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