diff --git a/scripts/runAllBoostsOptimization.sh b/scripts/runAllBoostsOptimization.sh old mode 100644 new mode 100755 index abdce1be..81bfadfb --- a/scripts/runAllBoostsOptimization.sh +++ b/scripts/runAllBoostsOptimization.sh @@ -1,12 +1,11 @@ #!/bin/bash -whats="disease gene fields posneg additional extra" +whats="genedis fields posneg additional extra pmclass mutation drug" -mvn clean compile - -#srun scripts/runBoostOptimizer.sh extra +mvn compile for i in $whats; do echo "Starting boost optimization of $i" - sbatch scripts/runBoostOptimizer.sh $i + sbatch scripts/runBoostOptimizer.sh $i 2017 + sbatch scripts/runBoostOptimizer.sh $i 2018 done diff --git a/scripts/runAllPmClassExperimentsLiterature.sh b/scripts/runAllPmClassExperimentsLiterature.sh index fc68642c..0a4dc2b8 100755 --- a/scripts/runAllPmClassExperimentsLiterature.sh +++ b/scripts/runAllPmClassExperimentsLiterature.sh @@ -2,8 +2,16 @@ mvn compile # For the best_fields, the slop does not do anything, but a argument value is expected -sbatch --exclude=h5,h6 scripts/runPmClassExperimentsLiterature.sh best_fields OR -sbatch --exclude=h5,h6 scripts/runPmClassExperimentsLiterature.sh best_fields AND +sbatch --exclude=h5,h6 scripts/runPmClassExperimentsLiterature.sh best_fields OR 2017 +sbatch --exclude=h5,h6 scripts/runPmClassExperimentsLiterature.sh best_fields AND 2017 # Here, the boolean operator has no effect -sbatch --exclude=h5,h6 scripts/runPmClassExperimentsLiterature.sh phrase OR +sbatch --exclude=h5,h6 scripts/runPmClassExperimentsLiterature.sh phrase OR 2017 + + +# For the best_fields, the slop does not do anything, but a argument value is expected +sbatch --exclude=h5,h6 scripts/runPmClassExperimentsLiterature.sh best_fields OR 2018 +sbatch --exclude=h5,h6 scripts/runPmClassExperimentsLiterature.sh best_fields AND 2018 + +# Here, the boolean operator has no effect +sbatch --exclude=h5,h6 scripts/runPmClassExperimentsLiterature.sh phrase OR 2018 \ No newline at end of file diff --git a/scripts/runAllTermBoostExperimentsLiterature.sh b/scripts/runAllTermBoostExperimentsLiterature.sh index b7f072a8..e3c575bc 100755 --- a/scripts/runAllTermBoostExperimentsLiterature.sh +++ b/scripts/runAllTermBoostExperimentsLiterature.sh @@ -2,8 +2,16 @@ mvn compile # For the best_fields, the slop does not do anything, but a argument value is expected -sbatch --exclude=h5,h6 scripts/runTermBoostExperimentsLiterature.sh best_fields OR -sbatch --exclude=h5,h6 scripts/runTermBoostExperimentsLiterature.sh best_fields AND +sbatch --exclude=h5,h6 scripts/runTermBoostExperimentsLiterature.sh best_fields OR 2017 +sbatch --exclude=h5,h6 scripts/runTermBoostExperimentsLiterature.sh best_fields AND 2017 # Here, the boolean operator has no effect -sbatch --exclude=h5,h6 scripts/runTermBoostExperimentsLiterature.sh phrase OR +sbatch --exclude=h5,h6 scripts/runTermBoostExperimentsLiterature.sh phrase OR 2017 + + +# For the best_fields, the slop does not do anything, but a argument value is expected +sbatch --exclude=h5,h6 scripts/runTermBoostExperimentsLiterature.sh best_fields OR 2018 +sbatch --exclude=h5,h6 scripts/runTermBoostExperimentsLiterature.sh best_fields AND 2018 + +# Here, the boolean operator has no effect +sbatch --exclude=h5,h6 scripts/runTermBoostExperimentsLiterature.sh phrase OR 2018 \ No newline at end of file diff --git a/scripts/runBoostOptimizer.sh b/scripts/runBoostOptimizer.sh index 98971bb8..de32d165 100755 --- a/scripts/runBoostOptimizer.sh +++ b/scripts/runBoostOptimizer.sh @@ -1,6 +1,7 @@ #!