├── .gitignore ├── LICENSE ├── README.md ├── checkpoint ├── ERNIE-RNA_3d_clossness_checkpoint │ └── ERNIE-RNA_3D_closeness_attnmap_dp16_finetuned.txt ├── ERNIE-RNA_UTR_MRL_checkpoint │ ├── ERNIE-RNA_UTR_MRL_checkpoint.txt │ └── scaler.save ├── ERNIE-RNA_checkpoint │ └── ERNIE-RNA_checkpoint.txt └── ERNIE-RNA_ss_prediction_checkpoint │ └── ERNIE-RNA_ss_prediction_checkpoint.txt ├── data ├── MRL_data │ └── seqs.fasta ├── ss_prediction │ ├── bpRNA-1m_testseqs.fasta │ ├── bpRNA-new_testseqs.fasta │ └── rna3db_testseqs.fasta └── test_seqs.txt ├── docs └── model.png ├── environment.yml ├── environment_CPU_mac.yml ├── environment_CPU_windows.yml ├── extract_embedding.py ├── predict_3d_clossness.py ├── predict_MRL.py ├── predict_ss_rna.py ├── results ├── ernie_rna_3d_clossness │ ├── 1gax_D_closeness_pred.npy │ ├── 5gup_EC_closeness_pred.npy │ ├── closeness_plots │ │ ├── 1gax_D_closeness_pred.png │ │ └── 5gup_EC_closeness_pred.png │ └── example.fasta ├── ernie_rna_representations │ └── test_seqs │ │ ├── all_embedding.npy │ │ ├── attnmap.npy │ │ └── cls_embedding.npy ├── ernie_rna_ss_prediction │ ├── bpRNA-1m_test_results │ │ ├── test_seq_1_finetune_prediction.ct │ │ ├── test_seq_1_zeroshot_prediction.ct │ │ ├── test_seq_2_finetune_prediction.ct │ │ └── test_seq_2_zeroshot_prediction.ct │ ├── bpRNA-new_test_results │ │ ├── URS0000D6861F_12908_1_pemk_RF02913_finetune_prediction.ct │ │ └── URS0000D6861F_12908_1_pemk_RF02913_zeroshot_prediction.ct │ └── rna3db_test_results │ │ ├── 4yb1_R_finetune_prediction.ct │ │ └── 4yb1_R_zeroshot_prediction.ct └── ernie_rna_utr_mrl │ └── prediction.txt └── src ├── dict └── dict.txt ├── downstream_heads ├── __init__.py └── closeness_model.py ├── ernie_rna ├── __init__.py ├── criterions │ ├── __init__.py │ └── ernie_rna.py ├── models │ ├── __init__.py │ ├── ernie_rna.py │ ├── ernie_rna_utils.py │ └── prediction.py └── tasks │ ├── __init__.py │ └── ernie_rna.py └── utils.py /.gitignore: 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