├── .github └── workflows │ └── docker-image.yml ├── .gitignore ├── Dockerfile_api ├── Dockerfile_cuda ├── Dockerfile_metal ├── LICENSE ├── README.md ├── app.py ├── config.yml ├── docker-compose-api.yml ├── docker-compose.yml ├── docs └── index.html ├── examples ├── annotation │ ├── anonymization_annotations.zip │ └── ie_annotation.xlsx ├── documents │ ├── 0090075.pdf │ ├── 1122334.pdf │ ├── 1342576.pdf │ ├── 2123242.pdf │ ├── 2425262.pdf │ ├── 3435369.pdf │ ├── 7756987.pdf │ └── 9874562.pdf ├── grammars │ ├── anonymize_grammar_entries.csv │ └── ie_grammar_entries.csv └── schemas │ └── ie_schema.csv ├── project.toml ├── requirements.txt ├── requirements_api.txt ├── setup.py ├── static ├── anonymization.md ├── hardware.md ├── ie_front_image.png ├── image_annotationhelper.png ├── image_anonymization_form.png ├── image_anonymization_grammarbuilder.png ├── image_anonymization_llm.png ├── image_anonymization_overview.png ├── image_anonymization_progress.png ├── image_anonymization_report.png ├── image_grammarbuilder.png ├── image_grammarbuilder_example.png ├── image_information_extraction.png ├── image_labelannotation_report.png ├── image_labelannotation_summary.png ├── image_labeltype_selection.png ├── image_redaction_view.png ├── information_extraction.md └── run_on_ukd.md ├── utils └── leaderboard_conversion.py └── webapp ├── __init__.py ├── annotationhelper ├── __init__.py ├── forms.py └── routes.py ├── input_processing ├── __init__.py ├── forms.py └── routes.py ├── labelannotation ├── __init__.py ├── forms.py ├── routes.py └── utils.py ├── llm_processing ├── __init__.py ├── forms.py ├── read_strange_csv.py ├── routes.py ├── tests │ ├── __init__.py │ └── test_pdf_redaction.py └── utils.py ├── main ├── __init__.py ├── routes.py └── utils.py ├── report_redaction ├── __init__.py ├── forms.py ├── routes.py ├── tests │ ├── __init__.py │ └── test_text_matching.py └── utils.py ├── static └── style.css └── templates ├── annotationhelper_form.html ├── annotationhelper_overview.html ├── annotationhelper_queue.html ├── annotationhelper_selector.html ├── annotationhelper_viewer.html ├── index.html ├── labelannotation_form.html ├── labelannotation_metrics.html ├── labelannotation_selector.html ├── labelannotation_viewer.html ├── layout.html ├── llm_processing.html ├── llm_results.html ├── report_redaction_form.html ├── report_redaction_metrics.html └── report_redaction_viewer.html /.github/workflows/docker-image.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/.github/workflows/docker-image.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/.gitignore -------------------------------------------------------------------------------- /Dockerfile_api: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/Dockerfile_api -------------------------------------------------------------------------------- /Dockerfile_cuda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/Dockerfile_cuda -------------------------------------------------------------------------------- /Dockerfile_metal: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/Dockerfile_metal -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/README.md -------------------------------------------------------------------------------- /app.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/app.py -------------------------------------------------------------------------------- /config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/config.yml -------------------------------------------------------------------------------- /docker-compose-api.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/docker-compose-api.yml -------------------------------------------------------------------------------- /docker-compose.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/docker-compose.yml -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/docs/index.html -------------------------------------------------------------------------------- /examples/annotation/anonymization_annotations.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/annotation/anonymization_annotations.zip -------------------------------------------------------------------------------- /examples/annotation/ie_annotation.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/annotation/ie_annotation.xlsx -------------------------------------------------------------------------------- /examples/documents/0090075.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/documents/0090075.pdf -------------------------------------------------------------------------------- /examples/documents/1122334.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/documents/1122334.pdf -------------------------------------------------------------------------------- /examples/documents/1342576.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/documents/1342576.pdf -------------------------------------------------------------------------------- /examples/documents/2123242.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/documents/2123242.pdf -------------------------------------------------------------------------------- /examples/documents/2425262.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/documents/2425262.pdf -------------------------------------------------------------------------------- /examples/documents/3435369.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/documents/3435369.pdf -------------------------------------------------------------------------------- /examples/documents/7756987.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/documents/7756987.pdf -------------------------------------------------------------------------------- /examples/documents/9874562.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/documents/9874562.pdf -------------------------------------------------------------------------------- /examples/grammars/anonymize_grammar_entries.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/grammars/anonymize_grammar_entries.csv -------------------------------------------------------------------------------- /examples/grammars/ie_grammar_entries.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/grammars/ie_grammar_entries.csv -------------------------------------------------------------------------------- /examples/schemas/ie_schema.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/examples/schemas/ie_schema.csv -------------------------------------------------------------------------------- /project.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/project.toml -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/requirements.txt -------------------------------------------------------------------------------- /requirements_api.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/requirements_api.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/setup.py -------------------------------------------------------------------------------- /static/anonymization.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/anonymization.md -------------------------------------------------------------------------------- /static/hardware.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/hardware.md -------------------------------------------------------------------------------- /static/ie_front_image.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/ie_front_image.png -------------------------------------------------------------------------------- /static/image_annotationhelper.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_annotationhelper.png -------------------------------------------------------------------------------- /static/image_anonymization_form.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_anonymization_form.png -------------------------------------------------------------------------------- /static/image_anonymization_grammarbuilder.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_anonymization_grammarbuilder.png -------------------------------------------------------------------------------- /static/image_anonymization_llm.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_anonymization_llm.png -------------------------------------------------------------------------------- /static/image_anonymization_overview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_anonymization_overview.png -------------------------------------------------------------------------------- /static/image_anonymization_progress.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_anonymization_progress.png -------------------------------------------------------------------------------- /static/image_anonymization_report.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_anonymization_report.png -------------------------------------------------------------------------------- /static/image_grammarbuilder.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_grammarbuilder.png -------------------------------------------------------------------------------- /static/image_grammarbuilder_example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_grammarbuilder_example.png -------------------------------------------------------------------------------- /static/image_information_extraction.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_information_extraction.png -------------------------------------------------------------------------------- /static/image_labelannotation_report.