### 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 # ESM model target_modules name: query key value # Bert_base(prot_bert) model target_modules name: query key value # T5_base(ankh, t5) model target_modules name: q k v export HF_ENDPOINT=https://hf-mirror.com dataset=eSOL pdb_type=ESMFold pooling_method=mean plm_source=model_ckpt plm_model=prot_t5_xl output_root=ckpt lr=5e-4 eval_method=plm-qlora test_result_dir=ckpt/debug_test/eSOL/test_res problem_type=regression num_labels=1 # python src/eval.py \ --plm_model $plm_source/$plm_model \ --dataset_config data/$dataset/"$dataset"_"$pdb_type"_HF.json \ --batch_token 12000 \ --output_root $output_root \ --output_dir debug_test/$dataset/$plm_model \ --output_model_name "$eval_method"_ESMFold_lr5e-4_bt12k_ga8.pt \ --eval_method $eval_method \ --test_result_dir $test_result_dir \ --problem_type $problem_type \ --metrics spearman_corr \ --pooling_method $pooling_method \ --num_labels $num_labels