Upload 14 files

hepg2_rag32_sparsity_0.1/batch_onehot_map.pkl

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hepg2_rag32_sparsity_0.1/checkpoints/final.ckpt

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hepg2_rag32_sparsity_0.1/checkpoints/last.ckpt

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hepg2_rag32_sparsity_0.1/config.yaml

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+data:
+  name: PerturbationDataModule
+  kwargs:
+    toml_config_path: /home/difrancesco/PT-RAG/datasets/repogle_nadig.toml
+    embed_key: X_hvg
+    output_space: gene
+    pert_rep: onehot
+    basal_rep: sample
+    num_workers: 4
+    pin_memory: true
+    n_basal_samples: 1
+    basal_mapping_strategy: random
+    should_yield_control_cells: true
+    batch_col: gem_group
+    pert_col: gene
+    cell_type_key: cell_line
+    control_pert: non-targeting
+    map_controls: true
+    perturbation_features_file: null
+    store_raw_basal: false
+    int_counts: false
+    barcode: true
+  output_dir: null
+  debug: true
+model:
+  name: state
+  checkpoint: null
+  device: cuda
+  kwargs:
+    cell_set_len: 64
+    blur: 0.05
+    hidden_dim: 128
+    loss: energy
+    confidence_head: false
+    n_encoder_layers: 1
+    n_decoder_layers: 1
+    predict_residual: true
+    softplus: true
+    freeze_pert_backbone: true
+    transformer_decoder: false
+    finetune_vci_decoder: false
+    residual_decoder: false
+    batch_encoder: true
+    use_batch_token: false
+    nb_decoder: false
+    mask_attn: false
+    use_effect_gating_token: false
+    distributional_loss: energy
+    init_from: /home/difrancesco/PT-RAG/pretrained_SE/se600m_epoch16.ckpt
+    transformer_backbone_key: llama
+    transformer_backbone_kwargs:
+      bidirectional_attention: false
+      max_position_embeddings: 64
+      hidden_size: 128
+      intermediate_size: 2784
+      num_hidden_layers: 8
+      num_attention_heads: 12
+      num_key_value_heads: 12
+      head_dim: 58
+      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
+    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
+training:
+  wandb_track: true
+  weight_decay: 0.0005
+  batch_size: 64
+  lr: 0.001
+  max_steps: 50001
+  train_seed: 42
+  val_freq: 2000
+  ckpt_every_n_steps: 5000
+  gradient_clip_val: 10
+  loss_fn: mse
+  devices: 1
+  strategy: auto
+  use_mfu: true
+  mfu_kwargs:
+    available_flops: 60000000000000.0
+    use_backward: true
+    logging_interval: 10
+    window_size: 2
+  cumulative_flops_use_backward: true
+  rag: true
+  topk_rag: 32
+  rag_weight: 0.0
+  use_genept: true
+  retrieve_than_predict: true
+  differentiable_rag: true
+  check_gradients: false
+  gradient_check_interval: 1
+  gumbel_sparsity_loss: true
+  gumbel_sparsity_weight: 0.1
+wandb:
+  entity: difra00
+  project: PT-RAG
+  local_wandb_dir: ./wandb_logs
+  tags:
+  - replogle_run
+  - rag
+  - topk32
+  - sparsity_0.1
+  - pretrained_se
+name: hepg2_rag32_sparsity_0.1
+output_dir: /home/difrancesco/PT-RAG/experiments/replogle
