├── .circleci └── config.yml ├── .gitignore ├── CODEOWNERS ├── LICENSE ├── Makefile ├── README.md ├── data ├── config-predict.properties ├── config-train.properties ├── parkinson-disease-filter │ ├── genes.txt │ ├── pathways.txt │ ├── predictions-short-list.txt │ ├── predictions.txt │ └── prioritised-edge-types.txt ├── test.txt └── triples.txt ├── java ├── LICENSE.md ├── mvnvm.properties ├── pom.xml └── src │ ├── main │ └── java │ │ └── de │ │ └── unima │ │ └── ki │ │ └── anyburl │ │ ├── Apply.java │ │ ├── Eval.java │ │ ├── LearnReinforced.java │ │ ├── RuleEngine.java │ │ ├── Settings.java │ │ ├── algorithm │ │ └── PathSampler.java │ │ ├── data │ │ ├── AnnotatedTriple.java │ │ ├── SampledPairedResultSet.java │ │ ├── Triple.java │ │ └── TripleSet.java │ │ ├── eval │ │ ├── AggregateEvaluation.java │ │ ├── Candidate.java │ │ ├── ComparativeEvaluation.java │ │ ├── CompletionResult.java │ │ ├── DiffRank1.java │ │ ├── GoldStandard.java │ │ ├── HitsAtK.java │ │ ├── RandomPrediction.java │ │ ├── ResultSet.java │ │ ├── ResultSetStats.java │ │ ├── TestHardnessEstimator.java │ │ └── XRYEvaluation.java │ │ ├── exceptions │ │ ├── TimeOutException.java │ │ └── Timer.java │ │ ├── io │ │ ├── IOHelper.java │ │ ├── RuleReader.java │ │ ├── RuleWriter.java │ │ └── Test.java │ │ ├── structure │ │ ├── Atom.java │ │ ├── Body.java │ │ ├── Dice.java │ │ ├── LinkedHashMapK.java │ │ ├── Negation.java │ │ ├── Path.java │ │ ├── Rule.java │ │ ├── RuleAcyclic.java │ │ ├── RuleAcyclic1.java │ │ ├── RuleAcyclic2.java │ │ ├── RuleCyclic.java │ │ ├── RuleFactory.java │ │ ├── RuleIndex.java │ │ ├── RuleUntyped.java │ │ ├── ScoreTree.java │ │ └── compare │ │ │ ├── BodyLexicalComparator.java │ │ │ └── RuleConfidenceComparator.java │ │ ├── threads │ │ ├── Predictor.java │ │ ├── RuleWriterAsThread.java │ │ └── ScorerReinforced.java │ │ └── util │ │ ├── DB500Filter.java │ │ ├── DB500Rewriter.java │ │ ├── HardTestCases.java │ │ ├── HepatitisEval.java │ │ ├── ObjectIdentity.java │ │ ├── RuleExplorer.java │ │ ├── RuleTriplePair.java │ │ ├── ScoreTreeTest.java │ │ ├── WSampling.java │ │ └── XX.java │ └── test │ └── java │ └── de │ └── unima │ └── ki │ └── anyburl │ └── ApplyTest.java ├── pyproject.toml ├── python ├── abegidd │ ├── __init__.py │ ├── cli │ │ ├── __init__.py │ │ ├── chains.py │ │ ├── chains_filter.py │ │ ├── predict.py │ │ └── train.py │ ├── entities.py │ ├── expanders.py │ ├── filters.py │ ├── generator.py │ ├── graph.py │ ├── io │ │ ├── __init__.py │ │ ├── anyburl.py │ │ └── chains.py │ ├── iterables.py │ ├── path_scorer.py │ └── system.py └── tests │ ├── cli │ └── test_cli_chains_filter.py │ ├── test_expanders.py │ ├── test_filters.py │ └── test_generator.py └── tox.ini /.circleci/config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/healx/automated-biological-evidence-generation-in-drug-discovery/HEAD/.circleci/config.yml 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