|
|
|
|
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seed_everything: 42 |
|
|
trainer: |
|
|
accelerator: auto |
|
|
strategy: |
|
|
class_path: lightning.pytorch.strategies.DDPStrategy |
|
|
init_args: |
|
|
find_unused_parameters: true |
|
|
devices: auto |
|
|
num_nodes: 1 |
|
|
precision: 32 |
|
|
logger: |
|
|
class_path: lightning.pytorch.loggers.WandbLogger |
|
|
init_args: |
|
|
name: isoform_expression |
|
|
save_dir: logs |
|
|
project: rna_tasks |
|
|
callbacks: |
|
|
- class_path: lightning.pytorch.callbacks.ModelCheckpoint |
|
|
init_args: |
|
|
dirpath: logs/ |
|
|
filename: best_val:{step}-{val_spearman:.3f}-{val_r2:.3f} |
|
|
monitor: val_spearman |
|
|
save_last: true |
|
|
save_top_k: 1 |
|
|
mode: max |
|
|
every_n_train_steps: 500 |
|
|
every_n_epochs: null |
|
|
save_on_train_epoch_end: true |
|
|
max_epochs: 3 |
|
|
max_steps: -1 |
|
|
val_check_interval: 499 |
|
|
check_val_every_n_epoch: null |
|
|
log_every_n_steps: 1 |
|
|
accumulate_grad_batches: 1 |
|
|
gradient_clip_val: 0.1 |
|
|
gradient_clip_algorithm: null |
|
|
default_root_dir: logs |
|
|
model: |
|
|
class_path: modelgenerator.tasks.MMSequenceRegression |
|
|
init_args: |
|
|
backbone: |
|
|
class_path: modelgenerator.backbones.enformer |
|
|
init_args: |
|
|
max_length: 196_608 |
|
|
frozen: false |
|
|
backbone1: |
|
|
class_path: modelgenerator.backbones.aido_rna_1b600m_cds |
|
|
init_args: |
|
|
max_length: 1024 |
|
|
frozen: false |
|
|
use_peft: true |
|
|
save_peft_only: true |
|
|
lora_r: 32 |
|
|
lora_alpha: 64 |
|
|
lora_dropout: 0.1 |
|
|
lora_target_modules: |
|
|
- query |
|
|
- value |
|
|
config_overwrites: |
|
|
hidden_dropout_prob: 0 |
|
|
attention_probs_dropout_prob: 0 |
|
|
model_init_args: null |
|
|
backbone2: |
|
|
class_path: modelgenerator.backbones.esm2_150m |
|
|
init_args: |
|
|
max_length: 1024 |
|
|
frozen: false |
|
|
use_peft: true |
|
|
save_peft_only: true |
|
|
lora_r: 32 |
|
|
lora_alpha: 64 |
|
|
lora_dropout: 0.1 |
|
|
lora_target_modules: |
|
|
- query |
|
|
- value |
|
|
config_overwrites: |
|
|
hidden_dropout_prob: 0 |
|
|
attention_probs_dropout_prob: 0 |
|
|
model_init_args: null |
|
|
backbone_order: |
|
|
- dna_seq |
|
|
- rna_seq |
|
|
- protein_seq |
|
|
adapter: |
|
|
class_path: modelgenerator.adapters.fusion.MMFusionTokenAdapter |
|
|
init_args: |
|
|
fusion: |
|
|
class_path: modelgenerator.adapters.fusion.ConcatFusion |
|
|
init_args: |
|
|
project_size: 1024 |
|
|
pooling: mean_pooling |
|
|
adapter: |
|
|
class_path: modelgenerator.adapters.MLPAdapter |
|
|
init_args: |
|
|
hidden_sizes: |
|
|
- 1024 |
|
|
bias: true |
|
|
dropout: 0.1 |
|
|
dropout_in_middle: false |
|
|
num_outputs: 30 |
|
|
optimizer: |
|
|
class_path: torch.optim.AdamW |
|
|
init_args: |
|
|
lr: 1e-4 |
|
|
betas: |
|
|
- 0.9 |
|
|
- 0.999 |
|
|
eps: 1.0e-08 |
|
|
weight_decay: 0.01 |
|
|
amsgrad: false |
|
|
maximize: false |
|
|
foreach: null |
|
|
capturable: false |
|
|
differentiable: false |
|
|
fused: null |
|
|
lr_scheduler: |
|
|
class_path: modelgenerator.lr_schedulers.CosineWithWarmup |
|
|
init_args: |
|
|
warmup_ratio: 0.01 |
|
|
num_warmup_steps: null |
|
|
last_epoch: -1 |
|
|
verbose: deprecated |
|
|
use_legacy_adapter: false |
|
|
strict_loading: true |
|
|
reset_optimizer_states: false |
|
|
data: |
|
|
class_path: modelgenerator.data.IsoformExpression |
|
|
init_args: |
|
|
path: genbio-ai/transcript_isoform_expression_prediction |
|
|
config_name: null |
|
|
valid_split_name: valid |
|
|
train_split_files: |
|
|
- train_*.tsv |
|
|
valid_split_files: |
|
|
- validation.tsv |
|
|
test_split_files: |
|
|
- test.tsv |
|
|
x_col: |
|
|
- rna_seq |
|
|
- dna_seq |
|
|
- protein_seq |
|
|
normalize: true |
|
|
random_seed: 42 |
|
|
batch_size: 2 |
|
|
shuffle: true |
|
|
sampler: null |
|
|
num_workers: 0 |
|
|
pin_memory: true |
|
|
persistent_workers: false |
|
|
cv_num_folds: 1 |
|
|
cv_test_fold_id: 0 |
|
|
cv_enable_val_fold: true |
|
|
cv_fold_id_col: null |
|
|
ckpt_path: null |
|
|
|
