2 |
| - ARL3 |
| - CEP55 |
| - KIF20B |
| - ENTPD1 |
| - ATIC |
| - STAT4 |
| - METTL5 |
| - WDR12 |
| - COX17 |
| - PARP9 |
| - PPCDC |
| - SEMA7A |
| - HERC3 |
| - HERC6 |
| - HERC5 |
| - SEC31A |
| - GPAT3 |
| - IL21 |
| - SEPTIN11 |
| - CCNG2 |
| - CNOT6L |
| - PPA2 |
| - CENPE |
| - LEF1 |
| - PPP3CA |
| - RGS3 |
| - PARVG |
| - ETV6 |
| - KIF21A |
| - CLSTN3 |
| - CD27 |
| - PHLDA1 |
| - DUSP6 |
| - SNRPF |
| - NEDD1 |
| - NUP58 |
| - SLC7A1 |
| - NABP2 |
| - ITGB7 |
| - LPAR6 |
| - ESD |
| - GPR65 |
| - WARS1 |
| - NIPA2 |
| - PSTPIP1 |
| - ETFA |
| - BCL2A1 |
| - DNAJA4 |
| - HAPLN3 |
| - MCTP2 |
| - FURIN |
| - ITGAX |
| - CDR2 |
| - MAP1LC3B |
| - MEAK7 |
| - IRF8 |
| - KSR1 |
| - TOB1 |
| - SKAP1 |
| - AFG3L2 |
| - GALNT1 |
| - ARRB2 |
| - PIK3R5 |
| - TP53 |
| - ARHGDIA |
| - SLC16A3 |
| - EIF4A3 |
| - RNF157 |
| - WDR45B |
| - TNFRSF11A |
| - PMAIP1 |
| - NT5C3B |
| - SAMD1 |
| - SLC39A3 |
| - ZIM3 |
| - DUS3L |
| - IFITM3 |
| - IFNAR1 |
| - SOD1 |
| - APP |
| - URB1 |
| - EMP3 |
| - GEMIN7 |
| - RNPEPL1 |
| - MYO1F |
| - CARM1 |
| - PSMB6 |
| - RERE |
| - EFHD2 |
| - SH3BGRL3 |
| - ZNF593 |
| - WDTC1 |
| - SERBP1 |
| - PRKACB |
| - KIF2C |
| - LMO4 |
| - PSMA5 |
| - CD53 |
| - CREG1 |
| - UCK2 |
| - MGST3 |
| - NUF2 |
| - PFDN2 |
| - RGS16 |
| - MCL1 |
| - DUSP10 |
| - JTB |
| - RAB13 |
| - HAX1 |
| - ILF2 |
| - SCCPDH |
| - LYST |
| - SNAP47 |
| - SRP9 |
| - DEGS1 |
| - PYCR2 |
| - LBR |
| - PTPN7 |
| - RHOB |
| - GALM |
| - ASXL2 |
| - RALB |
| - SLC20A1 |
| - CDCA7 |
| - HSPD1 |
| - OSBPL10 |
| - CSRNP1 |
| - IQSEC1 |
| - ARL6IP5 |
| - NFKBIZ |
| - SRPRB |
| - MANF |
| - EAF2 |
| - LYAR |
| - ENOPH1 |
| - CAMK2D |
| - TIFA |
| - CCNA2 |
| - NDUFS6 |
| - GZMA |
| - PIK3R1 |
| - TNFAIP8 |
| - ATG12 |
| - IL9 |
| - TIMD4 |
| - TNIP1 |
| - N4BP3 |
| - NHP2 |
| - PNRC1 |
| - ABRACL |
| - CCT6A |
| - PSPH |
| - SH3KBP1 |
| - KDM6A |
| - GPR174 |
| - NONO |
| - EBP |
| - IL2RG |
| - PRPS1 |
| - DOK2 |
| - MTDH |
| - POLR2K |
| - VLDLR |
| - SIGMAR1 |
| - STOM |
| - SURF4 |
| - PTGES2 |
| - RPP30 |
| - ADD3 |
| - MKI67 |
| - PPRC1 |
| - SSRP1 |
| - PTPRJ |
| - ZC3H12C |
| - ATM |
| - HYOU1 |
| - FADS1 |
| - INCENP |
| - COMMD7 |
| - ARID5B |
| - PDCD4 |
| - CD226 |
| - PRSS23 |
| - CCT5 |
| - DLAT |
| - TIMM8B |
| - SEC24D |
