├── .gitignore ├── CHANGELOG ├── Ideas.txt ├── LICENSE.md ├── Notes.txt ├── README ├── conf ├── log4j.properties └── neo4j.properties ├── doc ├── .gitignore ├── normalized-loss │ └── normalized-loss.tex ├── proppr-math │ ├── deriv.pdf │ └── deriv.tex └── publication-graphs │ ├── cikm-full.dot │ └── redblue.dot ├── examples ├── .gitignore ├── 20newsgroups │ ├── 20news.ppr │ ├── 20news.sparse │ │ ├── Makefile │ │ ├── README │ │ ├── bin │ │ │ ├── cfacts2sparse_index.pl │ │ │ └── index2sparse.pl │ │ ├── hasWord_doc_kw.cfacts.gz │ │ └── wordIn_kw_doc.cfacts │ ├── 20news.wam │ ├── Makefile │ ├── all.examples │ ├── hasLabel_doc_label.cfacts.gz │ ├── labels.cfacts │ ├── seed_doc_label.100per.cfacts.gz │ ├── seed_doc_label.10per.cfacts.gz │ ├── seed_doc_label.1per.cfacts.gz │ ├── test.examples │ └── train.examples ├── Makefile ├── README ├── adagrad │ ├── Makefile │ └── adagrad.properties ├── common.in ├── configure.sh ├── cora │ └── Makefile ├── hyperparameter_tuning │ └── plot.R ├── log4j.properties ├── review.sh ├── scripts │ └── makeResults.sh ├── textcat-ssl │ ├── Makefile │ ├── bin │ │ ├── config.json │ │ ├── dataset-builder.py │ │ ├── dataset-index.txt │ │ ├── getmutex.pl │ │ ├── param-stats.py │ │ ├── plot-results.py │ │ ├── sampleExample.bash │ │ ├── solution2graph.py │ │ ├── spearmint-config-builder.bash │ │ ├── split-train.pl │ │ └── summarize-diffs.pl │ ├── config.json │ ├── expt-getoor-spearmint.bash │ ├── expt-getoor.bash │ ├── mySpearmint.py │ ├── ppr │ │ ├── INDEX.txt │ │ ├── all.ppr │ │ └── all.wam │ ├── proppr.settings │ ├── raw-getoor │ │ ├── Makefile │ │ ├── citeseer │ │ │ ├── citeseer-all-examples.txt │ │ │ ├── citeseer-alltrain-examples.txt │ │ │ ├── citeseer-cites.graph │ │ │ ├── citeseer-corpus.graph │ │ │ ├── citeseer-labels.txt │ │ │ ├── citeseer-near.graph │ │ │ └── citeseer-test-examples.txt │ │ ├── cora │ │ │ ├── cora-all-examples.txt │ │ │ ├── cora-alltrain-examples.txt │ │ │ ├── cora-cites.graph │ │ │ ├── cora-corpus.graph │ │ │ ├── cora-labels.txt │ │ │ ├── cora-near.graph │ │ │ └── cora-test-examples.txt │ │ └── pubmed │ │ │ ├── pubmed-all-examples.txt │ │ │ ├── pubmed-alltrain-examples.txt │ │ │ ├── pubmed-cites.graph │ │ │ ├── pubmed-corpus.graph │ │ │ ├── pubmed-labels.txt │ │ │ ├── pubmed-near.graph │ │ │ └── pubmed-test-examples.txt │ ├── readme.md │ ├── settings.default.in │ ├── settings.in │ ├── steps.conf │ └── tmp_option ├── textcattoy │ ├── Makefile │ ├── results.20140516.txt │ ├── results.20141208.txt │ ├── test.examples │ ├── textcat.ppr │ ├── textcat.wam │ ├── toylabels.cfacts │ ├── toywords.graph │ └── train.examples ├── top-1000-near-google │ ├── Makefile │ ├── top-1000-near-google-fact.graph │ ├── top-1000-near-google-nonrecursive.ppr │ ├── top-1000-near-google-recursive.ppr │ ├── top-1000-near-google-recursive.wam │ ├── top-1000-near-google.cfacts │ ├── top-1000-near-google.facts │ ├── top-1000-near-google.test.examples │ └── top-1000-near-google.train.examples ├── top-1M-near-X │ ├── Makefile │ ├── top-1M-near-baseball-fact.graph │ ├── top-1M-near-baseball-recursive.ppr │ ├── top-1M-near-baseball-recursive.wam │ ├── top-1M-near-baseball.test.examples │ ├── top-1M-near-baseball.train.examples │ ├── top-1M-near-beatles-fact.graph │ ├── top-1M-near-beatles-recursive.ppr │ ├── top-1M-near-beatles-recursive.wam │ ├── top-1M-near-beatles.test.examples │ ├── top-1M-near-beatles.train.examples │ ├── top-1M-near-google-fact.graph │ ├── top-1M-near-google-recursive.ppr │ ├── top-1M-near-google-recursive.wam │ ├── top-1M-near-google.test.examples │ └── top-1M-near-google.train.examples ├── tuneAlpha.sh ├── tuneEpochs.sh ├── tuneEpsilon.sh ├── tuneMu.sh ├── walkthru │ └── Walkthru.txt ├── webkb │ ├── Makefile │ ├── test_cornell.data │ ├── test_texas.data │ ├── test_wash.data │ ├── test_wisc.data │ ├── train_no_cornell.data │ ├── train_no_texas.data │ ├── train_no_wash.data │ ├── train_no_wisc.data │ ├── webkb.cfacts │ ├── webkb.facts │ ├── webkb.graph │ ├── webkb0.ppr │ └── webkb0.wam └── weibo │ ├── Makefile │ ├── all │ ├── all.allowed │ ├── all.cfacts │ ├── all.dict │ ├── scripts │ ├── conll2proppr.pl │ ├── conll2proppr_weibo.pl │ ├── cookFrequencyThreshold.pl │ ├── cooked2featureFrequency.pl │ ├── evaluate_Malt.pl │ ├── postpass.pl │ ├── scoring.pl │ ├── tagged2conll.pl │ ├── typedDependencies2Conll.pl │ ├── wordcount.pl │ └── words2sentences.pl │ ├── timePerformance_l2p_l2plocal.sh │ ├── weibo.properties │ ├── weibo1.ppr │ ├── weibo1.rules │ └── weibo2.rules ├── init.sh ├── lib ├── bsh-2.0b4.jar ├── commons-cli-1.3.1.jar ├── concurrentlinkedhashmap-lru-1.3.1.jar ├── geronimo-jta_1.1_spec-1.1.1.jar ├── java-bloomfilter-javadoc.jar ├── java-bloomfilter-sources.jar ├── java-bloomfilter.jar ├── junit-4.11-SNAPSHOT.jar ├── junit-dep-4.11-SNAPSHOT.jar ├── la4j-0.4.5.jar ├── log4j-1.2.16.jar ├── lucene-core-3.6.2.jar ├── org.apache.servicemix.bundles.jline-0.9.94_1.jar ├── scala-library-2.10.0.jar ├── server-api-1.9.4.jar └── trove-3.0.3.jar ├── my_program ├── textcat.rules ├── toylabels.facts ├── toytest.data ├── toytrain.data └── toywords.graph ├── scripts ├── answermetrics.py ├── diffGraph.py ├── filterCookedFile.pl ├── ground2dot.py ├── grounded2featureFrequency.pl ├── listEdges.pl ├── proppr ├── proppr-helpers │ ├── cfacts2theano.py │ ├── graph2theano.py │ ├── pronghorn-wrapper.py │ ├── pronghorn.py │ ├── sg-interp-test-v1.ppr │ ├── sg-interp-test-v2.ppr │ ├── sg-interp-test.ppr │ ├── sg-interp-train-v1.ppr │ ├── sg-interp-train-v2.ppr │ ├── sg-interp-train.ppr │ ├── show.py │ ├── structured-gradient.py │ └── util.py ├── showLosses.sh ├── solutionFeatures.pl ├── solutions2labeled.pl └── solutions2train.pl ├── sparseGraphTools ├── Makefile ├── README └── bin │ ├── cfacts2sparse_index.pl │ └── index2sparse.pl ├── src ├── java │ ├── main │ │ ├── MANIFEST.MF │ │ ├── edu │ │ │ └── cmu │ │ │ │ └── ml │ │ │ │ └── proppr │ │ │ │ ├── CachingTrainer.java │ │ │ │ ├── Diagnostic.java │ │ │ │ ├── GradientFinder.java │ │ │ │ ├── Grounder.java │ │ │ │ ├── QueryAnswerer.java │ │ │ │ ├── Trainer.java │ │ │ │ ├── examples │ │ │ │ ├── DprExample.java │ │ │ │ ├── GroundedExample.java │ │ │ │ ├── InferenceExample.java │ │ │ │ ├── InferenceExampleStreamer.java │ │ │ │ ├── PosNegRWExample.java │ │ │ │ ├── PprExample.java │ │ │ │ └── RWExample.java │ │ │ │ ├── graph │ │ │ │ ├── ArrayLearningGraphBuilder.java │ │ │ │ ├── GraphFormatException.java │ │ │ │ ├── InferenceGraph.java │ │ │ │ ├── LearningGraph.java │ │ │ │ ├── LearningGraphBuilder.java │ │ │ │ ├── LightweightStateGraph.java │ │ │ │ └── RWOutlink.java │ │ │ │ ├── learn │ │ │ │ ├── AdaGradSRW.java │ │ │ │ ├── DprSRW.java │ │ │ │ ├── LocalRegularizationSchedule.java │ │ │ │ ├── LossFunction.java │ │ │ │ ├── NormalizedPosLoss.java │ │ │ │ ├── PairwiseL2SqLoss.java │ │ │ │ ├── PosNegLoss.java │ │ │ │ ├── RegularizationSchedule.java │ │ │ │ ├── Regularize.java │ │ │ │ ├── RegularizeL1.java │ │ │ │ ├── RegularizeL1GroupLasso.java │ │ │ │ ├── RegularizeL1Laplacian.java │ │ │ │ ├── RegularizeL2.java │ │ │ │ ├── SRW.java │ │ │ │ └── tools │ │ │ │ │ ├── ClippedExp.java │ │ │ │ │ ├── Exp.java │ │ │ │ │ ├── FixedWeightRules.java │ │ │ │ │ ├── LReLU.java │ │ │ │ │ ├── Linear.java │ │ │ │ │ ├── LossData.java │ │ │ │ │ ├── RWExampleParser.java │ │ │ │ │ ├── ReLU.java │ │ │ │ │ ├── Sigmoid.java │ │ │ │ │ ├── SquashingFunction.java │ │ │ │ │ ├── StoppingCriterion.java │ │ │ │ │ ├── Tanh.java │ │ │ │ │ └── Tanh1.java │ │ │ │ ├── prove │ │ │ │ ├── Backtrace.java │ │ │ │ ├── DfsProver.java │ │ │ │ ├── DprProver.java │ │ │ │ ├── FeatureDictWeighter.java │ │ │ │ ├── IdDprProver.java │ │ │ │ ├── IdPprProver.java │ │ │ │ ├── InnerProductWeighter.java │ │ │ │ ├── MinAlphaException.java │ │ │ │ ├── PathDprProver.java │ │ │ │ ├── PprProver.java │ │ │ │ ├── PriorityQueueProver.java │ │ │ │ ├── Prover.java │ │ │ │ ├── PruningIdDprProver.java │ │ │ │ ├── PruningIdPprProver.java │ │ │ │ ├── TracingDfsProver.java │ │ │ │ ├── UniformWeighter.java │ │ │ │ └── wam │ │ │ │ │ ├── Argument.java │ │ │ │ │ ├── CachingIdProofGraph.java │ │ │ │ │ ├── CallStackFrame.java │ │ │ │ │ ├── Compiler.java │ │ │ │ │ ├── ConstantArgument.java │ │ │ │ │ ├── Feature.java │ │ │ │ │ ├── FeatureBuilder.java │ │ │ │ │ ├── Goal.java │ │ │ │ │ ├── ImmutableState.java │ │ │ │ │ ├── Instruction.java │ │ │ │ │ ├── InvalidHeapException.java │ │ │ │ │ ├── LogicProgramException.java │ │ │ │ │ ├── MutableState.java │ │ │ │ │ ├── Outlink.java │ │ │ │ │ ├── ProofGraph.java │ │ │ │ │ ├── Query.java │ │ │ │ │ ├── Rule.java │ │ │ │ │ ├── State.java │ │ │ │ │ ├── StateProofGraph.java │ │ │ │ │ ├── VariableArgument.java │ │ │ │ │ ├── WamBaseProgram.java │ │ │ │ │ ├── WamInterpreter.java │ │ │ │ │ ├── WamProgram.java │ │ │ │ │ ├── WamQueryProgram.java │ │ │ │ │ └── plugins │ │ │ │ │ ├── FactsPlugin.java │ │ │ │ │ ├── GraphlikePlugin.java │ │ │ │ │ ├── LightweightGraphPlugin.java │ │ │ │ │ ├── SparseGraphPlugin.java │ │ │ │ │ ├── SparseMatrixIndex.java │ │ │ │ │ ├── SplitFactsPlugin.java │ │ │ │ │ ├── WamPlugin.java │ │ │ │ │ └── builtin │ │ │ │ │ ├── FilterPluginCollection.java │ │ │ │ │ ├── PluginCollection.java │ │ │ │ │ └── PluginFunction.java │ │ │ │ └── util │ │ │ │ ├── APROptions.java │ │ │ │ ├── ConcurrentSymbolTable.java │ │ │ │ ├── Configuration.java │ │ │ │ ├── CustomConfiguration.java │ │ │ │ ├── Dictionary.java │ │ │ │ ├── FileBackedIterable.java │ │ │ │ ├── MisconfigurationException.java │ │ │ │ ├── ModuleConfiguration.java │ │ │ │ ├── ParamsFile.java │ │ │ │ ├── ParsedFile.java │ │ │ │ ├── SRWOptions.java │ │ │ │ ├── SimpleSymbolTable.java │ │ │ │ ├── StatusLogger.java │ │ │ │ ├── SymbolTable.java │ │ │ │ ├── TimestampedWeight.java │ │ │ │ ├── math │ │ │ │ ├── LongDense.java │ │ │ │ ├── MuParamVector.java │ │ │ │ ├── ParamVector.java │ │ │ │ ├── SimpleParamVector.java │ │ │ │ ├── SimpleSparse.java │ │ │ │ └── SmoothFunction.java │ │ │ │ └── multithreading │ │ │ │ ├── Cleanup.java │ │ │ │ ├── Multithreading.java │ │ │ │ ├── NamedThreadFactory.java │ │ │ │ ├── Transformer.java │ │ │ │ └── WritingCleanup.java │ │ └── outlinks.2p │ └── test │ │ └── edu │ │ └── cmu │ │ └── ml │ │ └── proppr │ │ ├── .gitignore │ │ ├── GradientFinderTest.java │ │ ├── GrounderTest.java │ │ ├── NodeMergingTest.java │ │ ├── RedBlueGraph.java │ │ ├── TrainerTest.java │ │ ├── graph │ │ ├── CachingIdGraphTest.java │ │ ├── InferenceGraphTestTemplate.java │ │ ├── LearningGraphTest.java │ │ └── LightweightStateGraphTest.java │ │ ├── learn │ │ ├── DprSRWTest.java │ │ ├── ExampleFactory.java │ │ ├── FiniteDifferenceTest.java │ │ ├── L2PosNegLossSRWTest.java │ │ ├── LocalL2PosNegLossSRWTest.java │ │ ├── PairwiseL2LossSRWTest.java │ │ ├── RegularizedSRWTest.java │ │ ├── SRWRestartTest.java │ │ ├── SRWTest.java │ │ └── tools │ │ │ └── FixedWeightRulesTest.java │ │ ├── prove │ │ ├── ArgumentTest.java │ │ ├── DprProverTest.java │ │ ├── DuplicateSignatureRuleTest.java │ │ ├── EqualityTest.java │ │ ├── IdDprProverTest.java │ │ ├── IdPprProverTest.java │ │ ├── InnerProductWeighterTest.java │ │ ├── PathDprProverTest.java │ │ ├── PprProverTest.java │ │ ├── ProverTestTemplate.java │ │ ├── QueryParserTest.java │ │ ├── SimpleProgramProofGraphTest.java │ │ ├── SimpleProgramProverTest.java │ │ ├── TracingDfsProverTest.java │ │ ├── UngroundedSolutionsTest.java │ │ ├── WamInterpreterTest.java │ │ ├── WamProgramTest.java │ │ └── wam │ │ │ ├── GoalTest.java │ │ │ ├── QueryTest.java │ │ │ ├── StateCallStackTest.java │ │ │ └── plugins │ │ │ ├── BoundVariableGraphTest.java │ │ │ ├── FactsPluginTest.java │ │ │ ├── SparseGraphPluginTest.java │ │ │ ├── SplitFactsPluginTest.java │ │ │ ├── WeightedEdgeTest.java │ │ │ ├── WeightedFeaturesTest.java │ │ │ ├── WeightedRulesTest.java │ │ │ └── builtin │ │ │ └── TestNeqPlugin.java │ │ └── util │ │ ├── ConfigurationTest.java │ │ ├── DictionaryTest.java │ │ ├── MuParamVectorTest.java │ │ ├── ParamsFileTest.java │ │ └── PropertiesConfigurationTest.java ├── scripts │ ├── compiler.py │ ├── pyparsing.py │ ├── symtab.py │ └── util.py └── testcases │ ├── .gitignore │ ├── answermetrics │ ├── README.txt │ ├── duplicate.1_0.solutions.txt │ ├── duplicate.examples │ ├── multi.0_5.solutions.txt │ ├── multi.1_0.solutions.txt │ ├── multi.examples │ ├── test.alltie.solutions.txt │ ├── test.examples │ ├── test.none.solutions.txt │ ├── test.oneoff.solutions.txt │ ├── test.perfect.solutions.txt │ ├── test.twooff.solutions.txt │ └── test.withneg.examples │ ├── classifyEDB.cfacts │ ├── classifyIDB.ppr │ ├── classifyIDB.wam │ ├── classifyPredict.cfacts │ ├── classifyPredict.ppr │ ├── classifyPredict.wam │ ├── classifyPredict_minAlphaAdditions.cfacts │ ├── config.properties │ ├── duplicateSignatureTest.ppr │ ├── duplicateSignatureTest.wam │ ├── equalityTest.ppr │ ├── equalityTest.wam │ ├── memEDB.cfacts │ ├── memIDB.ppr │ ├── memIDB.wam │ ├── ne.ppr │ ├── ne.wam │ ├── nodeMerging │ ├── diamond.facts │ ├── diamond.ppr │ ├── diamond.wam │ ├── loop.facts │ ├── loop.ppr │ ├── loop.wam │ ├── multirankwalk.graph │ ├── multirankwalk.ppr │ ├── multirankwalk.wam │ ├── recursion.facts │ ├── recursion.ppr │ ├── recursion.wam │ ├── trapezoid.facts │ ├── trapezoid.ppr │ └── trapezoid.wam │ ├── sparseGraph │ ├── child_per_per.cfacts │ ├── family.ppr │ ├── family.sparse │ │ ├── child_per_per.colIndex │ │ ├── child_per_per.rce │ │ ├── child_per_per.rowOffset │ │ ├── per.i │ │ ├── sister_per_per.colIndex │ │ ├── sister_per_per.rce │ │ ├── sister_per_per.rowOffset │ │ ├── sparseIndex.txt │ │ ├── spouse_per_per.colIndex │ │ ├── spouse_per_per.rce │ │ └── spouse_per_per.rowOffset │ ├── family.wam │ ├── sister_per_per.cfacts │ └── spouse_per_per.cfacts │ ├── train.examples.grounded │ ├── ungroundedSolutionsTest │ ├── grand.cfacts │ └── grand.wam │ ├── wam │ ├── simpleProgram.ppr │ └── simpleProgram.wam │ └── weighted │ ├── dbWeights.ppr │ ├── dbWeights.wam │ ├── tiny.ppr │ ├── tiny.wam │ ├── tinycorpus.cfacts │ ├── tinycorpus.graph │ ├── tinylabels.cfacts │ ├── weightedRules.cfacts │ ├── weightedRules.ppr │ └── weightedRules.wam ├── theano ├── medical │ └── .gitignore ├── textcat │ ├── Makefile │ ├── proppr.settings │ ├── textcat.ppr │ ├── toycorpus.graph │ ├── toycorpus.txt │ ├── toylabels.cfacts │ ├── toytest.examples │ └── toytrain.examples └── wordsimilarity │ ├── Makefile │ ├── embeddings2theano.py │ ├── lexical.embeddings │ ├── proppr.settings │ ├── run.sh │ ├── test.examples │ ├── train.examples │ └── wordsimilarity.ppr └── tutorial ├── README ├── cora ├── Makefile ├── cora.ppr ├── scripts │ ├── getData.pl │ ├── getGraph.sh │ └── getLabel.sh ├── test.raw └── train.raw ├── labelprop ├── Makefile ├── Notes.txt ├── README ├── multirankwalk.ppr ├── naive.ppr ├── r8edges.graph ├── r8seeds.graph ├── r8test.examples ├── tinyedges.graph ├── tinyseeds.graph ├── tinytest.examples ├── toyedges.graph ├── toyseeds.graph └── toytest.examples ├── structureLearning ├── .gitignore ├── Makefile ├── README ├── kinship-2nd.cfacts ├── kinship-test.cfacts ├── kinship-test.examples ├── kinship-train.cfacts 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