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LICENSE.txt
README.md
pyproject.toml
setup.py
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.github/workflows/pages.yml
.github/workflows/release-docker.yml
biomedicus_client/LICENSE.txt
biomedicus_client/MANIFEST.in
biomedicus_client/README.md
biomedicus_client/pyproject.toml
biomedicus_client/src/biomedicus_client/__init__.py
biomedicus_client/src/biomedicus_client/__main__.py
biomedicus_client/src/biomedicus_client/cli.py
biomedicus_client/src/biomedicus_client/cli_tools/__init__.py
biomedicus_client/src/biomedicus_client/cli_tools/command.py
biomedicus_client/src/biomedicus_client/cli_tools/config_writing.py
biomedicus_client/src/biomedicus_client/cli_tools/parser.py
biomedicus_client/src/biomedicus_client/pipeline/__init__.py
biomedicus_client/src/biomedicus_client/pipeline/_run.py
biomedicus_client/src/biomedicus_client/pipeline/biomedicus_default_pipeline.yml
biomedicus_client/src/biomedicus_client/pipeline/default_pipeline.py
biomedicus_client/src/biomedicus_client/pipeline/rtf_to_text.py
biomedicus_client/src/biomedicus_client/pipeline/rtf_to_text_pipeline.yml
biomedicus_client/src/biomedicus_client/pipeline/scaleout_pipeline_config.yml
biomedicus_client/src/biomedicus_client/pipeline/sources.py
docs/sentences/Presentation.pptx
docs/sentences/Sentences.pdf
docs/sentences/Sentences_Annotation_Guidelines_20180409.pdf
docs/test_results/3.0-standard-data.yml
docs/test_results/3.0-umls-license-data.yml
docs/test_results/3.0b10-standard-data.yml
docs/test_results/3.0b10-umls-license-data.yml
docs/test_results/3.0b6.yml
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java/build.gradle
java/gradlew
java/gradlew.bat
java/settings.gradle
java/gradle/wrapper/gradle-wrapper.jar
java/gradle/wrapper/gradle-wrapper.properties
java/src/main/java/edu/umn/biomedicus/acronym/AcronymDetectorProcessor.java
java/src/main/java/edu/umn/biomedicus/acronym/Acronyms.java
java/src/main/java/edu/umn/biomedicus/acronym/AlignmentModel.java
java/src/main/java/edu/umn/biomedicus/acronym/HashSenseVectors.java
java/src/main/java/edu/umn/biomedicus/acronym/OrthographicAcronymModel.java
java/src/main/java/edu/umn/biomedicus/acronym/OrthographicAcronymModelTrainer.java
java/src/main/java/edu/umn/biomedicus/acronym/RocksDBSenseVectors.java
java/src/main/java/edu/umn/biomedicus/acronym/ScoredSense.java
java/src/main/java/edu/umn/biomedicus/acronym/SenseVectors.java
java/src/main/java/edu/umn/biomedicus/acronym/SparseVector.java
java/src/main/java/edu/umn/biomedicus/acronym/WordVectorSpace.java
java/src/main/java/edu/umn/biomedicus/common/config/Config.java
java/src/main/java/edu/umn/biomedicus/common/data/DataFiles.java
java/src/main/java/edu/umn/biomedicus/common/exc/BiomedicusException.java
java/src/main/java/edu/umn/biomedicus/common/exc/DataFilesException.java
java/src/main/java/edu/umn/biomedicus/common/grams/Bigram.java
java/src/main/java/edu/umn/biomedicus/common/grams/Ngram.java
java/src/main/java/edu/umn/biomedicus/common/grams/Trigram.java
java/src/main/java/edu/umn/biomedicus/common/pos/PartOfSpeech.java
java/src/main/java/edu/umn/biomedicus/common/pos/PartsOfSpeech.java
java/src/main/java/edu/umn/biomedicus/common/pos/UniversalPartOfSpeech.java
java/src/main/java/edu/umn/biomedicus/common/tokenization/TokenResult.java
java/src/main/java/edu/umn/biomedicus/common/tokenization/Tokenizer.java
java/src/main/java/edu/umn/biomedicus/common/tokenization/WhitespaceTokenizer.java
java/src/main/java/edu/umn/biomedicus/common/tuples/Pair.java
java/src/main/java/edu/umn/biomedicus/common/tuples/PosCap.java
java/src/main/java/edu/umn/biomedicus/common/tuples/WordCap.java
java/src/main/java/edu/umn/biomedicus/common/tuples/WordPos.java
java/src/main/java/edu/umn/biomedicus/common/tuples/WordPosCap.java
java/src/main/java/edu/umn/biomedicus/common/utilities/Patterns.java
