Initial model release

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README.md +9 -0
checkpoints/ccrcc.ckpt +3 -0
checkpoints/her2st.ckpt +3 -0
checkpoints/kidney.ckpt +3 -0
checkpoints/mouse_brain.ckpt +3 -0
checkpoints/prad.ckpt +3 -0
genes/ccrcc.txt +200 -0
genes/her2st.txt +200 -0
genes/kidney.txt +200 -0
genes/mouse_brain.txt +200 -0
genes/prad.txt +200 -0
models.json +25 -0

README.md ADDED Viewed

	@@ -0,0 +1,9 @@

+---
+library_name: pytorch
+tags:
+- spatial-transcriptomics
+---
+# GenAR
+Pretrained checkpoints for [GenAR](https://github.com/oyjr/genar).

checkpoints/ccrcc.ckpt ADDED Viewed

	@@ -0,0 +1,3 @@

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+size 179177335

checkpoints/her2st.ckpt ADDED Viewed

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+size 179177527

checkpoints/kidney.ckpt ADDED Viewed

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+version https://git-lfs.github.com/spec/v1
+oid sha256:dde807c3886beaa272d8422b4c991da9bbc7b381cf41e24fc5d6ddf6fd6ba09c
+size 173027319

checkpoints/mouse_brain.ckpt ADDED Viewed

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+version https://git-lfs.github.com/spec/v1
+oid sha256:8bd2a08980be9c8f873713786267e166e0e4614eb1434e90ac8514901a334557
+size 179177207

checkpoints/prad.ckpt ADDED Viewed

	@@ -0,0 +1,3 @@

+version https://git-lfs.github.com/spec/v1
+oid sha256:e840e075707f5bd656902870ae540386367953329e5bb76c599a1c92204f1b88
+size 179177335

genes/ccrcc.txt ADDED Viewed

	@@ -0,0 +1,200 @@

+APOC1
+APOE
+CTSB
+CTSD
+NPC2
+SAT1
+B2M
+C1QA
+CD74
+CST3
+HLA-A
+HLA-DPA1
+HLA-DPB1
+HLA-DRA
+HLA-DRB1
+HLA-F
+SERPING1
+TXNIP
+ATP1B1
+CLU
+ENPP3
+FTH1
+NUPR1
+PDK4
+PRR13
+A2M
+ADIRF
+DUSP1
+EIF1
+FXYD2
+GPX3
+RGS5
+RHOB
+VWF
+ANPEP
+APOL1
+APP
+ATP1A1
+ATP5F1B
+ATP5MC2
+BSG
+CANX
+CD63
+COL18A1
+COX6C
+CRYAB
+CYB5R3
+DDX17
+EEF1G
+HINT1
+HNRNPA2B1
+IGFBP3
+MIF
+NME2
+PCBP2
+PDZK1IP1
+PFDN5
+PTTG1IP
+RNASET2
+TMBIM6
+TOMM7
+TSC22D3
+UQCRQ
+IGHA1
+IGHG1
+IGHG2
+IGHG3
+IGHG4
+IGHM
+IGKC
+IGLC1
+JCHAIN
+ACTA2
+AEBP1
+BGN
+CALD1
+CCDC91
+CCN2
+COL4A1
+COL4A2
+DCN
+DEPP1
+FOS
+HSPG2
+HTRA1
+IGFBP5
+IGFBP7
+MGP
+MMP7
+MYL9
+PLTP
+SPARC
+SRRM2
+TAGLN
+TGFBI
+TIMP3
+TPM1
+TPM2
+BIRC3
+C1S
+C3
+CA12
+CEBPD
+CP
+FGB
+FKBP5
+LY6E
+PGF
+SCD
+SERPINA1
+SPP1
+ANGPTL4
+CD24
+CD81
+CYB5A
+DDIT4
+HPCAL1
+HSP90B1
+IFI27
+IGFBP4
+NDRG1
+NDUFA4L2
+P4HB
+PFKP
+PLIN2
+PTMA
+RARRES2
+SOD2
+SSR4
+TUBA1B
+VEGFA
+C1R
+CD99
+HSPA5
+IFITM2
+LGALS3BP
+MYH9
+PLOD2
+TAGLN2
+TGM2
+TIMP1
+C1QB
+C1QC
+CD68
+CTSZ
+FTL
+GLUL
+IFI30
+LAPTM5
+LYZ
+TMSB4X
+TYROBP
+ANXA2
+BST2
+C19orf33
+CD44
+CPE
+CSTB
+ITGA3
+PARK7
+PPDPF
+PRDX6
+S100A11
+S100A6
+VIM
+ACTB
+ARF1
+ARPC1B
+ARPC2
+ASPH
+CCNI
+CHCHD2
+COL6A1
+COL6A2
+EIF4G2
+EIF4H
+FLNA
+FN1
+GABARAP
+GSTP1
+HIST1H4C
+HNRNPA3
+HSP90AA1
+HSPA8
+HSPD1
+IL32
+ITGB1
+KRT8
+LGALS1
+PDIA6
+PGAM1
+PLEC
+PTMS
+SERPINE1
+SQSTM1
+UBC
+COL1A1
+COL1A2
+COL3A1
+COL6A3

