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### Dataset
# ESMFold & AlphaFold2: DeepLocBinary DeepLocMulti MetalIonBinding EC Thermostability
# ESMFold: DeepSol DeepSoluE
# No structure: FLIP_AAV FLIP_GB1
### Protein Language Model (PLM)
# facebook: esm2_t30_150M_UR50D esm2_t33_650M_UR50D esm2_t36_3B_UR50D
# RostLab: prot_bert prot_bert_bfd prot_t5_xl_uniref50 prot_t5_xl_bfd ankh-base ankh-large
# train with batch token
dataset=DeepLocBinary
pdb_type=AlphaFold2
plm_model=esm2_t30_150M_UR50D
lr=5e-4
python src/train.py \
--plm_model facebook/$plm_model \
--dataset_config data/$dataset/"$dataset"_"$pdb_type"_HF.json \
--learning_rate $lr \
--gradient_accumulation_steps 8 \
--batch_token 12000 \
--output_dir debug/$dataset/$plm_model \
--output_model_name af2_lr"$lr"_bt12k_ga8.pt
# train with batch_size
dataset=DeepLocBinary
pdb_type=AlphaFold2
plm_model=esm2_t30_150M_UR50D
lr=5e-4
python src/train.py \
--plm_model facebook/$plm_model \
--dataset_config data/$dataset/"$dataset"_"$pdb_type"_HF.json \
--learning_rate $lr \
--gradient_accumulation_steps 8 \
--batch_size 12 \
--max_seq_len 1024 \
--output_dir debug/$dataset/$plm_model \
--output_model_name af2_lr"$lr"_bs12_ga8.pt |