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  1. fewshot/hepg2/cell_type_onehot_map.pkl +3 -0
  2. fewshot/hepg2/eval_best.ckpt/hepg2_agg_results.csv +3 -0
  3. fewshot/hepg2/eval_best.ckpt/hepg2_results.csv +3 -0
  4. fewshot/hepg2/eval_last.ckpt/hepg2_results.csv +3 -0
  5. fewshot/hepg2/var_dims.pkl +3 -0
  6. fewshot/jurkat/batch_onehot_map.pkl +3 -0
  7. fewshot/jurkat/cell_type_onehot_map.pkl +3 -0
  8. fewshot/jurkat/eval_best.ckpt/jurkat_agg_results.csv +3 -0
  9. fewshot/jurkat/eval_best.ckpt/jurkat_results.csv +3 -0
  10. fewshot/jurkat/eval_last.ckpt/jurkat_agg_results.csv +3 -0
  11. fewshot/jurkat/pert_onehot_map.pt +3 -0
  12. fewshot/jurkat/var_dims.pkl +3 -0
  13. fewshot/k562/cell_type_onehot_map.pkl +3 -0
  14. fewshot/k562/eval_best.ckpt/k562_agg_results.csv +3 -0
  15. fewshot/k562/eval_best.ckpt/k562_results.csv +3 -0
  16. fewshot/k562/eval_last.ckpt/k562_agg_results.csv +3 -0
  17. fewshot/k562/eval_last.ckpt/k562_results.csv +3 -0
  18. fewshot/k562/pert_onehot_map.pt +3 -0
  19. fewshot/k562/var_dims.pkl +3 -0
  20. fewshot/rpe1/cell_type_onehot_map.pkl +3 -0
  21. fewshot/rpe1/config.yaml +116 -0
  22. fewshot/rpe1/eval_best.ckpt/rpe1_results.csv +3 -0
  23. fewshot/rpe1/eval_last.ckpt/rpe1_results.csv +3 -0
  24. fewshot/rpe1/pert_onehot_map.pt +3 -0
  25. fewshot/rpe1/var_dims.pkl +3 -0
  26. zeroshot/hepg2/cell_type_onehot_map.pkl +3 -0
  27. zeroshot/hepg2/eval_best.ckpt/hepg2_agg_results.csv +3 -0
  28. zeroshot/hepg2/eval_last.ckpt/hepg2_agg_results.csv +3 -0
  29. zeroshot/hepg2/eval_last.ckpt/hepg2_results.csv +3 -0
  30. zeroshot/hepg2/pert_onehot_map.pt +3 -0
  31. zeroshot/hepg2/var_dims.pkl +3 -0
  32. zeroshot/jurkat/cell_type_onehot_map.pkl +3 -0
  33. zeroshot/jurkat/eval_best.ckpt/jurkat_agg_results.csv +3 -0
  34. zeroshot/jurkat/eval_last.ckpt/jurkat_agg_results.csv +3 -0
  35. zeroshot/jurkat/eval_last.ckpt/jurkat_results.csv +3 -0
  36. zeroshot/jurkat/pert_onehot_map.pt +3 -0
  37. zeroshot/jurkat/var_dims.pkl +3 -0
  38. zeroshot/k562/batch_onehot_map.pkl +3 -0
  39. zeroshot/k562/cell_type_onehot_map.pkl +3 -0
  40. zeroshot/k562/eval_best.ckpt/k562_agg_results.csv +3 -0
  41. zeroshot/k562/eval_best.ckpt/k562_results.csv +3 -0
  42. zeroshot/k562/eval_last.ckpt/k562_agg_results.csv +3 -0
  43. zeroshot/k562/pert_onehot_map.pt +3 -0
  44. zeroshot/rpe1/batch_onehot_map.pkl +3 -0
  45. zeroshot/rpe1/cell_type_onehot_map.pkl +3 -0
  46. zeroshot/rpe1/eval_best.ckpt/rpe1_agg_results.csv +3 -0
  47. zeroshot/rpe1/eval_best.ckpt/rpe1_results.csv +3 -0
  48. zeroshot/rpe1/eval_last.ckpt/rpe1_agg_results.csv +3 -0
  49. zeroshot/rpe1/pert_onehot_map.pt +3 -0
  50. zeroshot/rpe1/var_dims.pkl +3 -0
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+ data:
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+ name: PerturbationDataModule
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+ kwargs:
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+ toml_config_path: /large_storage/ctc/userspace/aadduri/revisions/replogle_nogwps_v2/rpe1.toml
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+ embed_key: X_hvg
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+ output_space: gene
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+ pert_rep: onehot
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+ basal_rep: sample
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+ num_workers: 12
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+ pin_memory: true
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+ n_basal_samples: 1
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+ basal_mapping_strategy: random
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+ should_yield_control_cells: true
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+ batch_col: gem_group
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+ pert_col: gene
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+ cell_type_key: cell_line
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+ control_pert: non-targeting
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+ map_controls: true
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+ perturbation_features_file: null
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+ store_raw_basal: false
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+ int_counts: false
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+ barcode: true
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+ output_dir: null
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+ debug: true
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+ model:
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+ name: state
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+ checkpoint: null
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+ device: cuda
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+ kwargs:
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+ cell_set_len: 64
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+ blur: 0.05
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+ hidden_dim: 328
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+ loss: energy
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+ confidence_token: false
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+ n_encoder_layers: 1
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+ n_decoder_layers: 1
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+ predict_residual: true
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+ softplus: true
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+ freeze_pert_backbone: false
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+ transformer_decoder: false
