├── .gitignore ├── LICENSE ├── README.md ├── downstream ├── structure │ ├── data.py │ ├── lm.py │ ├── predictor.py │ └── resnet.py ├── train_contact_map.py ├── train_crispr_off_target.py ├── train_crispr_on_target.py ├── train_degradation.py ├── train_distance_map.py ├── train_isoform.py ├── train_mean_ribosome_loading.py ├── train_modification.py ├── train_ncrna.py ├── train_programmable_rna_switches.py ├── train_secondary_structure.py ├── train_spliceai.py └── train_structural_score_imputation.py ├── images ├── exp1.png ├── exp2.png └── main.png ├── model ├── configuration_utils.py ├── modeling_auto.py ├── modeling_utils.py ├── rnabert │ ├── configuration_rnabert.py │ └── modeling_rnabert.py ├── rnafm │ ├── configuration_rnafm.py │ └── modeling_rnafm.py ├── rnalm │ ├── __init__.py │ ├── bert_padding.py │ ├── config │ │ ├── rnalm-6mer-alibi │ │ │ ├── config.json │ │ │ └── vocab.txt │ │ ├── rnalm-6mer-ape │ │ │ ├── config.json │ │ │ └── vocab.txt │ │ ├── rnalm-6mer-rope │ │ │ ├── config.json │ │ │ └── vocab.txt │ │ ├── rnalm-bpe-alibi │ │ │ ├── config.json │ │ │ └── vocab.txt │ │ ├── rnalm-bpe-ape │ │ │ ├── config.json │ │ │ └── vocab.txt │ │ ├── rnalm-bpe-rope │ │ │ ├── config.json │ │ │ └── vocab.txt │ │ ├── rnalm-non-overlap-alibi │ │ │ ├── config.json │ │ │ └── vocab.txt │ │ ├── rnalm-non-overlap-ape │ │ │ ├── config.json │ │ │ └── vocab.txt │ │ ├── rnalm-non-overlap-rope │ │ │ ├── config.json │ │ │ └── vocab.txt │ │ ├── rnalm-single-alibi │ │ │ ├── config.json │ │ │ └── vocab.txt │ │ ├── rnalm-single-ape │ │ │ ├── config.json │ │ │ └── vocab.txt │ │ └── rnalm-single-rope │ │ │ ├── config.json │ │ │ └── vocab.txt │ ├── flash_attn_triton.py │ ├── modeling_rnalm.py │ ├── rnalm_config.py │ └── rnalm_tokenizer.py ├── rnamsm │ ├── configuration_rnamsm.py │ └── modeling_rnamsm.py ├── splicebert │ ├── configuration_splicebert.py │ └── modeling_splicebert.py ├── utrbert │ ├── configuration_utrbert.py │ └── modeling_utrbert.py └── utrlm │ ├── configuration_utrlm.py │ └── modeling_utrlm.py ├── requirements.txt ├── scripts ├── BEACON-B │ └── all_task.sh └── opensource │ └── UTR-LM-mrl │ └── ncrna.sh └── tokenizer ├── tokenization_opensource.py ├── utils.py └── vocab.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/terry-r123/RNABenchmark/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/terry-r123/RNABenchmark/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/terry-r123/RNABenchmark/HEAD/README.md -------------------------------------------------------------------------------- /downstream/structure/data.py: 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