| - RILPL2 |
| - ITPR1 |
| - SLC7A11 |
| - NGLY1 |
| - ANK3 |
| - EIF4E |
| - TEX30 |
| - CDC123 |
| - SCLT1 |
| - QDPR |
| - ADAM8 |
| - RNF144A |
| - CENPU |
| - ACSL1 |
| - GUF1 |
| - SETBP1 |
| - PSTPIP2 |
| - PDK1 |
| - PDE3B |
| - JMY |
| - NMT2 |
| - USP12 |
| - CCDC50 |
| - CAMK4 |
| - ZFP36L2 |
| - PELO |
| - PRDM8 |
| - UTRN |
| - PTPRK |
| - SRP19 |
| - CENPH |
| - CARHSP1 |
| - BCL2L11 |
| - CAST |
| - CD96 |
| - RMND5A |
| - RPIA |
| - CFDP1 |
| - CMIP |
| - CEBPG |
| - MCOLN2 |
| - DGKE |
| - MSI2 |
| - NUS1 |
| - ANKH |
| - UBASH3B |
| - GPR15 |
| - PITPNC1 |
| - PRKCA |
| - TNIK |
| - GBP5 |
| - BUB3 |
| - ATP5MC3 |
| - LY96 |
| - DPH3 |
| - SKA1 |
| - KLF10 |
| - GTF3C6 |
| - TTC39B |
| - HSPA13 |
| - SAMSN1 |
| - C16orf87 |
| - RHOC |
| - SLC16A1 |
| - NIFK |
| - LARP1 |
| - CNOT8 |
| - ELMO1 |
| - SLA |
| - CARNMT1 |
| - BATF |
| - DCK |
| - DRAM2 |
| - CCT8 |
| - TIAM1 |
| - HK1 |
| - CD109 |
| - UBE2L6 |
| - ZFAND3 |
| - NPTN |
| - RAB11FIP1 |
| - ATAD2 |
| - FBXO32 |
| - MALSU1 |
| - EIF4A2 |
| - LRP8 |
| - CCNB2 |
| - MYO1E |
| - TSC22D3 |
| - MX1 |
| - PALM2AKAP2 |
| - DGKI |
| - PSMG3 |
| - SLC37A3 |
| - BABAM2 |
| - DUSP2 |
| - EIF5B |
| - B4GALT5 |
| - COPG2 |
| - GPAT4 |
| - NBL1 |
| - F11R |
| - CDC42SE2 |
| - CFAP298 |
| - IFNAR2 |
| - GART |
| - RCAN1 |
| - RUNX1 |
| - CBR1 |
| - CBR3 |
| - PTMS |
| - BTG2 |
| - HK2 |
| - NAE1 |
| - ADGRG5 |
| - PTGIR |
| - CALM3 |
| - DFFA |
| - MIX23 |
| - TMPRSS3 |
| - RRP1B |
| - CSTB |
| - RRP1 |
| - ITGB2 |
| - ST6GALNAC6 |
| - JAML |
| - LMNA |
| - GPATCH4 |
| - IER2 |
| - LY6E |
| - SQSTM1 |
| - FDXR |
| - SRSF2 |
| - ITGA5 |
| - LARP4 |
| - SPC24 |
| - SENP3 |
| - FGF11 |
| - EIF4A1 |
| - POLR3K |
| - SNRNP25 |
| - CCNF |
| - BEND5 |
| - AK4 |
| - JAK1 |
| - DHRS3 |
| - LAPTM5 |
| - GBP2 |
| - PEA15 |
| - ATF3 |
| - DENND2D |
| - IER5 |
| - FCMR |
| - CAPN2 |
| - REL |
| - H3-3A |
| - CDC42EP3 |
| - S100A11 |
| - ARHGAP25 |
| - ANTXR2 |
| - COL6A3 |
| - KBTBD8 |
| - EIF4E3 |
| - CCT3 |
| - SSR2 |
| - TGFBR2 |
| - ANKZF1 |
| - TRAT1 |
| - SGO2 |
| - PYHIN1 |
| - IFI16 |
| - AIM2 |
| - CTLA4 |
| - ICOS |
| - RYBP |
| - PSMD6 |
| - RBM47 |
| - U2SURP |
| - WDR43 |
| - DTX3L |
| - POLR2H |
| - GNL3 |
| - SLBP |
| - RNF168 |
| - H2AZ1 |
| - CDC25A |
| - SPRY1 |