+use_wandb: true
+overwrite: false
+return_adatas: false
+pred_adata_path: null
+true_adata_path: null

hepg2_rag32_sparsity_0.1/eval_last.ckpt/adata_pred.h5ad

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hepg2_rag32_sparsity_0.1/eval_last.ckpt/adata_real.h5ad

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hepg2_rag32_sparsity_0.1/pert_onehot_map.pt

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hepg2_rag32_sparsity_0.1/version_0/hparams.yaml

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+input_dim: 2000
+hidden_dim: 128
+output_dim: 2000
+pert_dim: 1536
+batch_dim: 56
+dropout: 0.1
+lr: 0.001
+loss_fn: mse
+control_pert: non-targeting
+embed_key: X_hvg
+output_space: gene
+gene_names:
+- HES4
+- ISG15
+- MIB2
+- CEP104
+- RERE
+- ENO1
+- SLC25A33
+- CTNNBIP1
+- KIF1B
+- KIAA2013
+- PRDM2
+- SPEN
+- NBPF1
+- RCC2
+- CAMK2N1
+- DDOST
+- RPL11
+- LYPLA2
+- GALE
+- HMGCL
+- FUCA1
+- NIPAL3
+- CLIC4
+- RSRP1
+- STMN1
+- SH3BGRL3
+- HMGN2
+- ARID1A
+- FAM76A
+- RPA2
+- SNHG3
+- TRNAU1AP
+- SNHG12
+- GMEB1
+- EPB41
+- PTP4A2
+- HDAC1
+- MARCKSL1
+- BSDC1
+- ZBTB8A
+- RBBP4
+- YARS
+- S100PBP
+- AK2
+- ZMYM6
+- SFPQ
+- ZMYM4
+- CLSPN
+- AGO1
+- AGO3
+- MRPS15
+- SNIP1
+- C1orf109
+- CDCA8
+- YRDC
+- FHL3
+- RRAGC
+- MYCBP
+- AKIRIN1
+- MACF1
+- PPIE
+- TRIT1
+- RLF
+- SMAP2
+- YBX1
+- SLC2A1
+- CDC20
+- KIF2C
+- RPS8
+- UROD
+- PRDX1
+- NASP
+- UQCRH
+- EFCAB14
+- STIL
+- FAF1
+- RNF11
+- ORC1
+- PRPF38A
+- MAGOH
+- LRP8
+- SSBP3
+- DHCR24
+- MYSM1
+- JUN
+- NFIA
+- USP1
+- DOCK7
+- GADD45A
+- ACADM
+- SSX2IP
+- BCL10
+- HS2ST1
+- LMO4
+- ZNF644
+- RPAP2
+- MTF2
+- CCDC18
+- FNBP1L
+- PTBP2
+- AGL
+- SASS6
+- TRMT13
+- DBT
+- SLC30A7
+- RNPC3
+- SLC25A24
+- PRPF38B
+- GPSM2
+- PSRC1
+- GSTM3
+- LRIF1
+- CEPT1
+- RHOC
+- SLC16A1-AS1
+- LRIG2
+- RSBN1
+- HIPK1
+- ATP1A1
+- TTF2
+- PHGDH
+- SEC22B
+- LINC02802
+- PDE4DIP
+- HIST2H2AC
+- PLEKHO1
+- ANP32E
+- PRPF3
+- MCL1
+- CDC42SE1
+- MLLT11
+- SCNM1
+- RFX5
+- POGZ
+- S100A10
+- ADAR
+- SHC1
+- CKS1B
+- FDPS
+- RIT1
+- KHDC4
+- ARHGEF2
+- TAGLN2
+- PEA15
+- UAP1
+- NUF2
+- MGST3
+- POGK
+- POU2F1
+- NME7
+- SUCO
+- CENPL
+- GAS5
+- ZBTB37
+- RABGAP1L
+- CACYBP
+- FAM20B
+- TOR3A
+- ABL2
+- CEP350
+- MR1
+- IER5
+- GLUL
+- ARPC5
+- EDEM3
+- TRMT1L
+- UCHL5
+- ASPM
+- ZBTB41
+- NEK7
+- KIF14
+- UBE2T
+- KDM5B
+- PPP1R15B
+- MDM4
+- ELK4
+- RAB29
+- CD55
+- RCOR3
+- NEK2
+- DTL
+- PPP2R5A
+- PACC1
+- TATDN3
+- CENPF
+- BPNT1
+- WDR26
+- DNAH14
+- LBR
+- EPHX1
+- TMEM63A
+- SDE2
+- H3F3A
+- PARP1
+- C1orf35
+- TRIM11
+- CCSAP
+- ABCB10
+- GALNT2
+- ARV1
+- SPRTN
+- NTPCR
+- TARBP1
+- IRF2BP2
+- TOMM20
+- ARID4B
+- B3GALNT2
+- LGALS8
+- OPN3
+- CHML
+- CEP170
+- SMYD3
+- CNST
+- TMEM18
+- RPS7
+- RRM2
+- HPCAL1
+- PDIA6
+- ROCK2
+- LPIN1
+- LAPTM4A
+- TP53I3
+- ITSN2
+- NCOA1
+- CENPA
+- ZNF512
+- MAP4K3-DT
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+- ZFP36L2
+- LRPPRC
+- RHOQ
+- MCFD2
+- CALM2
+- MSH6
+- SPTBN1
+- RTN4
+- FAM161A
+- EHBP1
+- VPS54
+- AFTPH
+- SERTAD2
+- AAK1
+- ANXA4
+- GMCL1
+- PCYOX1
+- NAGK
+- MTHFD2
