all_presets_with_paths = { # ESM2 models (from esm2.py) 'ESM2-8': 'Synthyra/ESM2-8M', 'ESM2-35': 'Synthyra/ESM2-35M', 'ESM2-150': 'Synthyra/ESM2-150M', 'ESM2-650': 'Synthyra/ESM2-650M', 'ESM2-3B': 'Synthyra/ESM2-3B', # DSM models (from esm2.py) 'DSM-150': 'GleghornLab/ESM_diff_150', 'DSM-650': 'GleghornLab/ESM_diff_650', 'DSM-PPI': 'Synthyra/DSM_ppi_full', # ESMC models (from esmc.py) 'ESMC-300': 'Synthyra/ESMplusplus_small', 'ESMC-600': 'Synthyra/ESMplusplus_large', # E1 models (from e1.py) 'E1-150': 'Synthyra/Profluent-E1-150M', 'E1-300': 'Synthyra/Profluent-E1-300M', 'E1-600': 'Synthyra/Profluent-E1-600M', # ProtBert models (from protbert.py) 'ProtBert': 'Rostlab/prot_bert', 'ProtBert-BFD': 'Rostlab/prot_bert_bfd', # ProtT5 models (from prott5.py) 'ProtT5': 'Rostlab/prot_t5_xl_half_uniref50-enc', 'ProtT5-XL-UniRef50-full-prec': 'Rostlab/prot_t5_xl_uniref50', 'ProtT5-XXL-UniRef50': 'Rostlab/prot_t5_xxl_uniref50', 'ProtT5-XL-BFD': 'Rostlab/prot_t5_xl_bfd', 'ProtT5-XXL-BFD': 'Rostlab/prot_t5_xxl_bfd', # ANKH models (from ankh.py) 'ANKH-Base': 'Synthyra/ANKH_base', 'ANKH-Large': 'Synthyra/ANKH_large', 'ANKH2-Large': 'Synthyra/ANKH2_large', # GLM2 models (from glm.py) 'GLM2-150': 'tattabio/gLM2_150M', 'GLM2-650': 'tattabio/gLM2_650M', 'GLM2-GAIA': 'tattabio/gLM2_650M_embed', # DPLM models (from dplm.py) 'DPLM-150': 'airkingbd/dplm_150m', 'DPLM-650': 'airkingbd/dplm_650m', 'DPLM-3B': 'airkingbd/dplm_3b', # DPLM2 models (from dplm2.py) 'DPLM2-150': 'airkingbd/dplm2_150m', 'DPLM2-650': 'airkingbd/dplm2_650m', 'DPLM2-3B': 'airkingbd/dplm2_3b', # AMPLIFY models (from amplify.py) 'AMPLIFY-120': 'GleghornLab/AMPLIFY_120M', 'AMPLIFY-350': 'GleghornLab/AMPLIFY_350M', # Random models (from random.py) 'Random': 'random', 'Random-Transformer': 'facebook/esm2_t12_35M_UR50D', 'Random-ESM2-8': 'facebook/esm2_t6_8M_UR50D', 'Random-ESM2-35': 'facebook/esm2_t12_35M_UR50D', 'Random-ESM2-150': 'facebook/esm2_t30_150M_UR50D', 'Random-ESM2-650': 'facebook/esm2_t36_650M_UR50D', # OneHot models (from one_hot.py) - internal implementations 'OneHot-Protein': 'OneHot-Protein', 'OneHot-DNA': 'OneHot-DNA', 'OneHot-RNA': 'OneHot-RNA', 'OneHot-Codon': 'OneHot-Codon', # Vec2Vec models (from vec2vec.py) 'vec2vec-ESM2-8-ESM2-35': 'Synthyra/ESM2-8-ESM2-35-sequence-sequence', 'vec2vec-ESM2-8-ESM2-150': 'Synthyra/ESM2-8-ESM2-150-sequence-sequence', 'vec2vec-ESM2-8-ESM2-650': 'Synthyra/ESM2-8-ESM2-650-sequence-sequence', 'vec2vec-ESM2-8-ESM2-3B': 'Synthyra/ESM2-8-ESM2-3B-sequence-sequence', 'vec2vec-ESM2-35-ESM2-150': 'Synthyra/ESM2-35-ESM2-150-sequence-sequence', 'vec2vec-ESM2-35-ESM2-650': 'Synthyra/ESM2-35-ESM2-650-sequence-sequence', 'vec2vec-ESM2-35-ESM2-3B': 'Synthyra/ESM2-35-ESM2-3B-sequence-sequence', 'vec2vec-ESM2-150-ESM2-650': 'Synthyra/ESM2-150-ESM2-650-sequence-sequence', 'vec2vec-ESM2-150-ESM2-3B': 'Synthyra/ESM2-150-ESM2-3B-sequence-sequence', 'vec2vec-ESM2-650-ESM2-3B': 'Synthyra/ESM2-650-ESM2-3B-sequence-sequence', # CaLM models (from calm.py) 'CaLM': 'multimolecule/calm', } currently_supported_models = [ 'ESM2-8', 'ESM2-35', 'ESM2-150', 'ESM2-650', 'ESM2-3B', 'Random', 'Random-Transformer', 'Random-ESM2-8', 'Random-ESM2-35', # same as Random-Transformer 'Random-ESM2-150', 'Random-ESM2-650', 'ESMC-300', 'ESMC-600', 'E1-150', 'E1-300', 'E1-600', 'ProtBert', 'ProtBert-BFD', 'ProtT5', 'ProtT5-XL-UniRef50-full-prec', 'ProtT5-XXL-UniRef50', 'ProtT5-XL-BFD', 'ProtT5-XXL-BFD', 'ANKH-Base', 'ANKH-Large', 'ANKH2-Large', 'GLM2-150', 'GLM2-650', 'GLM2-GAIA', 'DPLM-150', 'DPLM-650', 'DPLM-3B', 'DPLM2-150', 'DPLM2-650', 'DPLM2-3B', 'DSM-150', 'DSM-650', 'DSM-PPI', 'OneHot-Protein', 'OneHot-DNA', 'OneHot-RNA', 'OneHot-Codon', 'AMPLIFY-120', 'AMPLIFY-350', 'CaLM', ] standard_models = [ 'AMPLIFY-120', 'AMPLIFY-350', 'GLM2-150', 'GLM2-650', 'GLM2-GAIA', 'DSM-150', 'DSM-650', 'DSM-PPI', 'E1-150', 'E1-300', 'E1-600', 'DSM-150', 'DSM-650', 'DSM-PPI', 'ESM2-8', 'ESM2-35', 'ESM2-150', 'ESM2-650', 'ESM2-3B', 'ESMC-300', 'ESMC-600', 'ProtBert-BFD', 'ProtT5', 'ANKH-Base', 'ANKH-Large', 'ANKH2-Large', 'DPLM-150', 'DPLM-650', 'DPLM-3B', 'DPLM2-150', 'DPLM2-650', 'DPLM2-3B', 'Random', 'Random-Transformer', 'OneHot-Protein', ] experimental_models = []