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Some changes to learn standalone

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leandrohw 2017-12-29 10:06:31 -07:00
parent 4e54490a85
commit 445024befe
1 changed files with 27 additions and 3 deletions
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30
learn/src/main/java/edu/utah/ece/async/ibiosim/learn/Learn.java
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@ -44,6 +44,29 @@ import edu.utah.ece.async.ibiosim.learn.parameterestimator.ParameterEstimator;
* <p>
* -e: when specified, the program will run parameter estimation.
* -l: when specified, parameter estimation will use the estimate the value of the parameters in the list.
* -ta [num]: Sets the activation threshold. Default 1.15
* -tr [num]: Sets the repression threshold. Default 0.75
* -ti [num]: Sets how high a score must be to be considered a parent. Default 0.5
* -tm [num]: Sets how close IVs must be in score to be considered for combination. Default 0.01
* -tn [num]: Sets minimum number of parents to allow through in SelectInitialParents. Default 2
* -tj [num]: Sets the max parents of merged influence vectors, Default 2
* -tt [num]: Sets how fast the bound is relaxed for ta and tr, Default 0.025
* -d [num]: Sets the debug or output level. Default 0
* -wr [num]: Sets how much larger a number must be to be considered as a rise. Default 1
* -ws [num]: Sets how far the TSD points are when compared. Default 1
* -nb [num]: Sets how many bins are used in the evaluation. Default 4
* --lvl: Writes out the suggested levels for every specie
* --readLevels: Reads the levels from level.lvl file for every specie
* --cpp_harshenBoundsOnTie: Determines if harsher bounds are used when parents tie in CPP.
* --cpp_cmp_output_donotInvertSortOrder: Sets the inverted sort order in the 3 places back to normal--cpp_seedParents Determines if parents should be ranked by score, not tsd order in CPP.
* --cmp_score_mustNotWinMajority: Determines if score should be used when following conditions are not met a > r+n || r > a + n
* --score_donotTossSingleRatioParents: Determines if single ratio parents should be kept
* --output_donotTossChangedInfluenceSingleParents: Determines if parents that change influence should not be tossed
* -binNumbers: Equal spacing per bin
* -noSUCC: to not use successors in calculating probabilities
* -PRED: use preicessors in calculating probabilities
* -basicFBP: to use the basic FindBaseProb function
*
*
* @author Leandro Watanabe
* @author Tramy Nguyen
@ -55,9 +78,9 @@ public class Learn {
private static void usage() {
System.err.println("Description:");
System.err.println("\tExecutes bayesian methods for structural learning using GeneNet or parameter estimation using SRES.");
System.err.println("\tExecutes bayesian methods for structural learning of regulatory networks using GeneNet or parameter estimation using SRES.");
System.err.println("Usage:");
System.err.println("\tjava -jar iBioSim-learn-3.0.0-SNAPSHOT-jar-with-dependencies.jar [options] <Input File> <Project Directory>");
System.err.println("\tjava -jar iBioSim-learn-3.0.0-SNAPSHOT-jar-with-dependencies.jar [options] <Input SBML File> <Project Directory>");
System.err.println("Required:");
System.err.println("\t<Input File> the input SBML file.");
System.err.println("\t<Project Directory> the directory where the experimental data is located.");
@ -69,7 +92,8 @@ public class Learn {
System.exit(1);
}
public static void main(String[] args) {
public static void main(String[] args)
{
if(args.length < 2)
{