+- WBP1
+- TMSB10
+- MAT2A
+- C2orf68
+- KDM3A
+- RMND5A
+- CYTOR
+- KRCC1
+- RPIA
+- LINC00342
+- ANKRD36C
+- NCAPH
+- ARID5A
+- MITD1
+- MAP4K4
+- UXS1
+- CCDC138
+- BUB1
+- MIR4435-2HG
+- ZC3H8
+- SLC20A1
+- CKAP2L
+- INSIG2
+- DBI
+- MGAT5
+- CCNT2
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+- MBD5
+- ARL6IP6
+- BAZ2B
+- STK39
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+- KLHL23
+- MAP3K20
+- CDCA7
+- NFE2L2
+- ITPRID2
+- ITGAV
+- GLS
+- NABP1
+- HSPD1
+- HSPE1
+- SGO2
+- CLK1
+- FAM126B
+- CFLAR
+- TMEM237
+- BMPR2
+- CREB1
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+- BARD1
+- ARPC2
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+- PTMA
+- HJURP
+- LRRFIP1
+- ITPR1
+- EDEM1
+- THUMPD3-AS1
+- FANCD2
+- VHL
+- XPC
+- CCDC174
+- EAF1
+- SGO1
+- NR1D2
+- TOP2B
+- SLC4A7
+- STT3B
+- CMTM6
+- DYNC1LI1
+- CRTAP
+- EPM2AIP1
+- ACAA1
+- EXOG
+- SLC25A38
+- RPL14
+- NKTR
+- SNRK
+- ZNF445
+- KIF15
+- LIMD1
+- SACM1L
+- SETD2
+- CDC25A
+- IP6K2
+- NDUFAF3
+- TCTA
+- GNAI2
+- RASSF1
+- MANF
+- ACY1
+- ALAS1
+- BAP1
+- PBRM1
+- DCP1A
+- CCDC66
+- ARF4
+- DENND6A
+- FLNB
+- ATXN7
+- ARL6IP5
+- FOXP1
+- RYBP
+- SHQ1
+- ZNF654
+- ARL13B
+- CLDND1
+- DCBLD2
+- TRMT10C
+- ZBTB11
+- BBX
+- CIP2A
+- USF3
+- POLQ
+- GOLGB1
+- PARP14
+- HACD2
+- CHCHD6
+- MCM2
+- H1FX
+- MBD4
+- ATP2C1
+- DNAJC13
+- TOPBP1
+- CEP63
+- MSL2
+- STAG1
+- NCK1
+- CEP70
+- RASA2
+- TFDP2
+- GK5
+- XRN1
+- DIPK2A
+- HLTF
+- SIAH2
+- RAP2B
+- SSR3
+- CCNL1
+- SMC4
+- PHC3
+- SKIL
+- RPL22L1
+- ECT2
+- ZMAT3
+- PIK3CA
+- TTC14
+- ATP11B
+- EIF4A2
+- RFC4
+- HES1
+- ATP13A3
+- TFRC
+- TCTEX1D2
+- UBXN7
+- RNF168
+- FBXO45
+- PIGX
+- SENP5
+- DLG1
+- ZNF721
+- CTBP1-DT
+- SLBP
+- TACC3
+- NSD2
+- MXD4
+- LYAR
+- AC093323.1
+- WDR1
+- BOD1L1
+- FAM200B
+- TAPT1
+- MED28
+- NCAPG
+- LCORL
+- STIM2
+- KLF3
+- UGDH
+- SMIM14
+- N4BP2
+- GNPDA2
+- FRYL
+- DANCR
+- CHIC2
+- SRD5A3
+- CEP135
+- CENPC
+- RUFY3
+- MOB1B
+- DCK
+- MTHFD2L
+- RCHY1
+- SCARB2
+- CNOT6L
+- BMP2K
+- THAP9-AS1
+- LIN54
+- AFF1
+- HSD17B11
+- PPM1K
+- SMARCAD1
+- PDLIM5
+- RAP1GDS1
+- H2AFZ
+- PPP3CA
+- NFKB1
+- BDH2
+- CENPE
+- TET2
+- HADH
+- MCUB
+- AP1AR
+- SNHG8
+- C4orf3
+- MAD2L1
+- ANXA5
+- EXOSC9
+- CCNA2
+- KIAA1109
+- ANKRD50
+- HSPA4L
+- PLK4
+- SCLT1
+- SLC7A11
+- ELF2
+- USP38
+- FBXW7
+- MND1
+- TMEM131L
+- FNIP2
+- RAPGEF2
+- MSMO1
+- CBR4
+- NEK1
+- CLCN3
+- HPF1
+- HMGB2
+- SAP30
+- CEP44
+- CDKN2AIP
+- ING2
+- IRF2
+- CASP3
+- CENPU
+- CLPTM1L
+- TRIO
+- SKP2
+- RICTOR
+- HMGCS1
+- NNT-AS1
+- IL6ST
+- DEPDC1B
+- KIF2A
+- CENPK
+- PIK3R1
+- CCNB1
+- CENPH
+- RAD17
+- HMGCR
+- POLK
+- F2R
+- JMY
+- DHFR
+- ATG10
+- RASA1
+- TMEM161B
+- TMEM161B-AS1
+- POLR3G
+- SLF1
+- RHOBTB3
+- GLRX
+- CAST
+- LNPEP
+- RIOK2
+- CHD1
+- PPIP5K2
+- FER
+- PJA2
+- MAN2A1
+- SLC25A46
+- EPB41L4A-AS1
+- DCP2
+- CCDC112
+- TNFAIP8
+- LMNB1
+- LINC01184
+- SLC12A2
+- LYRM7
+- CDC42SE2
+- RAPGEF6
+- IRF1
+- KIF3A
+- AFF4
+- ZCCHC10
+- TCF7
+- SEC24A
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+- BRD8
+- KIF20A
+- CTNNA1