genes/her2st.txt ADDED Viewed

	@@ -0,0 +1,200 @@

+EDF1
+GPX4
+GUK1
+KRT19
+MUC1
+P4HB
+TMSB10
+ACTN4
+AES
+BSG
+CLDN4
+H2AFJ
+MDK
+MIDN
+PSMD3
+PTBP1
+PTMS
+SEC61A1
+SERF2
+SNRPB
+SYNGR2
+ATP5B
+ATP5E
+CALR
+CD63
+CHCHD2
+COPE
+COPS9
+CTTN
+FTL
+GNAS
+LMAN2
+PPDPF
+PSMB4
+PTMA
+RACK1
+SEPW1
+STARD10
+TMED9
+ATP6V0B
+CALM2
+CD24
+DDX5
+FASN
+HNRNPA2B1
+HSP90AB1
+HSP90B1
+INTS1
+KRT81
+LAPTM4A
+LASP1
+MGP
+MLLT6
+MMACHC
+PIP4K2B
+PPP1R1B
+PRDX1
+PSMB3
+TFF3
+ACTB
+ACTG1
+CFL1
+COX4I1
+COX5B
+COX6C
+DBI
+DDIT4
+HSPA8
+IDH2
+KRT18
+LGALS3
+MYL6
+MZT2B
+NACA
+PEBP1
+PFDN5
+SLC2A4RG
+SSR2
+COX6B1
+ENO1
+LLGL2
+SLC9A3R1
+BGN
+C3
+CHPF
+COL6A2
+COMP
+FLNA
+LGALS1
+MYL9
+NBL1
+A2M
+APOE
+B2M
+CD74
+CST3
+CTSB
+HLA-DRA
+LAPTM5
+PLD3
+SH3BGRL3
+AP000769.1
+ARHGDIA
+BEST1
+CALML5
+CLDN3
+EEF1D
+FAU
+FTH1
+GRINA
+HSPB1
+IGFBP2
+LMNA
+MAPKAPK2
+NUCKS1
+PFKL
+PPP1CA
+S100A14
+SCAND1
+SDC1
+AEBP1
+COL18A1
+COL1A1
+COL1A2
+COL3A1
+FN1
+LUM
+MMP14
+POSTN
+SPARC
+TAGLN
+C1QA
+CTSD
+CYBA
+DHCR24
+HLA-E
+IFI27
+IGHA1
+IGHG1
+IGHG3
+IGHG4
+IGHM
+IGKC
+IGLC2
+IGLC3
+LGALS3BP
+LY6E
+S100A8
+S100A9
+SSR4
+TAPBP
+APOC1
+BST2
+HLA-A
+HLA-B
+HLA-C
+ISG15
+TIMP1
+FNBP1L
+PTPRF
+SF3B5
+SUPT6H
+CCT3
+COX7C
+CRIP2
+EEF2
+ERBB2
+ERGIC1
+GRB7
+HSP90AA1
+JTB
+KDELR1
+MIEN1
+MUCL1
+ORMDL3
+PCGF2
+PERP
+PGAP3
+PHB
+PRRC2A
+PRSS8
+S100A6
+SCD
+SPDEF
+SPINT2
+STARD3
+TPT1
+ADAM15
+ALDOA
+ATG10
+AZGP1
+C12orf57
+CIB1
+EIF4G1
+ELOVL1
+GAPDH
+KRT7
+NDUFB9
+NUPR1
+TSPO