| - C4orf3 |
| - HMGB2 |
| - SAP30 |
| - ANXA5 |
| - HPGD |
| - NAA15 |
| - ABCE1 |
| - LSM6 |
| - MOCS2 |
| - SLC25A46 |
| - STARD4 |
| - WDR41 |
| - CASP3 |
| - IL3 |
| - CSF2 |
| - SEPTIN8 |
| - CGAS |
| - CITED2 |
| - SAMD3 |
| - STK17A |
| - PTTG1 |
| - CDCA7L |
| - SYTL3 |
| - FABP5 |
| - TAGAP |
| - CTSB |
| - ADCY1 |
| - RAD21 |
| - SLC25A32 |
| - TP53INP1 |
| - NFIL3 |
| - FXN |
| - TMEM71 |
| - HNRNPK |
| - DYNLT3 |
| - MID1IP1 |
| - CARD19 |
| - STOML2 |
| - GJB2 |
| - ARF6 |
| - ENTR1 |
| - ZMYND19 |
| - DDX21 |
| - BMS1 |
| - NSMF |
| - PSMC3 |
| - TC2N |
| - CPSF2 |
| - IFI27 |
| - ARL5B |
| - SMCO4 |
| - TAF1D |
| - GPT2 |
| - RAB8B |
| - NOLC1 |
| - CCT2 |
| - PCBD1 |
| - TPP1 |
| - IDH3A |
| - XRRA1 |
| - PRKCB |
| - HDGFL3 |
| - SEC11C |
| - CENPV |
| - HSP90B1 |
| - BEX3 |
| - B2M |
| - SLFN5 |
| - PPIB |
| - FAM111A |
| - PLK1 |
| - STX3 |
| - C15orf48 |
| - SMAD3 |
| - MAPRE2 |
| - MARS1 |
| - C15orf39 |
| - FBXO22 |
| - TBC1D2B |
| - SNX20 |
| - CD3D |
| - ACAA2 |
| - RRM1 |
| - GNG8 |
| - MVD |
| - CDT1 |
| - TUBA1C |
| - RAB4B |
| - NFKBID |
| - LENG8 |
| - SPINT2 |
| - TSR1 |
| - ANGPTL4 |
| - CD320 |
| - PRDX2 |
| - CD300A |
| - TK1 |
| - MLST8 |
| - NLRC3 |
| - FTH1 |
| - SLC3A2 |
| - ATG16L2 |
| - LTBP3 |
| - RNF187 |
| - DDIT4 |
| - RBPJ |
| - TTC39C |
| - NT5DC2 |
| - COA6 |
| - BMI1 |
| - PXK |
| - H1-4 |
| - TAP1 |
| - RHOH |
| - FEN1 |
| - STAT3 |
| - IL7R |
| - GFM1 |
| - TNIP2 |
| - VAMP5 |
| - MAT2A |
| - MAP2K1 |
| - ASMTL |
| - NSMCE1 |
| - IL13 |
| - LMAN2 |
| - PRELID1 |
| - CXCL10 |
| - NMD3 |
| - B3GALNT1 |
| - CXCL8 |
| - CD52 |
| - PLEKHA2 |
| - CLIC4 |
| - GPR183 |
| - ZEB2 |
| - CKAP2L |
| - BUB1 |
| - FASN |
| - CNBP |
| - DUS1L |
| - SF3B5 |
| - IFFO2 |
| - TMEM154 |
| - YWHAG |
| - ZNF282 |
| - CRTAP |
| - ELP5 |
| - GABARAP |
| - CDK1 |
| - B3GNT2 |
| - FOS |
| - MGMT |
| - MZB1 |
| - PA2G4 |
| - PFKFB3 |
| - ARL6IP1 |
| - SERPINB9 |
| - EMB |
| - HSPA4 |
| - GTSF1 |
| - POLH |
| - RIOX2 |
| - TRIAP1 |
| - MTSS1 |
| - GSTA4 |
| - S1PR1 |
| - PKIA |
| - TMEM126A |
| - NETO2 |
| - JUNB |
| - NPTX1 |
| - FAM98B |
| - CHST11 |
| - CHD7 |
| - HOPX |
| - PPID |
| - PTGER4 |
| - BCL2L1 |
| - PIK3CD |
| - SLC25A33 |
| - ATF7IP |
| - BCL2 |
| - CTPS1 |
| - MLLT3 |
| - RRM2 |
| - RNASEH1 |