+- SNHG4
+- TAF7
+- DIAPH1
+- NR3C1
+- YIPF5
+- TNIP1
+- ANXA6
+- GALNT10
+- CNOT8
+- SLU7
+- PTTG1
+- HMMR
+- PANK3
+- SPDL1
+- NPM1
+- CREBRF
+- CPEB4
+- ZNF346
+- GRK6
+- PDLIM7
+- PHYKPL
+- CLK4
+- MGAT4B
+- SQSTM1
+- RNF130
+- TRIM41
+- TRIM52
+- GMDS
+- TUBB2A
+- ECI2
+- CDYL
+- RREB1
+- RIOK1
+- TMEM14C
+- HIVEP1
+- TBC1D7
+- JARID2
+- DTNBP1
+- FAM8A1
+- SOX4
+- GMNN
+- TRIM38
+- HIST1H1C
+- HIST1H4C
+- HIST1H2AC
+- HIST1H1E
+- BTN2A1
+- HIST1H1B
+- ZSCAN16-AS1
+- ZKSCAN8
+- ZNRD1
+- HLA-E
+- PPP1R10
+- PPP1R18
+- MDC1
+- TUBB
+- FLOT1
+- IER3
+- HLA-C
+- DDAH2
+- SNHG32
+- NEU1
+- ATF6B
+- BRD2
+- TAPBP
+- KIFC1
+- HMGA1
+- SMIM29
+- RPS10
+- FKBP5
+- CCND3
+- TAF8
+- UBR2
+- HSP90AB1
+- MCM3
+- TRAM2
+- ELOVL5
+- GCLC
+- DST
+- TMEM30A
+- PHIP
+- TTK
+- CYB5R4
+- CEP162
+- SNHG5
+- ZNF292
+- SMIM8
+- PNRC1
+- MDN1
+- CASP8AP2
+- MMS22L
+- ASCC3
+- PDSS2
+- OSTM1
+- FOXO3
+- CEP57L1
+- ZBTB24
+- CDK19
+- MFSD4B
+- REV3L
+- FAM229B
+- TSPYL4
+- TSPYL1
+- KPNA5
+- ASF1A
+- MAN1A1
+- SERINC1
+- NCOA7
+- CENPW
+- EPB41L2
+- AHI1
+- IFNGR1
+- ABRACL
+- SHPRH
+- STXBP5
+- KATNA1
+- FBXO5
+- SYNJ2
+- EZR
+- SOD2
+- ACAT2
+- TCP1
+- MPC1
+- RNASET2
+- ZFAND2A
+- NUDT1
+- CHST12
+- RBAK
+- TNRC18
+- ACTB
+- PMS2
+- KDELR2
+- ZNF12
+- PHF14
+- TMEM106B
+- ARL4A
+- TSPAN13
+- FAM126A
+- IGF2BP3
+- CYCS
+- NFE2L3
+- PLEKHA8
+- GARS-DT
+- RP9
+- ANLN
+- STK17A
+- CCM2
+- PSPH
+- ERV3-1
+- ZNF92
+- BAZ1B
+- TRIM73
+- RHBDD2
+- POR
+- HSPB1
+- DMTF1
+- TMEM243
+- DBF4
+- AKAP9
+- ANKIB1
+- PEX1
+- RBM48
+- FAM133B
+- CDK6
+- CASD1
+- BRI3
+- TRRAP
+- ARPC1A
+- ZNF394
+- ZKSCAN5
+- ZKSCAN1
+- MCM7
+- AP4M1
+- TSC22D4
+- LRCH4
+- GIGYF1
+- SRRT
+- TRIM56
+- ORAI2
+- LRWD1
+- POLR2J3
+- KMT2E
+- SRPK2
+- HBP1
+- CBLL1
+- PNPLA8
+- THAP5
+- DNAJB9
+- IFRD1
+- SMIM30
+- ING3
+- FAM3C
+- NDUFA5
+- HILPDA
+- CALU
+- UBE2H
+- KLHDC10
+- CREB3L2
+- TRIM24
+- ZC3HAV1
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+- LUC7L2
+- HIPK2
+- ADCK2
+- BRAF
+- CASP2
+- ZYX
+- TCAF1
+- EZH2
+- PDIA4
+- ATP6V0E2
+- CDK5
+- KMT2C
+- XRCC2
+- PAXIP1
+- NCAPG2
+- ESYT2
+- WDR60
+- FBXO25
+- ERICH1
+- AC100810.1
+- MCPH1
+- MFHAS1
+- TNKS
+- MTMR9
+- FDFT1
+- CTSB
+- PCM1
+- ASAH1
+- ATP6V1B2
+- SLC39A14
+- SORBS3
+- PDLIM2
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+- CDCA2
+- BNIP3L
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+- ESCO2
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+- HMBOX1
+- WRN
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+- FGFR1
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+- SDCBP
+- NSMAF
+- PDE7A
+- SGK3
+- CSPP1
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+- FABP5
+- LRRCC1
+- PIP4P2
+- FAM92A
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+- LAPTM4B
+- VPS13B
+- RNF19A
+- RRM2B
+- UTP23
+- RAD21
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+- C8orf76
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+- PTK2
+- JRK
+- LY6E
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+- GRINA
+- BOP1
+- DGAT1
