File size: 929 Bytes
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seed: 42
report_to: "none"
dataset:
dataset: "ptm"
dataset_type: "csv"
dataset_loc: "protein_lm/dataset/ptm_labels.csv"
subsample_size: null
split_seed: 2
val_size: 100
test_size: 0
sequence_column_name: "ori_seq"
max_sequence_length: 1024
cache_dir: "protein_lm/dataset/cache/ptm"
training_arguments:
save_dir: "checkpoints/ptm-mamba"
num_train_epochs: 3000
lr: 2.0e-4
per_device_train_batch_size: 256 # 64 if 1 GPU
resume_from_checkpoint: null
use_esm: true
max_tokens_per_batch: 80000 # 80G GPU
sort_by_seq: true
sample_len_ascending: true
log_steps: 100
max_sequence_length: null
model: # default mamba 130M
model_type: "mamba" # ["mamba", "bidirectional_mamba"]
d_model: 768
n_layer: 24
vocab_size: null # will be set by tokenizer
ssm_cfg: {}
rms_norm: true
residual_in_fp32: true
fused_add_norm: true
esm_embed_dim: 1280
pretrained_checkpoint: null
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