| - PRNP |
| - ZNF217 |
| - MAL |
| - ORMDL3 |
| - MOB3A |
| - KRCC1 |
| - CYCS |
| - SNTB1 |
| - ISG20 |
| - CXCR6 |
| - CEBPB |
| - COPRS |
| - BPGM |
| - RCAN2 |
| - IL16 |
| - CTSW |
| - RASGRP1 |
| - KLHL6 |
| - TMEM134 |
| - ZMAT3 |
| - THEMIS |
| - SLFN11 |
| - RAB37 |
| - DHCR7 |
| - GRK2 |
| - HPSE |
| - LRRN3 |
| - NOC3L |
| - PARP14 |
| - CKS1B |
| - ABCD2 |
| - GLRX |
| - NAA20 |
| - MICOS10 |
| - EHBP1L1 |
| - VEGFB |
| - GMPPB |
| - CHD2 |
| - PSMD1 |
| - HEG1 |
| - AGFG1 |
| - STAT5B |
| - CD7 |
| - RNF213 |
| - GPR160 |
| - GOLIM4 |
| - ATP2A2 |
| - AKIRIN1 |
| - RESF1 |
| - FAM241A |
| - ODAPH |
| - GPR171 |
| - DDIT3 |
| - CKAP5 |
| - SMAD2 |
| - TBC1D10C |
| - UCP2 |
| - CCDC85B |
| - MTLN |
| - TOMM5 |
| - LINC02694 |
| - RUVBL1 |
| - YES1 |
| - TMEM39A |
| - SMIM19 |
| - SYNE3 |
| - B3GNT5 |
| - MEX3C |
| - METRNL |
| - WSB2 |
| - TYMS |
| - MTX3 |
| - FAM210A |
| - RIMKLA |
| - PUS1 |
| - SAMD9L |
| - ZBED2 |
| - ATOX1 |
| - JUN |
| - CSTF2T |
| - AGTRAP |
| - AP3S1 |
| - IMPDH2 |
| - NDUFV2 |
| - ZC3H12D |
| - PLEC |
| - CD28 |
| - MAF |
| - ERN1 |
| - GPR35 |
| - GRINA |
| - MPI |
| - TUFM |
| - AURKB |
| - RRS1 |
| - CYC1 |
| - PER1 |
| - FARSA |
| - GIMAP7 |
| - CALR |
| - GADD45GIP1 |
| - EGR3 |
| - PCED1B |
| - APOBEC3B |
| - CCR8 |
| - PUF60 |
| - DCTPP1 |
| - RCC1 |
| - FUT7 |
| - MB21D2 |
| - PRF1 |
| - SHISA2 |
| - AEN |
| - SIAH2 |
| - RELL1 |
| - TIGIT |
| - COA4 |
| - RTKN2 |
| - IDH2 |
| - ERCC6L2 |
| - P2RY8 |
| - PLCXD1 |
| - NPLOC4 |
| - TSHZ2 |
| - KPNA2 |
| - FES |
| - GLRX5 |
| - MXRA7 |
| - SATB1 |
| - ANXA2 |
| - LCK |
| - C11orf54 |
| - PYCR1 |
| - NAA38 |
| - RUVBL2 |
| - PTTG1IP |
| - DAZAP2 |
| - BCOR |
| - PMCH |
| - SF3A3 |
| - TENT5C |
| - PSMG1 |
| - ALYREF |
| - RFLNB |
| - UPP1 |
| - CBX6 |
| - TBL3 |
| - SLC35F3 |
| - CCR4 |
| - UTY |
| - SH2D1A |
| - PRKX |
| - ACTG1 |
| - UBE2F |
| - PGP |
| - IRAK1 |
| - CMSS1 |
| - H1-5 |
| - CSF1 |
| - SOCS3 |
| - XPOT |
| - STING1 |
| - PDE4B |
| - NELL2 |
| - SEPTIN9 |
| - CDCA2 |
| - H1-10 |
| - FMNL1 |
| - USP18 |
| - SIGIRR |
| - IFITM2 |
| - PRMT3 |
| - IL3RA |
| - SOCS1 |
| - ATP6V0A2 |
| - SP140L |
| - GPRIN3 |
| - IKZF1 |
| - EVI2B |
| - ZNF267 |
| - RASA3 |
| - CYP2R1 |
| - POLR1D |
| - ZNRF1 |
| - GPAT2 |
| - RXRA |
