| """ | |
| Input config for pipeline | |
| """ | |
| def config_file() -> dict: | |
| config = { | |
| "BERT_config": { | |
| "model_emb": 'bert', | |
| "model_option": { | |
| "PathologyEmoryPubMedBERT": { | |
| "model_folder":"models/higher_order_hierarchy/PathologyEmoryPubMedBERT/" | |
| }, | |
| "PathologyEmoryBERT": { | |
| "model_folder":"models/higher_order_hierarchy/PathologyEmoryBERT/" | |
| }, | |
| "ClinicalBERT": { | |
| "model_folder":"models/higher_order_hierarchy/ClinicalBERT/" | |
| }, | |
| "BlueBERT": { | |
| "model_folder":"models/higher_order_hierarchy/BlueBERT/" | |
| }, | |
| "BioBERT": { | |
| "model_folder":"models/higher_order_hierarchy/BioBERT/" | |
| }, | |
| "BERT": { | |
| "model_folder":"models/higher_order_hierarchy/BERT/" | |
| }, | |
| }, | |
| "max_seq_length": "64", | |
| "threshold_prediction":0.5, | |
| "classes": ['Invasive breast cancer-IBC','Non-breast cancer-NBC','In situ breast cancer-ISC', | |
| 'Borderline lesion-BLL','High risk lesion-HRL','Benign-B','Negative'], | |
| "worst_rank" : ['Invasive breast cancer-IBC', 'In situ breast cancer-ISC', 'High risk lesion-HRL', | |
| 'Borderline lesion-BLL','Benign-B','Non-breast cancer-NBC','Negative'] | |
| }, | |
| "ibc_config": { | |
| "model_option": { | |
| "single_tfidf": { | |
| "path_model":"models/all_labels_hierarchy/single_tfidf/classifiers", | |
| "model": "ibc_xgboost_classifier.pkl", | |
| "path_vectorizer":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "vectorizer":"vectorizer_all_branches.pkl", | |
| "path_bigrmas":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "bigrams":"best_bigrams.csv", | |
| "path_phrase_bigrams":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "phrase_bigrams" : "phrase_bigrams.pkl" | |
| }, | |
| "branch_tfidf": { | |
| "path_model":"models/all_labels_hierarchy/branch_tfidf/classifiers", | |
| "model": "ibc_xgboost_classifier.pkl", | |
| "path_vectorizer":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "vectorizer":"ibc_vectorizer.pkl", | |
| "path_bigrmas":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "bigrams":"best_bigrams.csv", | |
| "path_phrase_bigrams":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "phrase_bigrams" : "phrase_bigrams.pkl" | |
| } | |
| }, | |
| "classes": ['apocrine carcinoma','grade i','grade ii','grade iii','invasive ductal carcinoma','invasive lobular carcinoma','medullary carcinoma','metaplastic carcinoma','mucinous carcinoma','tubular carcinoma','lymph node - metastatic'] | |
| }, | |
| "isc_config": { | |
| "model_option": { | |
| "single_tfidf": { | |
| "path_model":"models/all_labels_hierarchy/single_tfidf/classifiers", | |
| "model": "isc_xgboost_classifier.pkl", | |
| "path_vectorizer":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "vectorizer":"vectorizer_all_branches.pkl", | |
| "path_bigrmas":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "bigrams":"best_bigrams.csv", | |
| "path_phrase_bigrams":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "phrase_bigrams" : "phrase_bigrams.pkl" | |
| }, | |
| "branch_tfidf": { | |
| "path_model":"models/all_labels_hierarchy/branch_tfidf/classifiers", | |
| "model": "isc_xgboost_classifier.pkl", | |
| "path_vectorizer":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "vectorizer":"isc_vectorizer.pkl", | |
| "path_bigrmas":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "bigrams":"best_bigrams.csv", | |
| "path_phrase_bigrams":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "phrase_bigrams" : "phrase_bigrams.pkl" | |
| } | |
| }, | |
| "classes": ['ductal carcinoma in situ','high','intermediate','intracystic papillary carcinoma','intraductal papillary carcinoma','low','pagets','fna - malignant'] | |
| }, | |
| "hrl_config": { | |
| "model_option": { | |
| "single_tfidf": { | |
| "path_model":"models/all_labels_hierarchy/single_tfidf/classifiers", | |
| "model": "hrl_xgboost_classifier.pkl", | |
| "path_vectorizer":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "vectorizer":"vectorizer_all_branches.pkl", | |
| "path_bigrmas":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "bigrams":"best_bigrams.csv", | |
| "path_phrase_bigrams":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "phrase_bigrams" : "phrase_bigrams.pkl" | |
| }, | |
| "branch_tfidf": { | |
| "path_model":"models/all_labels_hierarchy/branch_tfidf/classifiers", | |
| "model": "hrl_xgboost_classifier.pkl", | |
