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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 | |
| # 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 |