genes/kidney.txt ADDED Viewed

	@@ -0,0 +1,200 @@

+ACADVL
+ATP5F1D
+ATP5MC3
+ATP5MD
+ATP5ME
+ATP5MF
+ATP5MPL
+BSG
+CHCHD10
+CKB
+COX5B
+COX6B1
+COX6C
+COX7A2
+COX7B
+COX7C
+CYSTM1
+EIF3K
+MAL
+MGST3
+NDUFA1
+NDUFA13
+NDUFA4
+NDUFB2
+NDUFB7
+NDUFB8
+NDUFB9
+PEBP1
+SLC25A3
+SLC25A5
+SLC25A6
+SOD1
+TPI1
+UQCRB
+UQCRFS1
+AQP2
+CA2
+CALB1
+HSD11B2
+NDRG1
+OGDHL
+RTN4
+SPINK1
+ATP1A1
+ATP1B1
+CLCNKB
+COX5A
+DEFB1
+FXYD2
+IDH2
+MUC1
+SERPINA5
+SLC12A3
+CALM2
+CFL1
+FTH1
+GSTP1
+H3F3A
+HINT1
+LDHA
+OAZ1
+OST4
+S100A10
+S100A6
+SRP14
+SSR4
+TMA7
+KNG1
+PPP1R1A
+SLC12A1
+UMOD
+ATP6V0C
+CRYAB
+MALAT1
+PCK1
+PTH1R
+SERPINA1
+SLC5A12
+ALDOB
+ANPEP
+APOE
+AQP1
+ASS1
+CTSB
+CTSH
+CXCL14
+FTL
+GATM
+GPX3
+LAMTOR5
+LRP2
+MIOX
+NAT8
+PDZK1IP1
+PEPD
+SELENOP
+SLC13A3
+SLC3A1
+SUCLG1
+UGT2B7
+IGHA1
+IGHG1
+IGHG3
+IGHG4
+IGKC
+IGLC1
+IGLC2
+IGLC3
+B2M
+C7
+CD74
+EEF1G
+GABARAP
+HLA-A
+HLA-B
+HLA-DRA
+HLA-DRB1
+LAMP1
+LAPTM4A
+NEAT1
+NME2
+PIGR
+TMSB10
+TSPAN1
+ADGRG1
+CD24
+CLU
+S100A2
+SAT1
+SFRP1
+SOD2
+SPP1
+WFDC2
+AEBP1
+COL1A2
+COL3A1
+COL4A2
+LUM
+MMP7
+TIMP1
+TPM1
+ACTB
+ACTG1
+APP
+CANX
+CIRBP
+CST3
+DDX5
+DSTN
+DYNLL1
+EEF1D
+EEF2
+EZR
+HNRNPA1
+HNRNPA2B1
+HSPA8
+HSPB1
+IGFBP7
+ITM2B
+MYL6
+P4HB
+PFN1
+PGK1
+RHOA
+TPT1
+UBA52
+A2M
+ACTA2
+ADIRF
+BGN
+CD151
+CD81
+DCN
+FLNA
+HLA-C
+IGFBP4
+LGALS1
+MGP
+MYL9
+RNASE1
+TAGLN
+TMSB4X
+VIM
+ANXA2
+BCAM
+CRIM1
+DUSP1
+ENG
+EPAS1
+HLA-E
+HTRA1
+IFITM2
+IFITM3
+IGFBP2
+IGFBP5
+PODXL
+PTGDS
+REN
+SPARC
+TIMP3

