File size: 2,293 Bytes
4f44389 cd43b57 4f44389 cd43b57 4f44389 cd43b57 4f44389 cd43b57 4f44389 cd43b57 4f44389 cd43b57 4f44389 cd43b57 4f44389 cd43b57 4f44389 cd43b57 4f44389 cd43b57 4f44389 cd43b57 4f44389 cd43b57 4f44389 cd43b57 4f44389 cd43b57 4f44389 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 |
data:
name: PerturbationDataModule
kwargs:
toml_config_path: /large_storage/ctc/userspace/aadduri/datasets/basak_tahoe/generalization.toml
embed_key: X_hvg
output_space: gene
pert_rep: onehot
basal_rep: sample
num_workers: 24
pin_memory: true
n_basal_samples: 1
basal_mapping_strategy: random
should_yield_control_cells: true
batch_col: plate
pert_col: drugname_drugconc
cell_type_key: cell_name
control_pert: DMSO_TF
map_controls: true
perturbation_features_file: null
store_raw_basal: false
int_counts: false
barcode: true
output_dir: null
debug: true
model:
name: PertSets
checkpoint: null
device: cuda
kwargs:
cell_set_len: 256
blur: 0.05
hidden_dim: 1440
loss: energy
confidence_head: false
n_encoder_layers: 4
n_decoder_layers: 4
predict_residual: true
softplus: true
freeze_pert: false
transformer_decoder: false
finetune_vci_decoder: false
residual_decoder: false
decoder_loss_weight: 1.0
batch_encoder: true
nb_decoder: false
mask_attn: false
use_effect_gating_token: false
use_basal_projection: false
distributional_loss: energy
init_from: null
transformer_backbone_key: llama
transformer_backbone_kwargs:
max_position_embeddings: 256
hidden_size: 1440
intermediate_size: 4416
num_hidden_layers: 4
num_attention_heads: 12
num_key_value_heads: 12
head_dim: 120
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
training:
wandb_track: false
weight_decay: 0.0005
batch_size: 64
lr: 0.0001
max_steps: 400000
train_seed: 42
val_freq: 4000
ckpt_every_n_steps: 4000
gradient_clip_val: 10
loss_fn: mse
devices: 1
strategy: auto
wandb:
entity: your_entity_name
project: state
local_wandb_dir: ./wandb_logs
tags:
- basak_tahoe
name: cs256_batch_encoder
output_dir: /large_storage/ctc/userspace/aadduri/preprint/basak_tahoe
use_wandb: true
overwrite: false
return_adatas: false
pred_adata_path: null
true_adata_path: null
|