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{ |
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"Description": "This is a pre-training configuration for codon optimization model based on BART language model.", |
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"project_name": "COnTRA_SCPECBS3_wintest", |
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"dataset_path": "/mount/COnTRA/data/datasets/processed_data_SCPECBS3/homologs/SCPECBS3_SCPECBS3_ExprRefined30", |
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"tokenizer_path": "/mount/COnTRA/tokenizers/contra_tokenizer_gen_exprrefined", |
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"cai_refference_path": "/mount/COnTRA/data/datasets/processed_data_SCPECBS3/S_cerevisiae/S_cerevisiae.0.nt.fasta", |
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"checkpoint_flag": true, |
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"checkpoint_path": "/mount/COnTRA/models/Finetuned_oSiS_30_ExR/best_model/", |
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"special_token_th": 42, |
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"mask_all": true, |
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"sw_aa_size": 30, |
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"eval_type": "model", |
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"model_type": "COBaBExRi", |
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"cai_query_species": "S_cerevisiae", |
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"outdir": "/mount/COnTRA/models/Finetuned_oSiS_30_ExR/best_model/", |
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"outfile": "mask_model_eval.csv", |
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"out_dict": [ |
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"prot_len", |
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"num_of_correct_predicted_codons", |
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"accuracy", |
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"cross_entropy_loss", |
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"entropy", |
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"query_codons", |
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"subject_codons", |
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"pred_codons" |
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], |
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"orig_dict": [ |
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"qseqid", |
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"sseqid", |
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"query_species", |
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"subject_species", |
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"pident", |
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"length", |
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"mismatch", |
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"gapopen", |
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"qstart", |
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"qend", |
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"sstart", |
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"send", |
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"evalue", |
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"bitscore" |
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], |
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"debug": false |
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} |