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_labelannotation_report.png -------------------------------------------------------------------------------- /static/image_labelannotation_summary.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_labelannotation_summary.png -------------------------------------------------------------------------------- /static/image_labeltype_selection.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_labeltype_selection.png -------------------------------------------------------------------------------- /static/image_redaction_view.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/image_redaction_view.png -------------------------------------------------------------------------------- /static/information_extraction.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/information_extraction.md -------------------------------------------------------------------------------- /static/run_on_ukd.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/static/run_on_ukd.md -------------------------------------------------------------------------------- /utils/leaderboard_conversion.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/utils/leaderboard_conversion.py -------------------------------------------------------------------------------- /webapp/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/__init__.py -------------------------------------------------------------------------------- /webapp/annotationhelper/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/annotationhelper/__init__.py -------------------------------------------------------------------------------- /webapp/annotationhelper/forms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/annotationhelper/forms.py -------------------------------------------------------------------------------- /webapp/annotationhelper/routes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/annotationhelper/routes.py -------------------------------------------------------------------------------- /webapp/input_processing/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/input_processing/__init__.py -------------------------------------------------------------------------------- /webapp/input_processing/forms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/input_processing/forms.py -------------------------------------------------------------------------------- /webapp/input_processing/routes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/input_processing/routes.py -------------------------------------------------------------------------------- /webapp/labelannotation/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/labelannotation/__init__.py -------------------------------------------------------------------------------- /webapp/labelannotation/forms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/labelannotation/forms.py -------------------------------------------------------------------------------- /webapp/labelannotation/routes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/labelannotation/routes.py -------------------------------------------------------------------------------- /webapp/labelannotation/utils.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /webapp/llm_processing/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/llm_processing/__init__.py -------------------------------------------------------------------------------- /webapp/llm_processing/forms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/llm_processing/forms.py -------------------------------------------------------------------------------- /webapp/llm_processing/read_strange_csv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/llm_processing/read_strange_csv.py -------------------------------------------------------------------------------- /webapp/llm_processing/routes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/llm_processing/routes.py -------------------------------------------------------------------------------- /webapp/llm_processing/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /webapp/llm_processing/tests/test_pdf_redaction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/llm_processing/tests/test_pdf_redaction.py -------------------------------------------------------------------------------- /webapp/llm_processing/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/llm_processing/utils.py -------------------------------------------------------------------------------- /webapp/main/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/main/__init__.py -------------------------------------------------------------------------------- /webapp/main/routes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/main/routes.py -------------------------------------------------------------------------------- /webapp/main/utils.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /webapp/report_redaction/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/report_redaction/__init__.py -------------------------------------------------------------------------------- /webapp/report_redaction/forms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/report_redaction/forms.py -------------------------------------------------------------------------------- /webapp/report_redaction/routes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/report_redaction/routes.py -------------------------------------------------------------------------------- /webapp/report_redaction/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /webapp/report_redaction/tests/test_text_matching.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/report_redaction/tests/test_text_matching.py -------------------------------------------------------------------------------- /webapp/report_redaction/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/report_redaction/utils.py -------------------------------------------------------------------------------- /webapp/static/style.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/static/style.css -------------------------------------------------------------------------------- /webapp/templates/annotationhelper_form.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/annotationhelper_form.html -------------------------------------------------------------------------------- /webapp/templates/annotationhelper_overview.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/annotationhelper_overview.html -------------------------------------------------------------------------------- /webapp/templates/annotationhelper_queue.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/annotationhelper_queue.html -------------------------------------------------------------------------------- /webapp/templates/annotationhelper_selector.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/annotationhelper_selector.html -------------------------------------------------------------------------------- /webapp/templates/annotationhelper_viewer.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/annotationhelper_viewer.html -------------------------------------------------------------------------------- /webapp/templates/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/index.html -------------------------------------------------------------------------------- /webapp/templates/labelannotation_form.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/labelannotation_form.html -------------------------------------------------------------------------------- /webapp/templates/labelannotation_metrics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/labelannotation_metrics.html -------------------------------------------------------------------------------- /webapp/templates/labelannotation_selector.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/labelannotation_selector.html -------------------------------------------------------------------------------- /webapp/templates/labelannotation_viewer.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/labelannotation_viewer.html -------------------------------------------------------------------------------- /webapp/templates/layout.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/layout.html -------------------------------------------------------------------------------- /webapp/templates/llm_processing.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/llm_processing.html -------------------------------------------------------------------------------- /webapp/templates/llm_results.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/llm_results.html -------------------------------------------------------------------------------- /webapp/templates/report_redaction_form.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/report_redaction_form.html -------------------------------------------------------------------------------- /webapp/templates/report_redaction_metrics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/report_redaction_metrics.html -------------------------------------------------------------------------------- /webapp/templates/report_redaction_viewer.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KatherLab/LLMAIx/HEAD/webapp/templates/report_redaction_viewer.html --------------------------------------------------------------------------------