| - ANKRD37 |
| - KPNA4 |
| - GNG2 |
| - BTN3A2 |
| - INSIG1 |
| - ARAP1 |
| - BCR |
| - CXCR3 |
| - TNFRSF4 |
| - TNFRSF18 |
| - FNBP1 |
| - ISG15 |
| - SEMA4D |
| - H1-2 |
| - EIF4EBP1 |
| - ARL4C |
| - TUBB4B |
| - SELL |
| - H2AX |
| - NBR1 |
| - PTAR1 |
| - PARVB |
| - UROS |
| - SMIM15 |
| - CALHM6 |
| - HACD4 |
| - FAM111B |
| - H1-0 |
| - LITAF |
| - MAOA |
| - KIAA0408 |
| - IL1RAP |
| - SPATS2L |
| - S100A4 |
| - TMEM63A |
| - TUBB |
| - IARS1 |
| - GIMAP5 |
| - CD55 |
| - LONP1 |
| - EVL |
| - YRDC |
| - PLXNB2 |
| - TRAPPC4 |
| - HSH2D |
| - ADA |
| - ARID5A |
| - FLNA |
| - FAM3C |
| - FUT11 |
| - H4C3 |
| - LRRC8B |
| - PSMD12 |
| - TBC1D9B |
| - PELI1 |
| - GSTK1 |
| - HNRNPAB |
| - SPN |
| - RPF2 |
| - GZMM |
| - SIPA1L1 |
| - CDC42SE1 |
| - DPP4 |
| - S100A10 |
| - ATAD3A |
| - ERO1A |
| - PLCG2 |
| - S100A6 |
| - ZNF121 |
| - MAK16 |
| - SFI1 |
| - TFDP1 |
| - HSD17B11 |
| - OGA |
| - TXNRD1 |
| - LRBA |
| - CCDC69 |
| - STK39 |
| - EIF1AY |
| - MT-ND6 |
| - MT-CO2 |
| - MT-CYB |
| - F5 |
| - SLC5A3 |
| - RCSD1 |
| - MT-CO1 |
| - PNP |
| - SFT2D1 |
| - CD247 |
| - ARHGAP11A |
| - MT-ND3 |
| - CD3E |
| - OSTC |
| - SFMBT2 |
| - MT-ND4 |
| - CAPZA2 |
| - MT-ATP6 |
| - APRT |
| - CCDC167 |
| - MT-CO3 |
| - PJA2 |
| - INF2 |
| - TMEM273 |
| - PFDN6 |
| - TAP2 |
| - SNHG32 |
| - HSPA1B |
| - VARS1 |
| - AIF1 |
| - CFAP95 |
| - FAM216A |
| - MZT1 |
| - CCNI2 |
| - E2F4 |
| - PDE7A |
| - ADGRG1 |
| - TMSB4X |
| - RNPS1 |
| - JPT2 |
| - TRBC1 |
| - TRBC2 |
| - TRDC |
| - IGHM |
| - MT-ND4L |
| - SFT2D2 |
| - CRIP1 |
| - GIMAP1 |
| - CHUK |
| - ARHGAP19 |
| - ARL2 |
| - STIMATE |
| - VDAC1 |
| - LBH |
| - GPSM3 |
| - LAT |
| - CPNE1 |
| - SMIM30 |
| - FIS1 |
| - SOGA3 |
| - IFRD2 |
| - TOMM6 |
| - GOLGA8B |
| - TSTD1 |
| - IFI30 |
| - CKLF |
| - PAM16 |
| - PPP2R2A |
| - APOL6 |
| - NDUFAF8 |
| - NOL7 |
| - LTA |
| - WDR46 |
| - TRGC2 |
| - LTB |
| - FAM174C |
| - DHFR |
| - TAPBP |
| - TNF |
| - C12orf75 |
| - SMIM27 |
| - KIFC1 |
| - TXNDC5 |
| - NME1 |
| - TNFSF12 |
| - APOBEC3G |
| - ADSL |
| - PSMB9 |
| - PPIL3 |
| - MIF |
| - ARFGAP3 |
| - EIF6 |
| - GNG10 |
| - IL10RB |
| - P2RY11 |
| - APOBEC3C |
| - H2AJ |
| - PGAM5 |
| - BCKDHA |
| - LYN |
| - EID1 |
| - SMIM3 |
| - DENND11 |
| - CNPY2 |
| - C17orf49 |
| - BOP1 |
