├── .gitignore ├── README.md ├── cfgs └── cfg0.yaml ├── execute_training_cfgs.sh ├── helper_fns ├── __pycache__ │ ├── incorrect_annotations.cpython-39.pyc │ ├── load.cpython-39.pyc │ ├── scoring.cpython-39.pyc │ ├── split_data.cpython-39.pyc │ └── utils.cpython-39.pyc ├── additional_labels_pn.py ├── incorrect_annotations.py ├── load.py ├── load_split_data.py ├── scoring.py ├── split_data.py └── utils.py ├── imgs ├── annotated_text.png └── visualize_ner.png ├── inference.ipynb ├── input ├── deberta-v2-3-fast-tokenizer │ └── transformers__init__.py ├── microsoft │ └── deberta-v3-large │ │ ├── config.json │ │ └── tokenizer_config.json ├── nbme-2wbvmzdp │ └── 2wbvmzdp_13kelj6x │ │ ├── config.json │ │ ├── config.yaml │ │ └── inf_output_config.yaml └── nbme-score-clinical-patient-notes │ ├── features.csv │ └── sample_submission.csv ├── nlp ├── __pycache__ │ ├── datasets.cpython-39.pyc │ └── models.cpython-39.pyc ├── datasets.py └── models.py ├── pseudo_label_data.py ├── requirements.txt ├── training.py └── visualization_ner.ipynb /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/README.md -------------------------------------------------------------------------------- /cfgs/cfg0.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/cfgs/cfg0.yaml -------------------------------------------------------------------------------- /execute_training_cfgs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/execute_training_cfgs.sh -------------------------------------------------------------------------------- /helper_fns/__pycache__/incorrect_annotations.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/helper_fns/__pycache__/incorrect_annotations.cpython-39.pyc -------------------------------------------------------------------------------- /helper_fns/__pycache__/load.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/helper_fns/__pycache__/load.cpython-39.pyc -------------------------------------------------------------------------------- /helper_fns/__pycache__/scoring.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/helper_fns/__pycache__/scoring.cpython-39.pyc -------------------------------------------------------------------------------- /helper_fns/__pycache__/split_data.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/helper_fns/__pycache__/split_data.cpython-39.pyc -------------------------------------------------------------------------------- /helper_fns/__pycache__/utils.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/helper_fns/__pycache__/utils.cpython-39.pyc -------------------------------------------------------------------------------- /helper_fns/additional_labels_pn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/helper_fns/additional_labels_pn.py -------------------------------------------------------------------------------- /helper_fns/incorrect_annotations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/helper_fns/incorrect_annotations.py -------------------------------------------------------------------------------- /helper_fns/load.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/helper_fns/load.py -------------------------------------------------------------------------------- /helper_fns/load_split_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/helper_fns/load_split_data.py -------------------------------------------------------------------------------- /helper_fns/scoring.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/helper_fns/scoring.py -------------------------------------------------------------------------------- /helper_fns/split_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/helper_fns/split_data.py -------------------------------------------------------------------------------- /helper_fns/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/helper_fns/utils.py -------------------------------------------------------------------------------- /imgs/annotated_text.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/imgs/annotated_text.png -------------------------------------------------------------------------------- /imgs/visualize_ner.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/imgs/visualize_ner.png -------------------------------------------------------------------------------- /inference.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/inference.ipynb -------------------------------------------------------------------------------- /input/deberta-v2-3-fast-tokenizer/transformers__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/input/deberta-v2-3-fast-tokenizer/transformers__init__.py -------------------------------------------------------------------------------- /input/microsoft/deberta-v3-large/config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/input/microsoft/deberta-v3-large/config.json -------------------------------------------------------------------------------- /input/microsoft/deberta-v3-large/tokenizer_config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/input/microsoft/deberta-v3-large/tokenizer_config.json -------------------------------------------------------------------------------- /input/nbme-2wbvmzdp/2wbvmzdp_13kelj6x/config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/input/nbme-2wbvmzdp/2wbvmzdp_13kelj6x/config.json -------------------------------------------------------------------------------- /input/nbme-2wbvmzdp/2wbvmzdp_13kelj6x/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/input/nbme-2wbvmzdp/2wbvmzdp_13kelj6x/config.yaml -------------------------------------------------------------------------------- /input/nbme-2wbvmzdp/2wbvmzdp_13kelj6x/inf_output_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/input/nbme-2wbvmzdp/2wbvmzdp_13kelj6x/inf_output_config.yaml -------------------------------------------------------------------------------- /input/nbme-score-clinical-patient-notes/features.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/input/nbme-score-clinical-patient-notes/features.csv -------------------------------------------------------------------------------- /input/nbme-score-clinical-patient-notes/sample_submission.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/input/nbme-score-clinical-patient-notes/sample_submission.csv -------------------------------------------------------------------------------- /nlp/__pycache__/datasets.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/nlp/__pycache__/datasets.cpython-39.pyc -------------------------------------------------------------------------------- /nlp/__pycache__/models.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/nlp/__pycache__/models.cpython-39.pyc -------------------------------------------------------------------------------- /nlp/datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/nlp/datasets.py -------------------------------------------------------------------------------- /nlp/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/nlp/models.py -------------------------------------------------------------------------------- /pseudo_label_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/pseudo_label_data.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/requirements.txt -------------------------------------------------------------------------------- /training.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/training.py -------------------------------------------------------------------------------- /visualization_ner.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mddunlap924/HuggingFace-NLP-NBME/main/visualization_ner.ipynb --------------------------------------------------------------------------------