|
{ |
|
"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_ExprRefined30", |
|
"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_30_ExR/best_model/", |
|
"special_token_th": 42, |
|
"mask_all": false, |
|
"sw_aa_size": 30, |
|
"eval_type": "model", |
|
"model_type": "COBaBExRi", |
|
"cai_query_species": "S_cerevisiae", |
|
"outdir": "/mount/COnTRA/models/Finetuned2Steps_homologs_30_ExR/best_model/", |
|
"outfile": "model_eval_mimic.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 |
|
} |