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+ finetune_vci_decoder: false
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+ residual_decoder: false
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+ batch_encoder: true
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+ use_batch_token: false
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+ nb_decoder: false
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+ mask_attn: false
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+ use_effect_gating_token: false
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+ distributional_loss: energy
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+ init_from: null
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+ mmd_num_chunks: 1
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+ randomize_mmd_chunks: false
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+ transformer_backbone_key: llama
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+ transformer_backbone_kwargs:
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+ bidirectional_attention: true
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+ max_position_embeddings: 64
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+ hidden_size: 328
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+ intermediate_size: 3072
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+ num_hidden_layers: 8
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+ num_attention_heads: 12
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+ num_key_value_heads: 12
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+ head_dim: 64
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+ use_cache: false
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+ attention_dropout: 0.0
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+ hidden_dropout: 0.0
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+ layer_norm_eps: 1.0e-06
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+ pad_token_id: 0
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+ bos_token_id: 1
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+ eos_token_id: 2
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+ tie_word_embeddings: false
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+ rotary_dim: 0
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+ use_rotary_embeddings: false
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+ enable: false
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+ r: 16
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+ alpha: 32
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+ dropout: 0.05
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+ bias: none
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+ target: auto
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+ adapt_mlp: false
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+ task_type: FEATURE_EXTRACTION
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+ merge_on_eval: false
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+ training:
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+ wandb_track: true
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+ weight_decay: 0.0005
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+ batch_size: 64
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+ lr: 0.001
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+ max_steps: 100000
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+ train_seed: 42
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+ val_freq: 2000
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+ ckpt_every_n_steps: 4000
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+ gradient_clip_val: 10
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+ gradient_accumulation_steps: 1
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+ loss_fn: mse
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+ devices: 1
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+ strategy: auto
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+ use_mfu: true
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+ mfu_kwargs:
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+ available_flops: 60000000000000.0
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+ use_backward: true
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+ logging_interval: 10
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+ window_size: 2
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+ cumulative_flops_use_backward: true
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+ wandb:
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+ entity: arcinstitute
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+ project: vci1
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+ local_wandb_dir: ./wandb_logs
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+ tags:
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+ - release
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+ - replogle
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+ name: rpe1
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+ output_dir: /large_storage/ctc/userspace/aadduri/release/replogle_st_X_hvg/fewshot
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+ use_wandb: true
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+ overwrite: false
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+ return_adatas: false
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+ pred_adata_path: null
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+ true_adata_path: null
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