###------------------------------------------------- ### Input parameter settings file for ### ### BA Bayesian ### N Network Inference ### J with Java ### O Objects ### ### Banjo is licensed from Duke University. ### Copyright (c) 2005-07 by Alexander J. Hartemink. ### All rights reserved. ### ### Settings file consistent with version 2.0.0 ###------------------------------------------------- ###------------------------------------------------- ### Project information ###------------------------------------------------- project = banjo static example user = demo dataset = 43-proteins-4380-genes notes = static bayesian network inference ###------------------------------------------------- ### Search component specifications ###------------------------------------------------- searcherChoice = SimAnneal proposerChoice = RandomLocalMove evaluatorChoice = default deciderChoice = default ###------------------------------------------------- ### Input and output locations ###------------------------------------------------- inputDirectory = /Users/bvsteensel/Documents/BNI/input observationsFile = BanjoCore_P95_BS104.inputdata.txt outputDirectory = /Users/bvsteensel/Documents/BNI/output reportFile = BanjoCore_P95_BS104.report.txt ###------------------------------------------------- ### We require this only to validate the input ###------------------------------------------------- variableCount = 43 ###------------------------------------------------- ### Pre-processing options ###------------------------------------------------- discretizationPolicy = none discretizationExceptions = createDiscretizationReport = no ###------------------------------------------------- ### Network structure properties ###------------------------------------------------- minMarkovLag = 0 maxMarkovLag = 0 dbnMandatoryIdentityLags = equivalentSampleSize = 1.0 maxParentCount = 5 defaultMaxParentCount = 10 ###------------------------------------------------- ### Network structure properties, optional ###------------------------------------------------- initialStructureFile = mustBePresentEdgesFile = mustNotBePresentEdgesFile = ###------------------------------------------------- ### Stopping criteria ###------------------------------------------------- maxTime = maxProposedNetworks = 300000 maxRestarts = 10000 minNetworksBeforeChecking = 1000 ###------------------------------------------------- ### Search monitoring properties ###------------------------------------------------- nBestNetworks = 1 bestNetworksAre = screenReportingInterval = 20 s fileReportingInterval = 10 m ###------------------------------------------------- ### Parameters used by specific search methods ###------------------------------------------------- ### For simulated annealing: initialTemperature = 10000 coolingFactor = 0.7 reannealingTemperature = 800 maxAcceptedNetworksBeforeCooling = 2500 maxProposedNetworksBeforeCooling = 10000 minAcceptedNetworksBeforeReannealing = 500 ### For greedy: minProposedNetworksAfterHighScore = 1000 minProposedNetworksBeforeRestart = 3000 maxProposedNetworksBeforeRestart = 5000 restartWithRandomNetwork = yes maxParentCountForRestart = 3 ###------------------------------------------------- ### Command line user interface options ###------------------------------------------------- askToVerifySettings = no ###------------------------------------------------- ### Post-processing options ###------------------------------------------------- createDotOutput = no computeInfluenceScores = yes computeConsensusGraph = no createConsensusGraphAsHtml = no fileNameForTopGraph = top.graph.@TS@ fileNameForConsensusGraph = consensus.graph.@TS@ dotGraphicsFormat = jpg dotFileExtension = txt htmlFileExtension = html fullPathToDotExecutable = ### C:/Program Files/ATT/Graphviz/bin/dot.exe timeStampFormat = yyyy.MM.dd.HH.mm.ss ###------------------------------------------------- ### Memory management and performance options ###------------------------------------------------- precomputeLogGamma = yes useCache = fastLevel2 cycleCheckingMethod = dfs ###------------------------------------------------- ### Misc. options ###------------------------------------------------- displayMemoryInfo = yes displayStructures = yes