java/src/main/java/edu/umn/biomedicus/common/utilities/Resources.java
java/src/main/java/edu/umn/biomedicus/common/utilities/RocksToSLF4JLogger.java
java/src/main/java/edu/umn/biomedicus/common/utilities/Strings.java
java/src/main/java/edu/umn/biomedicus/common/viterbi/Ancestor.java
java/src/main/java/edu/umn/biomedicus/common/viterbi/CandidateProbability.java
java/src/main/java/edu/umn/biomedicus/common/viterbi/EmissionProbabilityModel.java
java/src/main/java/edu/umn/biomedicus/common/viterbi/HistoryChain.java
java/src/main/java/edu/umn/biomedicus/common/viterbi/SimpleCandidateProbability.java
java/src/main/java/edu/umn/biomedicus/common/viterbi/TransitionProbabilityModel.java
java/src/main/java/edu/umn/biomedicus/common/viterbi/Viterbi.java
java/src/main/java/edu/umn/biomedicus/common/viterbi/ViterbiProcessor.java
java/src/main/java/edu/umn/biomedicus/common/viterbi/ViterbiProcessorImpl.java
java/src/main/java/edu/umn/biomedicus/concepts/CUI.java
java/src/main/java/edu/umn/biomedicus/concepts/ConceptDictionary.java
java/src/main/java/edu/umn/biomedicus/concepts/ConceptDictionaryBuilder.java
java/src/main/java/edu/umn/biomedicus/concepts/ConceptRow.java
java/src/main/java/edu/umn/biomedicus/concepts/ConceptsUtility.java
java/src/main/java/edu/umn/biomedicus/concepts/DictionaryConceptDetector.java
java/src/main/java/edu/umn/biomedicus/concepts/PhraseConcept.java
java/src/main/java/edu/umn/biomedicus/concepts/RocksDbConceptDictionary.java
java/src/main/java/edu/umn/biomedicus/concepts/SUI.java
java/src/main/java/edu/umn/biomedicus/concepts/SemanticTypeNetwork.java
java/src/main/java/edu/umn/biomedicus/concepts/TN.java
java/src/main/java/edu/umn/biomedicus/concepts/TUI.java
java/src/main/java/edu/umn/biomedicus/modification/ContextCues.java
java/src/main/java/edu/umn/biomedicus/modification/ModificationDetector.java
java/src/main/java/edu/umn/biomedicus/modification/ModificationType.java
java/src/main/java/edu/umn/biomedicus/normalization/HashNormalizerModel.java
java/src/main/java/edu/umn/biomedicus/normalization/NormalizationProcessor.java
java/src/main/java/edu/umn/biomedicus/normalization/NormalizerModel.java
java/src/main/java/edu/umn/biomedicus/normalization/NormalizerModelBuilder.java
java/src/main/java/edu/umn/biomedicus/normalization/RocksDBNormalizerModel.java
java/src/main/java/edu/umn/biomedicus/normalization/TermPos.java
java/src/main/java/edu/umn/biomedicus/performance/WaitProcessor.java
java/src/main/java/edu/umn/biomedicus/rtf/MTAPDocumentsSink.java
java/src/main/java/edu/umn/biomedicus/rtf/RTF.java
java/src/main/java/edu/umn/biomedicus/rtf/RtfProcessor.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/ANSICodepageAction.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/AbstractKeywordAction.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/BinaryKeywordAction.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/ControlKeyword.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/ControlKeywordsDescription.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/DestinationKeywordAction.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/EncodingKeywordAction.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/HexKeywordAction.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/OutputKeywordAction.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/PropertyKeywordAction.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/PropertyResetKeywordAction.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/SkipDestinationIfUnknownKeywordAction.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/keywords/UnicodeKeywordAction.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/properties/PropertiesDescription.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/properties/PropertyDescription.java
java/src/main/java/edu/umn/biomedicus/rtf/beans/properties/PropertyGroupDescription.java