genes/mouse_brain.txt ADDED Viewed

	@@ -0,0 +1,200 @@

+Arpp19
+Arpp21
+Baiap2
+Hpca
+Malat1
+Pcp4
+Pde1b
+Penk
+Ppp1r1b
+Ppp3ca
+Gm42418
+Lars2
+Lrrc17
+Gnas
+Ndfip1
+Adgrb2
+Camkv
+Chst1
+Cplx2
+Ctxn1
+Fkbp1a
+Gpm6a
+Hpcal4
+Ncdn
+Nisch
+Pja2
+Ptprn
+Selenow
+Snca
+Syn2
+6330403K07Rik
+Gaa
+Gprasp1
+Ly6h
+Maged1
+Meg3
+Nnat
+Pea15a
+Sst
+Ap2s1
+Atp1b1
+Atp2a2
+Atp5g1
+Atp5o
+Atp6v0e2
+Atp6v1e1
+Bex2
+Bsg
+Calm3
+Cfl1
+Ctsd
+Dpysl2
+Dynll1
+Dynll2
+Eno1
+Eno2
+Fkbp8
+Gdi1
+Gnao1
+Gng3
+Gpi1
+Hspa8
+Kif1a
+Mlf2
+Mrfap1
+Myl6
+Nsf
+Ociad1
+Rab3a
+Reep5
+Sez6l2
+Slc22a17
+Snap47
+Snrpn
+Sod1
+Stmn3
+Stmn4
+Syt11
+1110008P14Rik
+Atp1a1
+Atp2b2
+Basp1
+Camk2a
+Camk2n1
+Cck
+Chn1
+Clstn1
+Cplx1
+Dclk1
+Dnm1
+Gabra1
+Nat8l
+Nrgn
+Prkar1b
+Rtn4
+Scn1b
+Snap25
+Stmn1
+Syn1
+Syngr1
+Tmem59l
+Chgb
+Nptxr
+Olfm1
+Slc17a7
+Apoe
+Cst3
+Mt1
+App
+Arf1
+Atp5b
+Atp5e
+Atp6v1f
+Calm2
+Ckb
+Cox5a
+Cox7b
+Cox7c
+Cox8a
+Eif4g2
+Fis1
+Gad1
+Grcc10
+H2afz
+Hint1
+Kif5a
+Mdh2
+Ndufa12
+Ndufa3
+Ndufa4
+Ndufb4
+Ndufb9
+Ndufc1
+Ndufc2
+Oaz1
+Rac1
+Rpl4
+Serf2
+Slc1a2
+Slc25a5
+Sparcl1
+Sub1
+Tmsb10
+Nap1l5
+Eef1a1
+Ftl1
+Naca
+Pfdn5
+Ptma
+Rpl13
+Rpl14
+Rpl18
+Rpl18a
+Rpl19
+Rpl22
+Rpl27
+Rpl32
+Rpl34
+Rpl5
+Rpl6
+Rpl7
+Rps12
+Rps15a
+Rps17
+Rps18
+Rps19
+Rps2
+Rps24
+Rps27a
+Rps3
+Rps4x
+Rps6
+Rps7
+Ndrg2
+Bc1
+Rpl10
+Rpl22l1
+Rpl23a
+Rpl36a
+Rpl37
+Rpl39
+Rpl9
+Rps23
+Apod
+Cd81
+Cnp
+Cryab
+Dbi
+Fth1
+Mbp
+Mobp
+Plp1
+Qdpr
+Scd2
+Sparc
+Atp1a2
+Hba-a1
+Hba-a2
+Hbb-bs
+Ptgds