/bin/bash #SBATCH --mem 10G #SBATCH --cpus-per-task 4 -WHAT=$1 +#SBATCH -J boostopt -mvn exec:java -Dexec.mainClass=at.medunigraz.imi.bst.trec.SigirPubmedExperimenterBoostOptimizer -Dexec.args="$1" + +mvn exec:java -Dexec.mainClass=at.medunigraz.imi.bst.trec.SigirPubmedExperimenterBoostOptimizer -Dexec.args="$1 $2" diff --git a/scripts/runPmClassExperimentsLiterature.sh b/scripts/runPmClassExperimentsLiterature.sh index 61eba2dd..164d62b0 100755 --- a/scripts/runPmClassExperimentsLiterature.sh +++ b/scripts/runPmClassExperimentsLiterature.sh @@ -1,6 +1,6 @@ #!/bin/bash #SBATCH --cpus-per-task 2 #SBATCH --mem 10G -#SBATCH -J termboostexp +#SBATCH -J pmclassexp -mvn exec:java -Dexec.mainClass=at.medunigraz.imi.bst.trec.SigirPubmedExperimenterPmClass -Dexec.args="$1 $2" +mvn exec:java -Dexec.mainClass=at.medunigraz.imi.bst.trec.SigirPubmedExperimenterPmClass -Dexec.args="$1 $2 $3" diff --git a/scripts/runTermBoostExperimentsLiterature.sh b/scripts/runTermBoostExperimentsLiterature.sh index 91fd17a3..78f31f43 100755 --- a/scripts/runTermBoostExperimentsLiterature.sh +++ b/scripts/runTermBoostExperimentsLiterature.sh @@ -3,4 +3,4 @@ #SBATCH --mem 10G #SBATCH -J termboostexp -mvn exec:java -Dexec.mainClass=at.medunigraz.imi.bst.trec.SigirPubmedTermBoostExperimenterDefaultBoosting -Dexec.args="$1 $2" +mvn exec:java -Dexec.mainClass=at.medunigraz.imi.bst.trec.SigirPubmedTermBoostExperimenterDefaultBoosting -Dexec.args="$1 $2 $3" diff --git a/src/main/java/at/medunigraz/imi/bst/trec/SigirPubmedExperimenterBoostOptimizer.java b/src/main/java/at/medunigraz/imi/bst/trec/SigirPubmedExperimenterBoostOptimizer.java index 1cff9bb3..31178326 100644 --- a/src/main/java/at/medunigraz/imi/bst/trec/SigirPubmedExperimenterBoostOptimizer.java +++ b/src/main/java/at/medunigraz/imi/bst/trec/SigirPubmedExperimenterBoostOptimizer.java @@ -2,6 +2,7 @@ import at.medunigraz.imi.bst.trec.experiment.Experiment; +import java.io.File; import java.text.DecimalFormat; import java.util.*; import java.util.stream.IntStream; @@ -19,8 +20,8 @@ public static void main(String[] args) { validParams.add("mutation"); validParams.add("drug"); - if (args.length != 1 || !validParams.contains(args[0])) { - System.err.println("Usage: " + SigirPubmedExperimenterBoostOptimizer.class.getSimpleName() + " "); + if (args.length != 2 || !validParams.contains(args[0])) { + System.err.println("Usage: " + SigirPubmedExperimenterBoostOptimizer.class.getSimpleName() + " "); System.err.println("Where is one of " + validParams); System.exit(1); } @@ -29,7 +30,7 @@ public static void main(String[] args) { final Experiment.GoldStandard goldStandard = Experiment.GoldStandard.OFFICIAL; final Experiment.Task target = Experiment.Task.PUBMED; - final int year = 2017; + final int year = Integer.parseInt(args[1]); Map templateProperties = Collections.unmodifiableMap(SigirParameters.LITERATURE_ES_DEFAULTS); @@ -58,7 +59,7 @@ public static void main(String[] args) { } } } - runExperimentsWithParameters(parameters, suffixes, year, what, goldStandard, target); + runExperimentsWithParameters("/templates/sigir19_experiments_biomed/baseline.json", parameters, suffixes, year, what, goldStandard, target); } else if (what.equals("fields")) { List> parameters = new ArrayList<>(); List suffixes = new ArrayList<>(); @@ -81,7 +82,7 @@ public static void main(String[] args) { } } } - runExperimentsWithParameters(parameters, suffixes, year, what, goldStandard, target); + runExperimentsWithParameters("/templates/sigir19_field_boost_optimization", parameters, suffixes, year, what, goldStandard, target); } else if (what.equals("posneg")) { List> parameters = new ArrayList<>(); List suffixes = new ArrayList<>(); @@ -95,7 +96,7 @@ public static void main(String[] args) { suffixes.add(suffix); } } - runExperimentsWithParameters(parameters, suffixes, year, what, goldStandard, target); + runExperimentsWithParameters("/templates/sigir19_boost_optimization/posneg.json",parameters, suffixes, year, what, goldStandard, target); } else if (what.equals("additional")) { List> parameters = new ArrayList<>(); List suffixes = new ArrayList<>(); @@ -112,7 +113,7 @@ public static void main(String[] args) { } } } - runExperimentsWithParameters(parameters, suffixes, year, what, goldStandard, target); + runExperimentsWithParameters("/templates/sigir19_boost_optimization/additional.json", parameters, suffixes, year, what, goldStandard, target); } else if (what.equals("extra")) { List> parameters = new ArrayList<>(); List suffixes = new ArrayList<>(); @@ -123,7 +124,7 @@ public static void main(String[] args) { parameters.add(paramcombination); suffixes.add(suffix); } - runExperimentsWithParameters(parameters, suffixes, year, what, goldStandard, target); + runExperimentsWithParameters("/templates/sigir19_experiments_biomed/extra.json",parameters, suffixes, year, what, goldStandard, target); } else if (what.equals("mutation")) { List> parameters = new ArrayList<>(); List suffixes = new ArrayList<>(); @@ -134,8 +135,10 @@ public static void main(String[] args) { parameters.add(paramcombination); suffixes.add(suffix); } - runExperimentsWithParameters(parameters, suffixes, year, what, goldStandard, target); + runExperimentsWithParameters("/templates/sigir19_experiments_biomed/mutations.json", parameters, suffixes, year, what, goldStandard, target); } else if (what.equals("pmclass")) { + List> parameters = new ArrayList<>(); + List suffixes = new ArrayList<>(); final List pmfields = Arrays.asList("pmclass2017lstm.keyword", "pmclass2017lstmatt.keyword", "pmclass2017lstmgru.keyword", @@ -144,22 +147,28 @@ public static void main(String[] args) { "pmclass2018lstmgru.keyword", "pmclass2017.keyword", "pmclass2018.keyword"); - //final List pmfields = Arrays.asList( "pmclass2017.keyword"); - pmfields.parallelStream().forEach(pmfield -> { - Map parameters = new HashMap<>(templateProperties); - parameters.put("pm_class_field", pmfield); - // runExperiments(parameters, false, goldStandard, target, year, what, "-" + pmfield); - }); + for (String pmfield : pmfields) { + for (double extrab = .5; extrab <= 3; extrab += .5) { + Map paramcombination = new HashMap<>(templateProperties); + paramcombination.put("pm_boost", String.valueOf(extrab)); + paramcombination.put("pm_class_field", pmfield); + String suffix = "--pm" + df.format(extrab) + "-pmf:"; + parameters.add(paramcombination); + suffixes.add(suffix); + } + } + runExperimentsWithParameters("/templates/sigir19_pmclass_biomed", parameters, suffixes, year, what, goldStandard, target); + } else throw new IllegalStateException("Unknown mode " + what); } - private static void runExperimentsWithParameters(List> parameters, List suffixes, int year, String what, Experiment.GoldStandard goldStandard, Experiment.Task target) { + private static void runExperimentsWithParameters(String template, List> parameters, List suffixes, int year, String what, Experiment.GoldStandard goldStandard, Experiment.Task target) { IntStream.range(0, parameters.size()).parallel().forEach(i -> { Map parameterset = parameters.get(i); String suffix = suffixes.get(i); - // runExperiments(parameterset, false, goldStandard, target, year, what, suffix); + runBoostExperiments(template, parameterset, goldStandard, target, year, what, suffix); }); } } diff --git a/src/main/java/at/medunigraz/imi/bst/trec/SigirPubmedExperimenterPmClass.java b/src/main/java/at/medunigraz/imi/bst/trec/SigirPubmedExperimenterPmClass.java index 51413141..af9a41fd 100644 --- a/src/main/java/at/medunigraz/imi/bst/trec/SigirPubmedExperimenterPmClass.java +++ b/src/main/java/at/medunigraz/imi/bst/trec/SigirPubmedExperimenterPmClass.java @@ -11,15 +11,15 @@ public class SigirPubmedExperimenterPmClass extends SuperSigirPubmedRecallExperimenter { public static void main(String[] args) { - if (args.length != 2) { - System.err.println("Parameters: "); + if (args.length != 3) { + System.err.println("Parameters: "); } String what = "pmclass"; final Experiment.GoldStandard goldStandard = Experiment.GoldStandard.OFFICIAL; final Experiment.Task target = Experiment.Task.PUBMED; - final int year = 2017; + final int year = Integer.parseInt(args[2]); diff --git a/src/main/java/at/medunigraz/imi/bst/trec/SigirPubmedTermBoostExperimenterDefaultBoosting.java b/src/main/java/at/medunigraz/imi/bst/trec/SigirPubmedTermBoostExperimenterDefaultBoosting.java index 26cfa2f1..d5230860 100644 --- a/src/main/java/at/medunigraz/imi/bst/trec/SigirPubmedTermBoostExperimenterDefaultBoosting.java +++ b/src/main/java/at/medunigraz/imi/bst/trec/SigirPubmedTermBoostExperimenterDefaultBoosting.java @@ -10,13 +10,13 @@ public class SigirPubmedTermBoostExperimenterDefaultBoosting extends SuperSigirPubmedRecallExperimenter { public static void main(String[] args) { - if (args.length != 2) { - System.err.println("Parameters: "); + if (args.length != 3) { + System.err.println("Parameters: "); } final Experiment.GoldStandard goldStandard = Experiment.GoldStandard.OFFICIAL; final Experiment.Task target = Experiment.Task.PUBMED; - final int year = 2018; + final int year = Integer.parseInt(args[2]); Map templateProperties = new HashMap<>(SigirParameters.LITERATURE_ES_DEFAULTS); diff --git a/src/main/java/at/medunigraz/imi/bst/trec/SuperSigirPubmedRecallExperimenter.java b/src/main/java/at/medunigraz/imi/bst/trec/SuperSigirPubmedRecallExperimenter.java index 5e8ea673..e0eff2f8 100644 --- a/src/main/java/at/medunigraz/imi/bst/trec/SuperSigirPubmedRecallExperimenter.java +++ b/src/main/java/at/medunigraz/imi/bst/trec/SuperSigirPubmedRecallExperimenter.java @@ -2,6 +2,7 @@ import at.medunigraz.imi.bst.trec.experiment.Experiment; import at.medunigraz.imi.bst.trec.experiment.ExperimentsBuilder; +import bsh.commands.dir; import com.google.common.collect.Sets; import org.apache.commons.lang.StringUtils; import org.apache.logging.log4j.LogManager; @@ -48,6 +49,7 @@ protected static void runPmClassifierExperiments(File template, Map templateProperties, Experiment.GoldStandard goldStandard, Experiment.Task target, int year, String what, String suffix) { + protected static void runBoostExperiments(String template, Map templateProperties, Experiment.GoldStandard goldStandard, Experiment.Task target, int year, String what, String suffix) { if (templateProperties.size() > numProperties) throw new IllegalArgumentException("There are more key in the properties map as there are known properties: " + templateProperties.keySet()); @@ -70,12 +72,22 @@ protected static void runBoostExperiments(File template, Map tem builder.setDefaultStatsDir("stats_" + what + "_" + year); builder.setDefaultResultsDir("results_" + what + "_" + year); } - final Map sigirTemplates = getSigirTemplates("/templates/sigir19_experiments_biomed"); + final File file = new File(PubmedExperimenter.class.getResource(template).getFile()); + Map sigirTemplates; + if (file.isDirectory()) { + sigirTemplates = getSigirTemplates(template); + } else { + final TemplateSet templateSet = new TemplateSet(); + templateSet.setBase(file); + sigirTemplates = new HashMap<>(); + sigirTemplates.put(file.getName(), templateSet); + } + // Switch everything on - except word removal - so that the boosters actually have a point. final Set> expansionSets = new HashSet<>(Arrays.asList(EnumSet.complementOf(EnumSet.of(Expansion.WR)))); - addExperiments(template, sigirTemplates, templateProperties, expansionSets, goldStandard, target, year, builder, suffix); + addExperiments(null, sigirTemplates, templateProperties, expansionSets, goldStandard, target, year, builder, suffix); Set experiments = builder.build(); final ExecutorService executorService = Executors.newFixedThreadPool(5); @@ -91,6 +103,7 @@ protected static void runBoostExperiments(File template, Map tem throw new RuntimeException(e); } } + executorService.shutdown(); } /** @@ -138,6 +151,7 @@ protected static void runTermBoostExperiments(Map templateProper throw new RuntimeException(e); } } + executorService.shutdown(); } /** diff --git a/src/main/resources/templates/sigir19_boost_optimization/additional.json b/src/main/resources/templates/sigir19_boost_optimization/additional.json new file mode 100644 index 00000000..06997ce2 --- /dev/null +++ b/src/main/resources/templates/sigir19_boost_optimization/additional.json @@ -0,0 +1,13 @@ +{ + "bool": { + "must": [ + {{sigir19_experiments_biomed/disease.json}}, + {{sigir19_experiments_biomed/gene.json}} + ], + "should": [ + {{sigir19_experiments_biomed/chemotherapy.json}}, + {{sigir19_experiments_biomed/cancer.json}}, + {{sigir19_experiments_biomed/dna.json}} + ] + } +} diff --git a/src/main/resources/templates/sigir19_boost_optimization/posneg.json b/src/main/resources/templates/sigir19_boost_optimization/posneg.json new file mode 100644 index 00000000..70ac7ada --- /dev/null +++ b/src/main/resources/templates/sigir19_boost_optimization/posneg.json @@ -0,0 +1,12 @@ +{ + "bool": { + "must": [ + {{sigir19_experiments_biomed/disease.json}}, + {{sigir19_experiments_biomed/gene.json}} + ], + "should": [ + {{sigir19_experiments_biomed/positive_boosters.json}}, + {{sigir19_experiments_biomed/negative_boosters.json}} + ] + } +} diff --git a/src/main/resources/templates/sigir19_experiments_biomed/cancer.json b/src/main/resources/templates/sigir19_experiments_biomed/cancer.json index c6d17cdd..bc4281df 100644 --- a/src/main/resources/templates/sigir19_experiments_biomed/cancer.json +++ b/src/main/resources/templates/sigir19_experiments_biomed/cancer.json @@ -2,7 +2,7 @@ "bool": { "must": [ {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}} + {{sigir19_experiments_biomed/gene.json}} ], "should": [ {{sigir19_experiments_biomed/cancer.json}}, diff --git a/src/main/resources/templates/sigir19_experiments_biomed/chemo.json b/src/main/resources/templates/sigir19_experiments_biomed/chemo.json index 91b7dc0d..5228f27a 100644 --- a/src/main/resources/templates/sigir19_experiments_biomed/chemo.json +++ b/src/main/resources/templates/sigir19_experiments_biomed/chemo.json @@ -2,7 +2,7 @@ "bool": { "must": [ {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}} + {{sigir19_experiments_biomed/gene.json}} ], "should": [ {{sigir19_experiments_biomed/chemotherapy.json}}, diff --git a/src/main/resources/templates/sigir19_experiments_biomed/dna.json b/src/main/resources/templates/sigir19_experiments_biomed/dna.json index 8c135ee3..8c5b90e5 100644 --- a/src/main/resources/templates/sigir19_experiments_biomed/dna.json +++ b/src/main/resources/templates/sigir19_experiments_biomed/dna.json @@ -2,7 +2,7 @@ "bool": { "must": [ {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}} + {{sigir19_experiments_biomed/gene.json}} ], "should": [ {{sigir19_experiments_biomed/dna.json}}, diff --git a/src/main/resources/templates/sigir19_pmclass_biomed/baseline_custompm_should.json b/src/main/resources/templates/sigir19_experiments_biomed/extra.json similarity index 75% rename from src/main/resources/templates/sigir19_pmclass_biomed/baseline_custompm_should.json rename to src/main/resources/templates/sigir19_experiments_biomed/extra.json index 888f693d..c157ddbb 100644 --- a/src/main/resources/templates/sigir19_pmclass_biomed/baseline_custompm_should.json +++ b/src/main/resources/templates/sigir19_experiments_biomed/extra.json @@ -5,7 +5,7 @@ {{sigir19_experiments_biomed/gene.json}} ], "should": [ - {{sigir19_experiments_biomed/pm.json}} + {{sigir19_experiments_biomed/extra.json}}, ] } } diff --git a/src/main/resources/templates/sigir19_experiments_biomed/genefield_custompm_must.json b/src/main/resources/templates/sigir19_experiments_biomed/genefield_custompm_must.json deleted file mode 100644 index 0fd107d9..00000000 --- a/src/main/resources/templates/sigir19_experiments_biomed/genefield_custompm_must.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "bool": { - "must": [ - {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}}, - {{sigir19_experiments_biomed/pm.json}} - ] - } -} diff --git a/src/main/resources/templates/sigir19_experiments_biomed/genefield_custompm_should.json b/src/main/resources/templates/sigir19_experiments_biomed/genefield_custompm_should.json deleted file mode 100644 index ab0ecb47..00000000 --- a/src/main/resources/templates/sigir19_experiments_biomed/genefield_custompm_should.json +++ /dev/null @@ -1,11 +0,0 @@ -{ - "bool": { - "must": [ - {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}} - ], - "should": [ - {{sigir19_experiments_biomed/pm.json}} - ] - } -} diff --git a/src/main/resources/templates/sigir19_experiments_biomed/mutations.json b/src/main/resources/templates/sigir19_experiments_biomed/mutations.json index 2b6f98e9..f58c644a 100644 --- a/src/main/resources/templates/sigir19_experiments_biomed/mutations.json +++ b/src/main/resources/templates/sigir19_experiments_biomed/mutations.json @@ -2,7 +2,7 @@ "bool": { "must": [ {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}} + {{sigir19_experiments_biomed/gene.json}} ], "should": [ {{sigir19_experiments_biomed/mutations.json}} diff --git a/src/main/resources/templates/sigir19_experiments_biomed/negative_boosters.json b/src/main/resources/templates/sigir19_experiments_biomed/negative_boosters.json index 507f5053..1a271aec 100644 --- a/src/main/resources/templates/sigir19_experiments_biomed/negative_boosters.json +++ b/src/main/resources/templates/sigir19_experiments_biomed/negative_boosters.json @@ -2,7 +2,7 @@ "bool": { "must": [ {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}} + {{sigir19_experiments_biomed/gene.json}} ], "should": [ {{sigir19_experiments_biomed/negative_boosters.json}}, diff --git a/src/main/resources/templates/sigir19_experiments_biomed/pos_boosters.json b/src/main/resources/templates/sigir19_experiments_biomed/pos_boosters.json index a2b3944c..dcbef559 100644 --- a/src/main/resources/templates/sigir19_experiments_biomed/pos_boosters.json +++ b/src/main/resources/templates/sigir19_experiments_biomed/pos_boosters.json @@ -2,7 +2,7 @@ "bool": { "must": [ {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}} + {{sigir19_experiments_biomed/gene.json}} ], "should": [ {{sigir19_experiments_biomed/positive_boosters.json}} diff --git a/src/main/resources/templates/sigir19_experiments_biomed/pos_boosters_custompm_must.json b/src/main/resources/templates/sigir19_experiments_biomed/pos_boosters_custompm_must.json deleted file mode 100644 index 57d4e959..00000000 --- a/src/main/resources/templates/sigir19_experiments_biomed/pos_boosters_custompm_must.json +++ /dev/null @@ -1,12 +0,0 @@ -{ - "bool": { - "must": [ - {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}}, - {{sigir19_experiments_biomed/pm.json}} - ], - "should": [ - {{sigir19_experiments_biomed/positive_boosters.json}} - ] - } -} diff --git a/src/main/resources/templates/sigir19_experiments_biomed/pos_boosters_custompm_should.json b/src/main/resources/templates/sigir19_experiments_biomed/pos_boosters_custompm_should.json deleted file mode 100644 index b5c66c73..00000000 --- a/src/main/resources/templates/sigir19_experiments_biomed/pos_boosters_custompm_should.json +++ /dev/null @@ -1,12 +0,0 @@ -{ - "bool": { - "must": [ - {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}} - ], - "should": [ - {{sigir19_experiments_biomed/positive_boosters.json}}, - {{sigir19_experiments_biomed/pm.json}} - ] - } -} diff --git a/src/main/resources/templates/sigir19_experiments_biomed/positive_boosters.json b/src/main/resources/templates/sigir19_experiments_biomed/positive_boosters.json index 0386a37b..63aa156e 100644 --- a/src/main/resources/templates/sigir19_experiments_biomed/positive_boosters.json +++ b/src/main/resources/templates/sigir19_experiments_biomed/positive_boosters.json @@ -2,7 +2,7 @@ "bool": { "must": [ {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}} + {{sigir19_experiments_biomed/gene.json}} ], "should": [ {{sigir19_experiments_biomed/positive_boosters.json}}, diff --git a/src/main/resources/templates/sigir19_experiments_biomed/with_pos_neg_boosters_additional_signals_extra_custompm_should.json b/src/main/resources/templates/sigir19_experiments_biomed/with_pos_neg_boosters_additional_signals_extra_custompm_should.json deleted file mode 100644 index 805b29e4..00000000 --- a/src/main/resources/templates/sigir19_experiments_biomed/with_pos_neg_boosters_additional_signals_extra_custompm_should.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "bool": { - "must": [ - {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}} - ], - "should": [ - {{sigir19_experiments_biomed/positive_boosters.json}}, - {{sigir19_experiments_biomed/negative_boosters.json}}, - {{sigir19_experiments_biomed/chemotherapy.json}}, - {{sigir19_experiments_biomed/cancer.json}}, - {{sigir19_experiments_biomed/dna.json}}, - {{sigir19_experiments_biomed/extra.json}}, - {{sigir19_experiments_biomed/pm.json}} - ] - } -} diff --git a/src/main/resources/templates/sigir19_experiments_biomed/with_pos_neg_boosters_additional_signals_extra_custompm_must.json b/src/main/resources/templates/sigir19_field_boost_optimization/all.json similarity index 71% rename from src/main/resources/templates/sigir19_experiments_biomed/with_pos_neg_boosters_additional_signals_extra_custompm_must.json rename to src/main/resources/templates/sigir19_field_boost_optimization/all.json index 64ce5b63..b7a8f9bf 100644 --- a/src/main/resources/templates/sigir19_experiments_biomed/with_pos_neg_boosters_additional_signals_extra_custompm_must.json +++ b/src/main/resources/templates/sigir19_field_boost_optimization/all.json @@ -2,8 +2,7 @@ "bool": { "must": [ {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}}, - {{sigir19_experiments_biomed/pm.json}} + {{sigir19_experiments_biomed/gene.json}} ], "should": [ {{sigir19_experiments_biomed/positive_boosters.json}}, @@ -11,7 +10,8 @@ {{sigir19_experiments_biomed/chemotherapy.json}}, {{sigir19_experiments_biomed/cancer.json}}, {{sigir19_experiments_biomed/dna.json}}, - {{sigir19_experiments_biomed/extra.json}} + {{sigir19_experiments_biomed/mutations.json}}, + {{sigir19_experiments_biomed/interactions.json}} ] } } diff --git a/src/main/resources/templates/sigir19_field_boost_optimization/baseline.json b/src/main/resources/templates/sigir19_field_boost_optimization/baseline.json new file mode 100644 index 00000000..91b7db6c --- /dev/null +++ b/src/main/resources/templates/sigir19_field_boost_optimization/baseline.json @@ -0,0 +1,8 @@ +{ + "bool": { + "must": [ + {{sigir19_experiments_biomed/disease.json}}, + {{sigir19_experiments_biomed/gene.json}} + ] + } +} diff --git a/src/main/resources/templates/sigir19_pmclass_biomed/all_custompm_must.json b/src/main/resources/templates/sigir19_pmclass_biomed/all_must.json similarity index 89% rename from src/main/resources/templates/sigir19_pmclass_biomed/all_custompm_must.json rename to src/main/resources/templates/sigir19_pmclass_biomed/all_must.json index cb36e4e5..b6b9107a 100644 --- a/src/main/resources/templates/sigir19_pmclass_biomed/all_custompm_must.json +++ b/src/main/resources/templates/sigir19_pmclass_biomed/all_must.json @@ -2,7 +2,7 @@ "bool": { "must": [ {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}}, + {{sigir19_experiments_biomed/gene.json}}, {{sigir19_experiments_biomed/pm.json}} ], "should": [ diff --git a/src/main/resources/templates/sigir19_pmclass_biomed/all_custompm_should.json b/src/main/resources/templates/sigir19_pmclass_biomed/all_should.json similarity index 89% rename from src/main/resources/templates/sigir19_pmclass_biomed/all_custompm_should.json rename to src/main/resources/templates/sigir19_pmclass_biomed/all_should.json index 5229e907..ed890310 100644 --- a/src/main/resources/templates/sigir19_pmclass_biomed/all_custompm_should.json +++ b/src/main/resources/templates/sigir19_pmclass_biomed/all_should.json @@ -2,7 +2,7 @@ "bool": { "must": [ {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene_plus_genefield.json}} + {{sigir19_experiments_biomed/gene.json}} ], "should": [ {{sigir19_experiments_biomed/positive_boosters.json}}, diff --git a/src/main/resources/templates/sigir19_pmclass_biomed/baseline_custompm_must.json b/src/main/resources/templates/sigir19_pmclass_biomed/baseline_custompm_must.json deleted file mode 100644 index 991d6ee6..00000000 --- a/src/main/resources/templates/sigir19_pmclass_biomed/baseline_custompm_must.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "bool": { - "must": [ - {{sigir19_experiments_biomed/disease.json}}, - {{sigir19_experiments_biomed/gene.json}}, - {{sigir19_experiments_biomed/pm.json}} - ] - } -} diff --git a/src/main/resources/templates/sigir19_experiments_biomed/baseline_custompm_must.json b/src/main/resources/templates/sigir19_pmclass_biomed/baseline_must.json similarity index 100% rename from src/main/resources/templates/sigir19_experiments_biomed/baseline_custompm_must.json rename to src/main/resources/templates/sigir19_pmclass_biomed/baseline_must.json diff --git a/src/main/resources/templates/sigir19_experiments_biomed/baseline_custompm_should.json b/src/main/resources/templates/sigir19_pmclass_biomed/baseline_should.json similarity index 100% rename from src/main/resources/templates/sigir19_experiments_biomed/baseline_custompm_should.json rename to src/main/resources/templates/sigir19_pmclass_biomed/baseline_should.json