| "path_vectorizer":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "vectorizer":"hrl_vectorizer.pkl", | |
| "path_bigrmas":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "bigrams":"best_bigrams.csv", | |
| "path_phrase_bigrams":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "phrase_bigrams" : "phrase_bigrams.pkl" | |
| } | |
| }, | |
| "classes": ['atypical ductal hyperplasia','atypical lobular hyperplasia','atypical papilloma','columnar cell change with atypia','flat epithelial atypia','hyperplasia with atypia','intraductal papilloma','lobular carcinoma in situ','microscopic papilloma','radial scar'] | |
| }, | |
| "bll_config": { | |
| "model_option": { | |
| "single_tfidf": { | |
| "path_model":"models/all_labels_hierarchy/single_tfidf/classifiers", | |
| "model": "bll_xgboost_classifier.pkl", | |
| "path_vectorizer":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "vectorizer":"vectorizer_all_branches.pkl", | |
| "path_bigrmas":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "bigrams":"best_bigrams.csv", | |
| "path_phrase_bigrams":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "phrase_bigrams" : "phrase_bigrams.pkl" | |
| }, | |
| "branch_tfidf": { | |
| "path_model":"models/all_labels_hierarchy/branch_tfidf/classifiers", | |
| "model": "bll_xgboost_classifier.pkl", | |
| "path_vectorizer":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "vectorizer":"bll_vectorizer.pkl", | |
| "path_bigrmas":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "bigrams":"best_bigrams.csv", | |
| "path_phrase_bigrams":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "phrase_bigrams" : "phrase_bigrams.pkl" | |
| } | |
| }, | |
| "classes": ['atypical phyllodes', 'granular cell tumor', 'mucocele'] | |
| }, | |
| "benign_config": { | |
| "model_option": { | |
| "single_tfidf": { | |
| "path_model":"models/all_labels_hierarchy/single_tfidf/classifiers", | |
| "model": "benign_xgboost_classifier.pkl", | |
| "path_vectorizer":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "vectorizer":"vectorizer_all_branches.pkl", | |
| "path_bigrmas":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "bigrams":"best_bigrams.csv", | |
| "path_phrase_bigrams":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "phrase_bigrams" : "phrase_bigrams.pkl" | |
| }, | |
| "branch_tfidf": { | |
| "path_model":"models/all_labels_hierarchy/branch_tfidf/classifiers", | |
| "model": "benign_xgboost_classifier.pkl", | |
| "path_vectorizer":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "vectorizer":"benign_vectorizer.pkl", | |
| "path_bigrmas":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "bigrams":"best_bigrams.csv", | |
| "path_phrase_bigrams":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "phrase_bigrams" : "phrase_bigrams.pkl" | |
| } | |
| }, | |
| "classes": ['apocrine metaplasia','biopsy site changes','columnar cell change without atypia','cyst','excisional or post-surgical change','fat necrosis','fibroadenoma','fibroadenomatoid','fibrocystic disease','fibromatoses','fibrosis','hamartoma','hemangioma','lactational change','lymph node - benign','myofibroblastoma','myxoma','phyllodes','pseudoangiomatous stromal hyperplasia','sclerosing adenosis','usual ductal hyperplasia','fna - benign','seroma'] | |
| }, | |
| "nbc_config": { | |
| "model_option": { | |
| "single_tfidf": { | |
| "path_model":"models/all_labels_hierarchy/single_tfidf/classifiers", | |
| "model": "nbc_xgboost_classifier.pkl", | |
| "path_vectorizer":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "vectorizer":"vectorizer_all_branches.pkl", | |
| "path_bigrmas":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "bigrams":"best_bigrams.csv", | |
| "path_phrase_bigrams":"models/all_labels_hierarchy/single_tfidf/vectorizers", | |
| "phrase_bigrams" : "phrase_bigrams.pkl" | |
| }, | |
| "branch_tfidf": { | |
| "path_model":"models/all_labels_hierarchy/branch_tfidf/classifiers", | |
| "model": "nbc_xgboost_classifier.pkl", | |
| "path_vectorizer":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "vectorizer":"nbc_vectorizer.pkl", | |
| "path_bigrmas":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "bigrams":"best_bigrams.csv", | |
| "path_phrase_bigrams":"models/all_labels_hierarchy/branch_tfidf/vectorizers", | |
| "phrase_bigrams" : "phrase_bigrams.pkl" | |
| } | |
| }, | |
| "classes": ['lymphoma', 'malignant(sarcomas)', 'non-breast metastasis'] | |
| }, | |
| } | |
| return config | |
| if __name__ == '__main__': | |
| pass | |