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+- ZFAND5
+- C9orf40
+- OSTF1
+- RFK
+- GNAQ
+- CEP78
+- PSAT1
+- TLE4
+- GKAP1
+- RMI1
+- AGTPBP1
+- TUT7
+- SPIN1
+- CKS2
+- SECISBP2
+- NFIL3
+- NINJ1
+- AL158152.1
+- ERCC6L2
+- MFSD14C
+- XPA
+- NANS
+- TRIM14
+- TGFBR1
+- MSANTD3
+- RNF20
+- SMC2
+- TMEM38B
+- ELP1
+- CTNNAL1
+- UGCG
+- CDK5RAP2
+- PSMD5
+- PHF19
+- CNTRL
+- RABGAP1
+- HSPA5
+- ZBTB43
+- RPL12
+- ODF2
+- SPTAN1
+- AL441992.1
+- C9orf78
+- FNBP1
+- NUP214
+- RAPGEF1
+- SETX
+- TTF1
+- TSC1
+- SURF2
+- UBAC1
+- AGPAT2
+- SNHG7
+- PHPT1
+- SAPCD2
+- DPP7
+- TUBB4B
+- IDI1
+- PFKP
+- KLF6
+- NET1
+- MCM10
+- DCLRE1C
+- NMT2
+- ARL5B
+- DNAJC1
+- MSRB2
+- MASTL
+- WAC-AS1
+- ZEB1
+- ARHGAP12
+- ITGB1
+- CREM
+- ZNF248
+- ZNF37A
+- ZNF32
+- NCOA4
+- ERCC6
+- PARG
+- ZWINT
+- CDK1
+- ARID5B
+- RTKN2
+- REEP3
+- SIRT1
+- HERC4
+- RUFY2
+- DNA2
+- TET1
+- KIF1BP
+- PCBD1
+- PSAP
+- DDIT4
+- P4HA1
+- DNAJC9
+- PPP3CB
+- ZSWIM8
+- KAT6B
+- SAMD8
+- RPS24
+- PPIF
+- PRXL2A
+- CCSER2
+- GLUD1
+- PTEN
+- KIF20B
+- PCGF5
+- KIF11
+- CEP55
+- FRA10AC1
+- HELLS
+- PDLIM1
+- ZNF518A
+- LCOR
+- ARHGAP19
+- PGAM1
+- GOT1
+- ERLIN1
+- BLOC1S2
+- SCD
+- HIF1AN
+- SLF2
+- DPCD
+- OGA
+- GBF1
+- CUEDC2
+- RPARP-AS1
+- TRIM8
+- ARL3
+- GSTO1
+- ADD3
+- MXI1
+- PDCD4
+- SHOC2
+- GPAM
+- TCF7L2
+- CCDC186
+- SHTN1
+- PDZD8
+- RAB11FIP2
+- BAG3
+- PLEKHA1
+- ACADSB
+- OAT
+- EDRF1
+- MKI67
+- BNIP3
+- STK32C
+- FUOM
+- ECHS1
+- IFITM2
+- HRAS
+- PHRF1
+- CD151
+- POLR2L
+- TSPAN4
+- CTSD
+- KCNQ1OT1
+- ZNF195
+- RHOG
+- STIM1
+- RRM1
+- MRPL17
+- TMEM41B
+- ZNF143
+- WEE1
+- SWAP70
+- CTR9
+- ZBED5
+- TEAD1
+- BTBD10
+- RRAS2
+- NUCB2
+- SAAL1
+- LDHA
+- SPTY2D1
+- SVIP
+- CCDC34
+- KIF18A
+- ARL14EP
+- RCN1
+- HIPK3
+- CD59
+- CAT
+- TTC17
+- ALKBH3
+- PHF21A
+- CKAP5
+- PTPMT1
+- UBE2L6
+- MED19
+- MRPL16
+- TMEM109
+- FEN1
+- FADS1
+- FADS3
+- FTH1
+- INCENP
+- MTA2
+- BSCL2
+- TTC9C
+- SNHG1
+- SLC3A2
+- MARK2
+- ATG2A
+- SAC3D1
+- CDCA5
+- TM7SF2
+- NEAT1
+- MALAT1
+- FAM89B
+- RNASEH2C
+- MUS81
+- CCDC85B
+- C11orf68
+- DRAP1
+- PACS1
+- ZDHHC24
+- LRFN4
+- GRK2
+- ANKRD13D
+- POLD4
+- TMEM134
+- AIP
+- CDK2AP2
+- CHKA
+- KMT5B
+- IGHMBP2
+- DHCR7
+- FCHSD2
+- UCP2
+- POLD3
+- XRRA1
+- AP002360.1
+- EMSY
+- NDUFC2
+- PCF11
+- PICALM
+- EED
+- CTSC
+- CHORDC1
+- CEP295
+- TAF1D
+- MED17
+- ENDOD1
+- FAM76B
+- CEP57
+- CCDC82
+- TMEM123
+- MSANTD4
+- NPAT
+- ATM
+- RDX
+- BUD13
+- PCSK7
+- KMT2A
+- CCDC84
+- H2AFX
+- CBL
+- SC5D
+- UBASH3B
+- HSPA8
+- CHEK1
+- NFRKB
+- APLP2
+- ZBTB44
+- NCAPD3
+- VPS26B
+- THYN1
+- KDM5A
+- ERC1
+- FOXM1
+- RAD51AP1
+- DYRK4
+- TNFRSF1A
+- MRPL51
+- NCAPD2
+- GAPDH
+- COPS7A
+- MLF2
+- PTMS
+- CDCA3
+- TPI1
+- ENO2
+- ATN1
+- C12orf57
+- GABARAPL1
+- YBX3
+- PRH1
+- ETV6
+- CDKN1B
+- ATF7IP
+- PLEKHA5
+- AEBP2
+- RECQL
+- GOLT1B
+- C2CD5
+- BCAT1
+- ITPR2
+- TM7SF3
+- STK38L
+- ARNTL2
+- PPFIBP1
+- KLHL42
+- DDX11
+- RESF1
+- GXYLT1
+- IRAK4
+- TWF1
+- ARID2
+- SLC38A1
+- SLC38A2
+- SLC48A1
+- HDAC7
+- TMEM106C
+- SENP1
+- ASB8
+- CCNT1
+- FKBP11
+- LMBR1L
+- TUBA1B
+- TUBA1A