genes/prad.txt ADDED Viewed

	@@ -0,0 +1,200 @@

+A2M
+CD74
+DUSP1
+FOS
+HLA-B
+HLA-DRA
+LTF
+MALAT1
+MGP
+NR4A1
+PLA2G2A
+TIMP1
+VIM
+IGHA1
+IGKC
+IGLC2
+ATP5IF1
+ATP5F1E
+ATP5MD
+ATP5MF
+ATP5MPL
+COPS9
+COX4I1
+COX6A1
+COX7B
+COX8A
+DDT
+KRT18
+MINOS1
+NDUFB1
+NDUFB11
+NDUFB9
+NDUFC1
+NUPR1
+OST4
+ROMO1
+SEC11C
+SEC61B
+SEC61G
+SELENOP
+SERF2
+SERP1
+TMEM258
+TRPM4
+TSPAN1
+TXN
+UQCR10
+UQCRQ
+COMMD6
+COX6C
+FABP5
+MPC2
+NDUFB4
+SLC25A6
+SNHG19
+SNHG25
+SNHG8
+SPON2
+TFF3
+TMSB4X
+TOMM7
+UBA52
+UQCRB
+UQCRH
+C12orf57
+CALM2
+COX5B
+DSTN
+ELOB
+FAU
+FTL
+H3F3B
+HSPB1
+MZT2B
+NDUFS5
+OAZ1
+PFDN5
+POLR2L
+S100A11
+TMSB10
+UBL5
+H2AFJ
+MIF
+PDLIM5
+CFL1
+CHCHD2
+COX7A2
+FTH1
+GPX4
+HMGN2
+PARK7
+PRDX2
+SKP1
+TSTD1
+AGR2
+ACTG1
+BTF3
+CIRBP
+COX7C
+EDF1
+EEF1A1
+EEF1B2
+EEF2
+EIF1
+EIF3L
+GAPDH
+H3F3A
+HINT1
+HNRNPA1
+HSPA8
+NACA
+NPM1
+PABPC1
+PPIA
+PRAC1
+PTMA
+RACK1
+SNRPD2
+SRP14
+TPT1
+ACTA2
+ACTB
+ACTG2
+CLU
+CNN1
+CSRP1
+DES
+FLNA
+LGALS1
+MYH11
+MYL6
+MYL9
+MYLK
+S100A6
+TAGLN
+TPM2
+CFD
+FBLN1
+PTGDS
+ACPP
+CD9
+CPE
+NKX3-1
+PMEPA1
+RDH11
+RPN2
+SARAF
+SORD
+SPINT2
+STEAP2
+TMBIM6
+TMEM59
+CD63
+CD81
+CKB
+CST3
+ITM2B
+MDK
+PPDPF
+SAT1
+SELENOW
+ADI1
+APLP2
+ATP6V0B
+CALR
+CD99
+DBI
+DHRS7
+FASN
+FXYD3
+HOXB13
+HSPA5
+KDELR2
+KLK2
+KLK3
+KLK4
+KRT8
+NEAT1
+NME4
+PLPP1
+PRDX6
+SLC45A3
+SPDEF
+SSR4
+TMEM141
+TMPRSS2
+UBB
+ADIRF
+AMD1
+AZGP1
+B2M
+HERPUD1
+HLA-C
+MSMB
+NBL1
+NDRG1
+NEFH
+TSC22D3
+VEGFA
+NPY

models.json ADDED Viewed

	@@ -0,0 +1,25 @@

+{
+  "repo_id": "ouyjr/GenAR",
+  "models": {
+    "prad": {
+      "checkpoint": "checkpoints/prad.ckpt",
+      "genes": "genes/prad.txt"
+    },
+    "her2st": {
+      "checkpoint": "checkpoints/her2st.ckpt",
+      "genes": "genes/her2st.txt"
+    },
+    "kidney": {
+      "checkpoint": "checkpoints/kidney.ckpt",
+      "genes": "genes/kidney.txt"
+    },
+    "mouse_brain": {
+      "checkpoint": "checkpoints/mouse_brain.ckpt",
+      "genes": "genes/mouse_brain.txt"
+    },
+    "ccrcc": {
+      "checkpoint": "checkpoints/ccrcc.ckpt",
+      "genes": "genes/ccrcc.txt"
+    }
+  }
+}