| - PECAM1 |
| - TIMM23 |
| - TXNIP |
| - CCL5 |
| - KMT2B |
| - SYNRG |
| - CCL4 |
| - H2BC9 |
| - UHRF1 |
| - CCL4L2 |
| - CCL3 |
| - TRAC |
| - ARHGAP11B |
| batch_size: 64 |
| gene_dim: 2001 |
| hvg_dim: 2001 |
| decoder_cfg: |
| latent_dim: 2001 |
| gene_dim: 2001 |
| hidden_dims: |
| - 1024 |
| - 1024 |
| - 512 |
| dropout: 0.1 |
| residual_decoder: false |
| cell_set_len: 64 |
| blur: 0.05 |
| loss: energy |
| confidence_token: true |
| n_encoder_layers: 1 |
| n_decoder_layers: 1 |
| softplus: true |
| freeze_pert_backbone: false |
| transformer_decoder: false |
| finetune_vci_decoder: false |
| residual_decoder: false |
| batch_encoder: true |
| use_batch_token: false |
| mask_attn: false |
| n_refine_rounds: 6 |
| halt_tau: 0.05 |
| halt_alpha: 0.5 |
| halt_beta: 0.1 |
| halt_gamma: 0.1 |
| halt_warmup_steps: 2000 |
| halt_magnitude_free: true |
| confidence_weight: 0.01 |
| confidence_target_scale: 10.0 |
| use_effect_gating_token: false |
| init_from: null |
| mmd_num_chunks: 1 |
| randomize_mmd_chunks: false |
| llm_name: null |
| lora: |
| enable: false |
| r: 16 |
| alpha: 32 |
| dropout: 0.05 |
| bias: none |
| target: auto |
| adapt_mlp: false |
| task_type: FEATURE_EXTRACTION |
| merge_on_eval: false |
| wandb_track: true |
| weight_decay: 0.0005 |
| max_steps: 15000 |
| train_seed: 42 |
| val_freq: 1000 |
| ckpt_every_n_steps: 1000 |
| gradient_clip_val: 10 |
| gradient_accumulation_steps: 1 |
| devices: 1 |
| strategy: auto |
| use_mfu: false |
| mfu_kwargs: |
| available_flops: 60000000000000.0 |
| use_backward: true |
| logging_interval: 10 |
| window_size: 2 |
| cumulative_flops_use_backward: true |
| basal_mapping_strategy: random |
| predict_residual: true |
| distributional_loss: energy |
| transformer_backbone_key: llama |
| transformer_backbone_kwargs: |
| bidirectional_attention: true |
| max_position_embeddings: 64 |
| hidden_size: 336 |
| intermediate_size: 3072 |
| num_hidden_layers: 8 |
| num_attention_heads: 12 |
| num_key_value_heads: 12 |
| head_dim: 28 |
| use_cache: false |
| attention_dropout: 0.0 |
| hidden_dropout: 0.0 |
| layer_norm_eps: 1.0e-06 |
| pad_token_id: 0 |
| bos_token_id: 1 |
| eos_token_id: 2 |
| tie_word_embeddings: false |
| rotary_dim: 0 |
| use_rotary_embeddings: false |
|
|