java/src/main/java/edu/umn/biomedicus/rtf/exc/EndOfFileException.java
java/src/main/java/edu/umn/biomedicus/rtf/exc/InvalidKeywordException.java
java/src/main/java/edu/umn/biomedicus/rtf/exc/InvalidParameterException.java
java/src/main/java/edu/umn/biomedicus/rtf/exc/RtfReaderException.java
java/src/main/java/edu/umn/biomedicus/rtf/reader/KeywordAction.java
java/src/main/java/edu/umn/biomedicus/rtf/reader/PlainTextSink.java
java/src/main/java/edu/umn/biomedicus/rtf/reader/RtfParser.java
java/src/main/java/edu/umn/biomedicus/rtf/reader/RtfParserFactory.java
java/src/main/java/edu/umn/biomedicus/rtf/reader/RtfSink.java
java/src/main/java/edu/umn/biomedicus/rtf/reader/RtfSource.java
java/src/main/java/edu/umn/biomedicus/rtf/reader/RtfState.java
java/src/main/java/edu/umn/biomedicus/rtf/reader/UnknownKeywordAction.java
java/src/main/java/edu/umn/biomedicus/sections/RuleBasedSectionHeaderDetector.java
java/src/main/java/edu/umn/biomedicus/serialization/YamlSerialization.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/DataStoreFactory.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/FilteredWordPosFrequencies.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/KnownWordProbabilityModel.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/KnownWordsDataStore.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/PosCapTrigramModel.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/PosCapTrigramModelTrainer.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/RocksDbDataStoreFactory.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/SuffixDataStore.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/SuffixWordProbabilityModel.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/TntModel.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/TntModelTrainer.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/TntPosTaggerProcessor.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/TntTrainerProcessor.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/WordCapAdapter.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/WordCapFilter.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/WordPosFrequencies.java
java/src/main/java/edu/umn/biomedicus/tagging/tnt/WordProbabilityModel.java
java/src/main/java/edu/umn/biomedicus/utilities/PtbReader.java
java/src/main/java/edu/umn/biomedicus/utilities/PtbReaderProcessor.java
java/src/main/resources/log4j2.xml
java/src/main/resources/edu/umn/biomedicus/defaultConfig.yml
java/src/main/resources/edu/umn/biomedicus/common/tokenization/unitsList.txt
java/src/main/resources/edu/umn/biomedicus/rtf/ControlKeywords.xml
java/src/main/resources/edu/umn/biomedicus/rtf/PropertiesDescription.xml
java/src/test/java/edu/umn/biomedicus/common/tokenization/TokenizerTest.java
java/src/test/java/edu/umn/biomedicus/common/tokenization/WhitespaceTokenizerTest.java
java/src/test/java/edu/umn/biomedicus/concepts/ConceptRowTest.java
java/src/test/java/edu/umn/biomedicus/concepts/DictionaryConceptDetectorTest.java
java/src/test/java/edu/umn/biomedicus/rtf/RTFTest.java
java/src/test/java/edu/umn/biomedicus/rtf/RtfProcessorTest.java
java/src/test/java/edu/umn/biomedicus/rtf/beans/keywords/BinaryKeywordActionTest.java
java/src/test/java/edu/umn/biomedicus/rtf/beans/keywords/DestinationKeywordActionTest.java
java/src/test/java/edu/umn/biomedicus/rtf/beans/keywords/HexKeywordActionTest.java
java/src/test/java/edu/umn/biomedicus/rtf/beans/keywords/OutputKeywordActionTest.java
java/src/test/java/edu/umn/biomedicus/rtf/beans/keywords/PropertyKeywordActionTest.java
java/src/test/java/edu/umn/biomedicus/rtf/beans/keywords/PropertyResetKeywordActionTest.java
java/src/test/java/edu/umn/biomedicus/rtf/beans/keywords/SkipDestinationIfUnknownKeywordActionTest.java
java/src/test/java/edu/umn/biomedicus/rtf/beans/keywords/UnicodeKeywordActionTest.java
