├── .gitignore ├── .idea ├── .gitignore ├── inspectionProfiles │ └── Project_Default.xml ├── misc.xml ├── modules.xml └── vcs.xml ├── LICENSE ├── LucaOneTasks.iml ├── NOTICE ├── README.md ├── README_v1.md ├── README_zh.md ├── README_zh_v1.md ├── config ├── .DS_Store ├── luca_base │ └── luca_base_config.json ├── lucappi │ └── ppi_config.json └── lucappi2 │ └── ppi_config.json ├── data └── test_data │ ├── gene │ ├── test_gene.csv │ └── test_gene.fasta │ └── prot │ ├── test_prot.csv │ └── test_prot.fasta ├── dataset └── README.md ├── pics ├── DownstreamNetworksAndMetrics.png ├── LucaTeam.jpg └── downstream_networds_and_tasks.png ├── requirements.txt ├── requirements_dnabert2.txt ├── requirements_full.txt ├── src ├── .DS_Store ├── args.py ├── batch_converter.py ├── common │ ├── .DS_Store │ ├── alphabet.py │ ├── alphabet_atom.py │ ├── classification_loss.py │ ├── cross_transformer.py │ ├── loss.py │ ├── luca_base.py │ ├── masked_loss.py │ ├── metrics.py │ ├── model_config.py │ ├── modeling_bert.py │ ├── modeling_utils.py │ ├── multi_label_metrics.py │ ├── multi_task_loss.py │ ├── pooling.py │ └── regression_loss.py ├── encoder.py ├── encoder_v1.py ├── evaluator.py ├── file_operator.py ├── llm │ ├── .DS_Store │ ├── README.md │ ├── README_zh.md │ ├── dnabert2 │ │ ├── .DS_Store │ │ └── inference_embedding.py │ ├── dnaberts │ │ ├── .DS_Store │ │ └── inference_embedding.py │ ├── esm │ │ ├── .DS_Store │ │ └── predict_embedding.py │ └── lucagplm │ │ ├── .DS_Store │ │ ├── common │ │ ├── .DS_Store │ │ ├── classification_loss.py │ │ ├── loss.py │ │ ├── masked_loss.py │ │ ├── metrics.py │ │ ├── multi_label_metrics.py │ │ ├── multi_task_loss.py │ │ ├── pairwise_loss.py │ │ ├── pairwise_metrics.py │ │ └── regression_loss.py │ │ ├── get_embedding.py │ │ ├── get_embedding_v1.py │ │ ├── v0_2 │ │ ├── .DS_Store │ │ ├── alphabet.py │ │ ├── lucaone_gplm.py │ │ ├── lucaone_gplm_config.py │ │ ├── model_utils.py │ │ ├── modeling_gplm.py │ │ └── pooling.py │ │ └── v2_0 │ │ ├── .DS_Store │ │ ├── alphabet.py │ │ ├── lucaone_gplm.py │ │ ├── lucaone_gplm_config.py │ │ ├── model_utils.py │ │ ├── modeling_gplm.py │ │ └── pooling.py ├── multi_files_stream_dataloader.py ├── ppi │ ├── .DS_Store │ ├── README.md │ └── models │ │ ├── .DS_Store │ │ ├── LucaPPI.py │ │ └── LucaPPI2.py ├── predict_v1.py ├── predict_v1_new.py ├── predict_v2.py ├── predict_v2_new.py ├── prediction.sh ├── run.py ├── tester.py ├── trainer.py ├── training │ ├── .DS_Store │ ├── downstream_tasks │ │ ├── run_CentralDogma_dnabert2_esm2_linear.sh │ │ ├── run_CentralDogma_lucaone_linear.sh │ │ ├── run_CentralDogma_lucaone_separated_linear.sh │ │ ├── run_CentralDogma_onehot_linear.sh │ │ ├── run_CentralDogma_onehot_transformer.sh │ │ ├── run_CentralDogma_transformer.sh │ │ ├── run_GenusTax_dnabert2_linear.sh │ │ ├── run_GenusTax_dnabert2_luca_base.sh │ │ ├── run_GenusTax_lucaone_linear.sh │ │ ├── run_GenusTax_lucaone_luca_base.sh │ │ ├── run_InfA_dnabert2_linear.sh │ │ ├── run_InfA_dnabert2_lucappi.sh │ │ ├── run_InfA_lucaone_linear.sh │ │ ├── run_InfA_lucaone_lucappi.sh │ │ ├── run_PPI_esm2_linear.sh │ │ ├── run_PPI_esm2_lucappi.sh │ │ ├── run_PPI_lucaone_linear.sh │ │ ├── run_PPI_lucaone_lucappi.sh │ │ ├── run_ProtLoc_esm2_linear.sh │ │ ├── run_ProtLoc_esm2_luca_base.sh │ │ ├── run_ProtLoc_lucaone_linear.sh │ │ ├── run_ProtLoc_lucaone_luca_base.sh │ │ ├── run_ProtStab_esm2_linear.sh │ │ ├── run_ProtStab_esm2_luca_base.sh │ │ ├── run_ProtStab_lucaone_linear.sh │ │ ├── run_ProtStab_lucaone_luca_base.sh │ │ ├── run_SpeciesTax_dnabert2_linear.sh │ │ ├── run_SpeciesTax_dnabert2_luca_base.sh │ │ ├── run_SpeciesTax_lucaone_linear.sh │ │ ├── run_SpeciesTax_lucaone_luca_base.sh │ │ ├── run_SupKTax_dnabert2_linear.sh │ │ ├── run_SupKTax_dnabert2_luca_base.sh │ │ ├── run_SupKTax_lucaone_linear.sh │ │ ├── run_SupKTax_lucaone_luca_base.sh │ │ ├── run_ncRNAFam_dnabert2_linear.sh │ │ ├── run_ncRNAFam_dnabert2_luca_base.sh │ │ ├── run_ncRNAFam_lucaone_linear.sh │ │ ├── run_ncRNAFam_lucaone_luca_base.sh │ │ ├── run_ncRPI_dnabert2_esm2_linear.sh │ │ ├── run_ncRPI_dnabert2_esm2_lucappi2.sh │ │ ├── run_ncRPI_lucaone_linear.sh │ │ └── run_ncRPI_lucaone_lucappi2.sh │ ├── downstream_tasks_v1 │ │ ├── run_CentralDogma_dnabert2_esm2_linear.sh │ │ ├── run_CentralDogma_lucaone_linear.sh │ │ ├── run_CentralDogma_lucaone_separated_linear.sh │ │ ├── run_CentralDogma_onehot_linear.sh │ │ ├── run_CentralDogma_onehot_transformer.sh │ │ ├── run_CentralDogma_transformer.sh │ │ ├── run_GenusTax_dnabert2_linear.sh │ │ ├── run_GenusTax_dnabert2_luca_base.sh │ │ ├── run_GenusTax_lucaone_linear.sh │ │ ├── run_GenusTax_lucaone_luca_base.sh │ │ ├── run_InfA_dnabert2_linear.sh │ │ ├── run_InfA_dnabert2_lucappi.sh │ │ ├── run_InfA_lucaone_linear.sh │ │ ├── run_InfA_lucaone_lucappi.sh │ │ ├── run_PPI_esm2_linear.sh │ │ ├── run_PPI_esm2_lucappi.sh │ │ ├── run_PPI_lucaone_linear.sh │ │ ├── run_PPI_lucaone_lucappi.sh │ │ ├── run_ProtLoc_esm2_linear.sh │ │ ├── run_ProtLoc_esm2_luca_base.sh │ │ ├── run_ProtLoc_lucaone_linear.sh │ │ ├── run_ProtLoc_lucaone_luca_base.sh │ │ ├── run_ProtStab_esm2_linear.sh │ │ ├── run_ProtStab_esm2_luca_base.sh │ │ ├── run_ProtStab_lucaone_linear.sh │ │ ├── run_ProtStab_lucaone_luca_base.sh │ │ ├── run_SpeciesTax_dnabert2_linear.sh │ │ ├── run_SpeciesTax_dnabert2_luca_base.sh │ │ ├── run_SpeciesTax_lucaone_linear.sh │ │ ├── run_SpeciesTax_lucaone_luca_base.sh │ │ ├── run_SupKTax_dnabert2_linear.sh │ │ ├── run_SupKTax_dnabert2_luca_base.sh │ │ ├── run_SupKTax_lucaone_linear.sh │ │ ├── run_SupKTax_lucaone_luca_base.sh │ │ ├── run_ncRNAFam_dnabert2_linear.sh │ │ ├── run_ncRNAFam_dnabert2_luca_base.sh │ │ ├── run_ncRNAFam_lucaone_linear.sh │ │ ├── run_ncRNAFam_lucaone_luca_base.sh │ │ ├── run_ncRPI_dnabert2_esm2_linear.sh │ │ ├── run_ncRPI_dnabert2_esm2_lucappi2.sh │ │ ├── run_ncRPI_lucaone_linear.sh │ │ └── run_ncRPI_lucaone_lucappi2.sh │ ├── lucaone │ │ ├── run_CentralDogma_lucaone_linear.sh │ │ ├── run_GenusTax_lucaone_luca_base.sh │ │ ├── run_InfA_lucaone_linear.sh │ │ ├── run_PPI_lucaone_linear.sh │ │ ├── run_ProtLoc_lucaone_linear.sh │ │ ├── run_ProtStab_lucaone_luca_base.sh │ │ ├── run_SpeciesTax_lucaone_luca_base.sh │ │ ├── run_SupKTax_lucaone_luca_base.sh │ │ ├── run_ncRNAFam_lucaone_luca_base.sh │ │ ├── run_ncRPI_lucaone_linear.sh │ │ └── test │ │ │ ├── run_test_lucaone_linear.sh │ │ │ └── run_test_lucaone_linear_2_gpu.sh │ ├── lucaone_separated │ │ └── run_CentralDogma_lucaone_separated_linear.sh │ ├── lucaone_separated_v1 │ │ └── run_CentralDogma_lucaone_separated_linear.sh │ └── lucaone_v1 │ │ ├── run_CentralDogma_lucaone_linear.sh │ │ ├── run_CentralDogma_lucaone_separated_linear.sh │ │ ├── run_GenusTax_lucaone_luca_base.sh │ │ ├── run_InfA_lucaone_linear.sh │ │ ├── run_PPI_lucaone_linear.sh │ │ ├── run_ProtLoc_lucaone_linear.sh │ │ ├── run_ProtStab_lucaone_luca_base.sh │ │ ├── run_SpeciesTax_lucaone_luca_base.sh │ │ ├── run_SupKTax_lucaone_luca_base.sh │ │ ├── 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