├── LICENSE ├── README.md ├── download.sh ├── embedding ├── README.md ├── img │ └── biobert_embedding.png ├── load_embedding.py ├── pubmed_entity_2048.txt ├── run_embedding.py └── utils_embedding.py ├── named-entity-recognition ├── README.md ├── preprocess.sh ├── run_ner.py ├── scripts │ └── preprocess.py └── utils_ner.py ├── question-answering ├── README.md ├── run_factoid.py ├── run_yesno.py ├── scripts │ └── bioasq_eval │ │ ├── README.txt │ │ ├── flat │ │ ├── BioASQEvaluation │ │ │ ├── BioASQ-task2bPhaseA-testset1.docs.concepts.documents.gold.json │ │ │ ├── BioASQ-task2bPhaseA-testset1.docs.concepts.multiple.json │ │ │ ├── build.xml │ │ │ ├── build │ │ │ │ ├── built-jar.properties │ │ │ │ └── classes │ │ │ │ │ ├── classifiers │ │ │ │ │ └── DummyClassifier.class │ │ │ │ │ ├── converters │ │ │ │ │ ├── MapMeshResults.class │ │ │ │ │ └── OBOToHier.class │ │ │ │ │ ├── core │ │ │ │ │ └── Graph.class │ │ │ │ │ ├── data │ │ │ │ │ ├── CalculatedMeasures.class │ │ │ │ │ ├── ExactAnswer.class │ │ │ │ │ ├── PreProcess │ │ │ │ │ │ └── ExtractVocabulary.class │ │ │ │ │ ├── PubMedDocument.class │ │ │ │ │ ├── Question.class │ │ │ │ │ ├── Snippet.class │ │ │ │ │ ├── Task1bData.class │ │ │ │ │ ├── TaskADataParser.class │ │ │ │ │ └── Triple.class │ │ │ │ │ ├── evaluation │ │ │ │ │ ├── ConfusionMatrix.class │ │ │ │ │ ├── Evaluator.class │ │ │ │ │ ├── EvaluatorTask1b.class │ │ │ │ │ └── QuestionAnswerEvaluator.class │ │ │ │ │ ├── stats │ │ │ │ │ └── WilcoxonSignedRanksTest.class │ │ │ │ │ └── tools │ │ │ │ │ ├── DrawStatisticsForPubMedData.class │ │ │ │ │ └── MathUtils.class │ │ │ ├── dist │ │ │ │ ├── BioASQEvaluation.jar │ │ │ │ ├── README.TXT │ │ │ │ └── lib │ │ │ │ │ ├── SnowBallStemmer.jar │ │ │ │ │ ├── commons-cli-1.2.jar │ │ │ │ │ └── gson-2.2.4.jar │ │ │ ├── manifest.mf │ │ │ ├── nbproject │ │ │ │ ├── build-impl.xml │ │ │ │ ├── configs │ │ │ │ │ ├── PreProcess.properties │ │ │ │ │ ├── converto_To_hier.properties │ │ │ │ │ ├── read_questions.properties │ │ │ │ │ └── run_evaluation.properties │ │ │ │ ├── genfiles.properties │ │ │ │ ├── private │ │ │ │ │ ├── config.properties │ │ │ │ │ ├── configs │ │ │ │ │ │ ├── PreProcess.properties │ │ │ │ │ │ ├── converto_To_hier.properties │ │ │ │ │ │ ├── read_questions.properties │ │ │ │ │ │ └── run_evaluation.properties │ │ │ │ │ ├── private.properties │ │ │ │ │ └── private.xml │ │ │ │ ├── project.properties │ │ │ │ └── project.xml │ │ │ ├── partalas_system.json │ │ │ ├── partalas_system_bioasq2.json │ │ │ ├── partalas_template.json │ │ │ ├── partalas_template_bioasq2.json │ │ │ └── src │ │ │ │ ├── classifiers │ │ │ │ └── DummyClassifier.java │ │ │ │ ├── converters │ │ │ │ ├── MapMeshResults.java │ │ │ │ └── OBOToHier.java │ │ │ │ ├── core │ │ │ │ └── Graph.java │ │ │ │ ├── data │ │ │ │ ├── CalculatedMeasures.java │ │ │ │ ├── ExactAnswer.java │ │ │ │ ├── PreProcess │ │ │ │ │ └── ExtractVocabulary.java │ │ │ │ ├── PubMedDocument.java │ │ │ │ ├── Question.java │ │ │ │ ├── Snippet.java │ │ │ │ ├── Task1bData.java │ │ │ │ ├── TaskADataParser.java │ │ │ │ └── Triple.java │ │ │ │ ├── evaluation │ │ │ │ ├── ConfusionMatrix.java │ │ │ │ ├── Evaluator.java │ │ │ │ ├── EvaluatorTask1b.java │ │ │ │ └── QuestionAnswerEvaluator.java │ │ │ │ ├── stats │ │ │ │ └── WilcoxonSignedRanksTest.java │ │ │ │ └── tools │ │ │ │ ├── DrawStatisticsForPubMedData.java │ │ │ │ └── MathUtils.java │ │ └── README.txt │ │ ├── hierarchical │ │ ├── COPYING.txt │ │ ├── README.txt │ │ ├── example files │ │ │ ├── Golden.txt │ │ │ ├── cat_hier.txt │ │ │ ├── result.txt │ │ │ └── result.txt~ │ │ └── software │ │ │ ├── NodeLength.h │ │ │ ├── bestPathfinder.cpp │ │ │ ├── bestPathfinder.h │ │ │ ├── bestPathfinder.o │ │ │ ├── coder.h │ │ │ ├── distanceCopmuter.h │ │ │ ├── graph.cpp │ │ │ ├── graph.h │ │ │ ├── graph.o │ │ │ ├── greatPath.h │ │ │ ├── main.cpp │ │ │ ├── main.o │ │ │ ├── makefile │ │ │ ├── matches.h │ │ │ ├── node.h │ │ │ ├── path.h │ │ │ ├── subGraphCreator.cpp │ │ │ ├── subGraphCreator.h │ │ │ ├── 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