+- TUBA1C
+- TROAP
+- RACGAP1
+- LIMA1
+- CBX5
+- CD63
+- GDF11
+- CDK2
+- RPL41
+- MYL6
+- PRIM1
+- STAT6
+- R3HDM2
+- DDIT3
+- MARCH9
+- GIHCG
+- USP15
+- SLC35E3
+- MDM2
+- AC025159.1
+- TMEM19
+- TBC1D15
+- CEP290
+- ATP2B1
+- BTG1
+- EEA1
+- NUDT4
+- CEP83
+- FGD6
+- ELK3
+- CDK17
+- NEDD1
+- TMPO
+- IKBIP
+- ACTR6
+- CHPT1
+- HELLPAR
+- HSP90B1
+- TDG
+- TXNRD1
+- TMEM263
+- CORO1C
+- SSH1
+- ALKBH2
+- UNG
+- GLTP
+- GIT2
+- IFT81
+- FAM216A
+- MAPKAPK5-AS1
+- HECTD4
+- MED13L
+- C12orf49
+- WSB2
+- PEBP1
+- TAOK3
+- CIT
+- BCL7A
+- CLIP1
+- ZCCHC8
+- RSRC2
+- KNTC1
+- C12orf65
+- RILPL2
+- CCDC92
+- SCARB1
+- UBC
+- BRI3BP
+- POLE
+- ZNF26
+- ZNF84
+- ZMYM5
+- ZMYM2
+- SKA3
+- MRPL57
+- ZDHHC20
+- SACS
+- CENPJ
+- MTMR6
+- NUP58
+- RNF6
+- GTF3A
+- UBL3
+- KATNAL1
+- HMGB1
+- USPL1
+- HSPH1
+- BRCA2
+- N4BP2L2
+- PDS5B
+- EXOSC8
+- NHLRC3
+- ELF1
+- NAA16
+- DGKH
+- AKAP11
+- TSC22D1
+- GPALPP1
+- TPT1
+- TPT1-AS1
+- ITM2B
+- RB1
+- DLEU2
+- TRIM13
+- DLEU1
+- RNASEH2B
+- INTS6
+- WDFY2
+- VPS36
+- CKAP2
+- DIAPH3
+- TDRD3
+- MZT1
+- CLN5
+- MYCBP2
+- OBI1
+- NDFIP2
+- ABCC4
+- DNAJC3
+- MBNL2
+- TPP2
+- ERCC5
+- ARGLU1
+- ING1
+- ANKRD10
+- ARHGEF7
+- ATP11A
+- TMCO3
+- TTC5
+- CCNB1IP1
+- PNP
+- LRP10
+- ACIN1
+- DHRS4
+- DHRS4L2
+- PSME1
+- EMC9
+- PSME2
+- MDP1
+- SDR39U1
+- G2E3
+- ARHGAP5
+- SPTSSA
+- BAZ1A
+- PSMA6
+- NFKBIA
+- MBIP
+- TRAPPC6B
+- PNN
+- FBXO33
+- PRPF39
+- FANCM
+- MIS18BP1
+- LRR1
+- KLHDC2
+- SOS2
+- NIN
+- ERO1A
+- FERMT2
+- DDHD1
+- CDKN3
+- WDHD1
+- SOCS4
+- DLGAP5
+- AP5M1
+- PSMA3-AS1
+- ARID4A
+- KIAA0586
+- PCNX4
+- DHRS7
+- PPM1A
+- HIF1A
+- SNAPC1
+- ZBTB1
+- FUT8
+- ATP6V1D
+- ZFP36L1
+- ACTN1
+- DCAF5
+- PCNX1
+- SIPA1L1
+- ELMSAN1
+- NPC2
+- ACYP1
+- ERG28
+- GPATCH2L
+- TMED8
+- AHSA1
+- SEL1L
+- FOXN3
+- NRDE2
+- CALM1
+- PPP4R3A
+- TRIP11
+- ATXN3
+- UBR7
+- DDX24
+- SNHG10
+- VRK1
+- EVL
+- WARS
+- DYNC1H1
+- HSP90AA1
+- RCOR1
+- TRAF3
+- SIVA1
+- CDCA4
+- NUDT14
+- UBE3A
+- NSMCE3
+- FAN1
+- ARHGAP11A
+- MEIS2
+- FAM98B
+- BUB1B
+- KNSTRN
+- KNL1
+- INO80
+- NUSAP1
+- LRRC57
+- TTBK2
+- UBR1
+- CCNDBP1
+- ADAL
+- TUBGCP4
+- TP53BP1
+- PDIA3
+- CTDSPL2
+- B2M
+- DUT
+- CEP152
+- SECISBP2L
+- DTWD1
+- GABPB1-IT1
+- GABPB1-AS1
+- TRPM7
+- TMOD3
+- RAB27A
+- RFX7
+- ZNF280D
+- TCF12
+- ADAM10
+- MINDY2
+- CCNB2
+- ANXA2
+- ICE2
+- VPS13C
+- TPM1
+- LACTB
+- RPS27L
+- RAB8B
+- HERC1
+- CSNK1G1
+- PCLAF
+- PIF1
+- TIPIN
+- SMAD3
+- ANP32A
+- KIF23
+- TLE3
+- PKM
+- PML
+- UBL7
+- SIN3A
+- SNUPN
+- UBE2Q2
+- SCAPER
+- TLNRD1
+- EFL1
+- SNHG21
+- AKAP13
+- AEN
+- MFGE8
+- FANCI
+- IDH2
+- IQGAP1
+- CRTC3
+- BLM
+- PRC1
+- LINC01578
+- CHD2
+- LRRC28
+- MEF2A
+- CHSY1
+- POLR3K
+- METRN
+- CIAO3
+- HAGH
+- MSRB1
+- SLC9A3R2
+- TSC2
+- SNHG19
+- CCNF
+- PKMYT1
+- PAQR4
+- HCFC1R1
+- ZNF263
+- EEF2KMT
+- CARHSP1
+- USP7
+- RRN3
+- MARF1
+- NDE1
+- ARL6IP1
+- CCP110
+- LYRM1
+- NPIPB5
+- PLK1
+- MAZ
+- KCTD13
+- HIRIP3
+- SEPHS2
+- VKORC1
+- ZNF720
+- ZNF267
+- SHCBP1
+- ORC6
+- C16orf87
+- NETO2
+- RBL2
+- CRNDE
+- MT2A
+- MT1X
+- HERPUD1
+- CKLF
