| { | |
| "Description": "This is a pre-training configuration for codon optimization model based on BART language model.", | |
| "project_name": "COnTRA_SCPECBS3_wintest", | |
| "dataset_path": "/mount/COnTRA/data/datasets/processed_data_SCPECBS3/homologs/SCPECBS3_SCPECBS3_ExprRefined50", | |
| "tokenizer_path": "/mount/COnTRA/tokenizers/contra_tokenizer_gen_exprrefined", | |
| "cai_refference_path": "/mount/COnTRA/data/datasets/processed_data_SCPECBS3/S_cerevisiae/S_cerevisiae.0.nt.fasta", | |
| "checkpoint_flag": true, | |
| "checkpoint_path": "/mount/COnTRA/models/Finetuned_oSiS_50_ExR/best_model/", | |
| "special_token_th": 42, | |
| "mask_all": true, | |
| "sw_aa_size": 50, | |
| "eval_type": "model", | |
| "model_type": "COBaBExRi", | |
| "cai_query_species": "S_cerevisiae", | |
| "outdir": "/mount/COnTRA/models/Finetuned_oSiS_50_ExR/best_model/", | |
| "outfile": "mask_model_eval.csv", | |
| "out_dict": [ | |
| "prot_len", | |
| "num_of_correct_predicted_codons", | |
| "accuracy", | |
| "cross_entropy_loss", | |
| "entropy", | |
| "query_codons", | |
| "subject_codons", | |
| "pred_codons" | |
| ], | |
| "orig_dict": [ | |
| "qseqid", | |
| "sseqid", | |
| "query_species", | |
| "subject_species", | |
| "pident", | |
| "length", | |
| "mismatch", | |
| "gapopen", | |
| "qstart", | |
| "qend", | |
| "sstart", | |
| "send", | |
| "evalue", | |
| "bitscore" | |
| ], | |
| "debug": false | |
| } |