java/src/test/resources/edu/umn/biomedicus/rtf/test.rtf
python/biomedicus/__init__.py
python/biomedicus/__main__.py
python/biomedicus/biomedicus-all.jar
python/biomedicus/cli.py
python/biomedicus/config.py
python/biomedicus/data_version.py
python/biomedicus/defaultConfig.yml
python/biomedicus/java_support.py
python/biomedicus/tokenization.py
python/biomedicus/version.py
python/biomedicus.egg-info/PKG-INFO
python/biomedicus.egg-info/SOURCES.txt
python/biomedicus.egg-info/dependency_links.txt
python/biomedicus.egg-info/entry_points.txt
python/biomedicus.egg-info/requires.txt
python/biomedicus.egg-info/top_level.txt
python/biomedicus/core/__init__.py
python/biomedicus/core/dawg.py
python/biomedicus/dependencies/__init__.py
python/biomedicus/dependencies/conllu_reader.py
python/biomedicus/dependencies/split_conllu.py
python/biomedicus/dependencies/stanza_parser.py
python/biomedicus/dependencies/stanza_selective_parser.py
python/biomedicus/deployment/__init__.py
python/biomedicus/deployment/_data_downloading.py
python/biomedicus/deployment/biomedicus_deploy_config.yml
python/biomedicus/deployment/default_deployment.py
python/biomedicus/deployment/rtf_to_text.py
python/biomedicus/deployment/rtf_to_text_deploy_config.yml
python/biomedicus/deployment/scaleout_deploy_config.yml
python/biomedicus/examples/__init__.py
python/biomedicus/examples/add_pos_tags.py
python/biomedicus/examples/dependencies.py
python/biomedicus/examples/mipacq_csv_reader.py
python/biomedicus/examples/sentences.py
python/biomedicus/examples/sql_pipeline.py
python/biomedicus/examples/sql_pipeline_rtf.py
python/biomedicus/examples/sql_pipeline_rtf_only.py
python/biomedicus/negation/__init__.py
python/biomedicus/negation/deepen.py
python/biomedicus/negation/i2b2_va2010.py
python/biomedicus/negation/negex.py
python/biomedicus/negation/negex_triggers.py
python/biomedicus/negation/negex_triggers.txt
python/biomedicus/sentences/__init__.py
python/biomedicus/sentences/bi_lstm.py
python/biomedicus/sentences/bi_lstm_torchserve.py
python/biomedicus/sentences/bilstm_handler.py
python/biomedicus/sentences/input.py
python/biomedicus/sentences/one_per_line_sentences.py
python/biomedicus/sentences/vocabulary.py
python/biomedicus/tagging/__init__.py
python/biomedicus/tagging/genia_xml_pipeline.py
python/biomedicus/tagging/ptb_evaluation_set.py
python/biomedicus/tagging/ptb_pipeline.py
python/biomedicus/utilities/__init__.py
python/biomedicus/utilities/embeddings.py
python/biomedicus/utilities/mimic.py
python/biomedicus/utilities/print_all_processors_metadata.py
python/biomedicus/utilities/pubmed.py
python/biomedicus/utilities/sample_batches.py
python/biomedicus/utilities/sample_mimic.py
python/biomedicus/utilities/train_eval_split.py
python/tests/conftest.py
python/tests/pytest.ini
python/tests/test_config.py
python/tests/acronyms/test_acronyms_performance.py
python/tests/concepts/test_concepts_performance.py
python/tests/core/test_dawg.py
python/tests/dependencies/3.0b6.yml
python/tests/dependencies/test_dependencies.py
python/tests/deployment/test_deployment.py
python/tests/deployment/test_rtf_to_text.py
python/tests/deployment/in/97_204.txt
python/tests/deployment/rtf_in/97_204.rtf
python/tests/negation/test_negation_i2b2.py
python/tests/negation/test_negex_tagger.py
python/tests/normalization/97_95.pickle
python/tests/normalization/test_normalization.py
python/tests/scaleout/test_scaleout.py
python/tests/sentences/test_sentences.py
python/tests/sentences/test_sentences_performance.py
python/tests/tnt_tagging/test_tnt_performance.py
tools/concepts/BannedTTYs.txt
tools/concepts/TUIsOfInterest.txt
tools/concepts/umls-level0.prop
tools/concepts/umls-snomed.prop
tools/docker/Dockerfile
tools/docker/Dockerfile-dev
tools/docker/docker-compose.yml
tools/docker/biomedicus-reverse-proxy/Dockerfile
tools/docker/biomedicus-reverse-proxy/default.conf