+- CMTM3
+- CES2
+- CTCF
+- GFOD2
+- PSMB10
+- SLC7A6OS
+- NFAT5
+- NQO1
+- ST3GAL2
+- CMTR2
+- GLG1
+- RFWD3
+- ZNRF1
+- TMEM170A
+- ADAT1
+- TERF2IP
+- GSE1
+- GINS2
+- MAP1LC3B
+- KLHDC4
+- SLC7A5
+- BANP
+- ZFPM1
+- MVD
+- RNF166
+- CDT1
+- ACSF3
+- ANKRD11
+- SPATA33
+- FANCA
+- VPS53
+- SMYD4
+- SMG6
+- MNT
+- METTL16
+- ZZEF1
+- CYB5D2
+- ARRB2
+- KIF1C
+- RPAIN
+- AC004148.1
+- MIS12
+- DVL2
+- GABARAP
+- ELP5
+- GPS2
+- POLR2A
+- SAT2
+- WRAP53
+- KDM6B
+- NAA38
+- CHD3
+- VAMP2
+- TMEM107
+- AURKB
+- RANGRF
+- STX8
+- ZNF286A
+- ZSWIM7
+- CENPV
+- LRRC75A
+- MPRIP
+- FLCN
+- GID4
+- TOP3A
+- LINC02693
+- TMEM97
+- SPAG5
+- PHF12
+- MYO18A
+- TP53I13
+- SSH2
+- ATAD5
+- SUZ12
+- C17orf75
+- ZNF830
+- LIG3
+- RAD51D
+- SNHG30
+- TAF15
+- DUSP14
+- SYNRG
+- MLLT6
+- CISD3
+- CWC25
+- FBXL20
+- ORMDL3
+- CDC6
+- TOP2A
+- TMEM99
+- NKIRAS2
+- ATP6V0A1
+- COASY
+- PSMC3IP
+- EZH1
+- VAT1
+- BRCA1
+- NBR1
+- UBTF
+- GRN
+- HEXIM1
+- AC005670.3
+- CDK5RAP3
+- CALCOCO2
+- IGF2BP1
+- ZNF652
+- KAT7
+- RSAD1
+- TOB1
+- STXBP4
+- TRIM25
+- MSI2
+- MTMR4
+- PRR11
+- VMP1
+- PPM1D
+- BRIP1
+- SNHG25
+- DDX5
+- CEP95
+- SMURF2
+- PRKCA
+- BPTF
+- KPNA2
+- SLC9A3R1
+- FDXR
+- JPT1
+- MIF4GD
+- UBALD2
+- MXRA7
+- SEPTIN9
+- TK1
+- AFMID
+- BIRC5
+- CBX4
+- RNF213
+- ENDOV
+- ACTG1
+- SLC25A10
+- P4HB
+- ALYREF
+- PCYT2
+- SIRT7
+- PYCR1
+- ASPSCR1
+- RFNG
+- FASN
+- CYBC1
+- TBCD
+- THOC1
+- TYMSOS
+- TYMS
+- ENOSF1
+- NDC80
+- MYL12A
+- MYL12B
+- TGIF1
+- ANKRD12
+- CHMP1B
+- PTPN2
+- CEP192
+- ROCK1
+- RBBP8
+- RIOK3
+- RNF138
+- MAPRE2
+- ZNF397
+- SLC39A6
+- HAUS1
+- PIAS2
+- SMAD2
+- C18orf32
+- CXXC1
+- SKA1
+- ME2
+- SEC11C
+- LMAN1
+- PMAIP1
+- KDSR
+- VPS4B
+- TMX3
+- RTTN
+- CYB5A
+- CDC34
+- BSG
+- R3HDM4
+- CNN2
+- MIDN
+- MKNK2
+- SPPL2B
+- SLC39A3
+- NFIC
+- CHAF1A
+- FEM1A
+- UHRF1
+- CLPP
+- ARHGEF18
+- CTXN1
+- ZNF121
+- ZNF562
+- SHFL
+- DNMT1
+- ICAM3
+- KRI1
+- CDKN2D
+- ILF3-DT
+- SMARCA4
+- LDLR
+- SPC24
+- ZNF791
+- DHPS
+- JUNB
+- FARSA
+- IER2
+- CCDC130
+- SAMD1
+- ASF1B
+- DDX39A
+- GIPC1
+- DNAJB1
+- AKAP8L
+- TPM4
+- JUND
+- PGPEP1
+- SSBP4
+- HOMER3
+- NR2C2AP
+- ZNF430
+- ZNF714
+- ZNF431
+- ZNF91
+- LINC00662
+- CEP89
+- CEBPG
+- KMT2B
+- ZNF260
+- FAM98C
+- ACTN4
+- ECH1
+- NFKBIB
+- PLD3
+- BLVRB
+- TGFB1
+- RABAC1
+- PAFAH1B3
+- ETHE1
+- ZNF226
+- VASP
+- SLC1A5
+- AP2S1
+- NOP53
+- SELENOW
+- EMP3
+- CYTH2
+- PPP1R15A
+- BAX
+- FTL
+- FCGRT
+- PNKP
+- ATF5
+- VRK3
+- POLD1
+- ETFB
+- ZNF766
+- ZNF480
+- MYADM
+- TFPT
+- LENG1
+- LENG8
+- PPP6R1
+- UBE2S
+- AC005261.1
+- A1BG
+- TRIB3
+- RBCK1
+- MRPS26
+- CDC25B
+- RNF24
+- SLC23A2
+- PCNA
+- GPCPD1
+- MCM8
+- CRLS1
+- TMX4
+- PLCB1
+- ESF1
+- DSTN
+- RRBP1
+- SNX5
+- CRNKL1
+- CST3
+- PYGB
+- ID1
+- BCL2L1
+- TPX2
+- PDRG1
+- NOL4L
+- E2F1
+- AHCY
+- DYNLRB1
+- MMP24OS
+- EIF6
+- CEP250
+- CPNE1
+- SCAND1
+- NORAD
+- RAB5IF
+- RBL1
+- MANBAL
+- CTNNBL1
+- SNHG17
+- FAM83D
+- CHD6
+- MYBL2
+- OSER1
+- PKIG
+- STK4
+- CTSA
+- ZMYND8
+- NCOA3
+- ARFGEF2
+- ZFAS1
+- CEBPB
+- ZNF217
+- FAM210B
+- AURKA
+- RAB22A
+- PRELID3B
