| { |
| "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_ExprRefined", |
| "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/Finetuned2Steps_homologs_75_ExR/best_model/", |
| "special_token_th": 42, |
| "mask_all": true, |
| "sw_aa_size": 75, |
| "eval_type": "model", |
| "model_type": "COBaBExRi", |
| "cai_query_species": "S_cerevisiae", |
| "outdir": "/mount/COnTRA/models/Finetuned2Steps_homologs_75_ExR/best_model/mask/", |
| "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 |
| } |
