.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
CHANGELOG.md
CONTRIBUTING.md
DAPT.md
LICENSE
Makefile
README.md
pyproject.toml
uv.lock
.github/workflows/build-and-test.yml
.github/workflows/lint-and-format.yml
docker/Dockerfile.cpu
docker/Dockerfile.gpu
docker/MAINTAINER.md
docker/__init__.py
docker/build.py
docker/compose.yaml
docker/model_download.py
docs/Makefile
docs/cnlpt.BaselineModels.rst
docs/cnlpt.CnlpModelForClassification.rst
docs/cnlpt.HierarchicalTransformer.rst
docs/cnlpt.api.cnlp_rest.rst
docs/cnlpt.api.dtr_rest.rst
docs/cnlpt.api.event_rest.rst
docs/cnlpt.api.hier_rest.rst
docs/cnlpt.api.negation_rest.rst
docs/cnlpt.api.rst
docs/cnlpt.api.temporal_rest.rst
docs/cnlpt.api.timex_rest.rst
docs/cnlpt.cnlp_args.rst
docs/cnlpt.cnlp_data.rst
docs/cnlpt.cnlp_metrics.rst
docs/cnlpt.cnlp_predict.rst
docs/cnlpt.cnlp_processors.rst
docs/cnlpt.data.preprocess_i2b2_2008.rst
docs/cnlpt.data.rst
docs/cnlpt.data.transform_prot.rst
docs/cnlpt.data.transform_uci_drug.rst
docs/cnlpt.rst
docs/cnlpt.thyme_eval.rst
docs/cnlpt.train_system.rst
docs/conf.py
docs/index.rst
docs/make.bat
docs/requirements.txt
docs/transformer_objects.inv
docs/transformer_objects.txt
examples/chemprot/README.md
examples/chemprot/chemprot_requirements.txt
examples/uci_drug/README.md
src/cnlp_transformers.egg-info/PKG-INFO
src/cnlp_transformers.egg-info/SOURCES.txt
src/cnlp_transformers.egg-info/dependency_links.txt
src/cnlp_transformers.egg-info/entry_points.txt
src/cnlp_transformers.egg-info/requires.txt
src/cnlp_transformers.egg-info/top_level.txt
src/cnlpt/BaselineModels.py
src/cnlpt/CnlpModelForClassification.py
src/cnlpt/HierarchicalTransformer.py
src/cnlpt/__init__.py
src/cnlpt/__main__.py
src/cnlpt/cnlp_args.py
src/cnlpt/cnlp_data.py
src/cnlpt/cnlp_metrics.py
src/cnlpt/cnlp_predict.py
src/cnlpt/cnlp_processors.py
src/cnlpt/dapt.py
src/cnlpt/select_hyperparameters.py
src/cnlpt/thyme_eval.py
src/cnlpt/train_system.py
src/cnlpt/_cli/main.py
src/cnlpt/_cli/rest.py
src/cnlpt/api/__init__.py
src/cnlpt/api/cnn_rest.py
src/cnlpt/api/current_rest.py
src/cnlpt/api/dtr_rest.py
src/cnlpt/api/event_rest.py
src/cnlpt/api/hier_rest.py
src/cnlpt/api/negation_rest.py
src/cnlpt/api/temporal_rest.py
src/cnlpt/api/termexists_rest.py
src/cnlpt/api/timex_rest.py
src/cnlpt/api/utils.py
src/cnlpt/data/__init__.py
src/cnlpt/data/preprocess_i2b2_2008.py
src/cnlpt/data/transform_prot.py
src/cnlpt/data/transform_uci_drug.py
src/cnlpt/notebooks/viz_negation.ipynb
src/cnlpt/notebooks/viz_params.ipynb
src/cnlpt/tests/test_multiple_systems.sh
test/test_api.py
test/test_init.py