+- FAM217B
+- OGFR
+- ARFGAP1
+- PPDPF
+- MHENCR
+- ZGPAT
+- TCEA2
+- CU638689.4
+- BTG3
+- GABPA
+- CCT8
+- BACH1
+- MIS18A
+- IFNAR2
+- GART
+- SLC5A3
+- RCAN1
+- RUNX1
+- MORC3
+- CHAF1B
+- PIGP
+- DYRK1A
+- ETS2
+- ZBTB21
+- PTTG1IP
+- C21orf58
+- PCNT
+- IL17RA
+- BID
+- ESS2
+- SLC25A1
+- HIRA
+- C22orf39
+- MRPL40
+- UFD1
+- CDC45
+- RTL10
+- COMT
+- DGCR8
+- TRMT2A
+- RANBP1
+- DGCR6L
+- MED15
+- PI4KA
+- SNAP29
+- CRKL
+- THAP7
+- UBE2L3
+- YDJC
+- SDF2L1
+- PPIL2
+- MAPK1
+- PPM1F
+- BCR
+- SLC2A11
+- MIF
+- CABIN1
+- SPECC1L
+- HPS4
+- TPST2
+- CCDC117
+- XBP1
+- GAS2L1
+- NIPSNAP1
+- SFI1
+- MCM5
+- RBFOX2
+- MYH9
+- TST
+- LGALS1
+- TRIOBP
+- GCAT
+- ATF4
+- TNRC6B
+- PHF5A
+- CENPM
+- TCF20
+- NUP50
+- Z95331.1
+- GTSE1
+- BRD1
+- ZBED4
+- PIM3
+- NCAPH2
+- PLCXD1
+- PPP2R3B
+- AKAP17A
+- CD99
+- MSL3
+- PRPS2
+- RAB9A
+- MOSPD2
+- AP1S2
+- SH3KBP1
+- RPS6KA3
+- SMS
+- SAT1
+- POLA1
+- MID1IP1
+- BCOR
+- CXorf38
+- USP11
+- EBP
+- GRIPAP1
+- PLP2
+- SMC1A
+- UBQLN2
+- NBDY
+- KIF4A
+- TAF1
+- OGT
+- FTX
+- RLIM
+- BRWD3
+- ARMCX3
+- TCEAL9
+- MORF4L2
+- RBM41
+- ACSL4
+- SEPTIN6
+- RNF113A
+- LAMP2
+- CUL4B
+- STAG2
+- SMARCA1
+- STK26
+- PHF6
+- HTATSF1
+- ATP11C
+- FMR1
+- IDS
+- HMGB3
+- MECP2
+- FLNA
+- TAZ
+- GDI1
+- LAGE3
+- G6PD
+- DKC1
+- MPP1
+- MT-ND2
+- MT-ATP8
+- MT-ATP6
+- MT-CO3
+- MT-ND3
+- MT-ND4L
+- MT-ND4
+- MT-ND5
+- MT-ND6
+batch_size: 64
+gene_dim: 2000
+hvg_dim: 2000
+decoder_cfg:
+  latent_dim: 2000
+  gene_dim: 2000
+  hidden_dims:
+  - 1024
+  - 1024
+  - 512
+  dropout: 0.1
+  residual_decoder: false
+cell_set_len: 64
+blur: 0.05
+loss: energy
+confidence_head: false
+n_encoder_layers: 1
+n_decoder_layers: 1
+softplus: true
+freeze_pert_backbone: true
+transformer_decoder: false
+finetune_vci_decoder: false
+residual_decoder: false
+batch_encoder: true
+use_batch_token: false
+nb_decoder: false
+mask_attn: false
+use_effect_gating_token: false
+init_from: /home/difrancesco/PT-RAG/pretrained_SE/se600m_epoch16.ckpt
+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: 50001
+train_seed: 42
+val_freq: 2000
+ckpt_every_n_steps: 5000
+gradient_clip_val: 10
+devices: 1
+strategy: auto
+use_mfu: true
+mfu_kwargs:
+  available_flops: 60000000000000.0
+  use_backward: true
+  logging_interval: 10
+  window_size: 2
+cumulative_flops_use_backward: true
+rag: true
+topk_rag: 32
+rag_weight: 0.0
+use_genept: true
+retrieve_than_predict: true
+differentiable_rag: true
+check_gradients: false
+gradient_check_interval: 1
+gumbel_sparsity_loss: true
+gumbel_sparsity_weight: 0.1
+basal_mapping_strategy: random
+predict_residual: true
+distributional_loss: energy
+transformer_backbone_key: llama
+transformer_backbone_kwargs:
+  bidirectional_attention: false
+  max_position_embeddings: 64
+  hidden_size: 128
+  intermediate_size: 2784
+  num_hidden_layers: 8
+  num_attention_heads: 12
+  num_key_value_heads: 12
+  head_dim: 58
+  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

hepg2_rag32_sparsity_0.1/wandb_path.txt

@@ -0,0 +1 @@
+difra00/PT-RAG/eesrf6c7