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Lc/add posterior tempering #2

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495f09b
Merge branch 'development'
julesjacobsen Dec 10, 2024
480975e
adapted to temperature
leokim-l Dec 18, 2025
dc238fd
Merge branch 'exomiser:master' into lc/add-posterior-tempering
leokim-l Dec 18, 2025
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23 changes: 17 additions & 6 deletions ...-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/BoqaPrioritiser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ public class BoqaPrioritiser implements Prioritiser<BoqaPriorityResult> {
private final Counter counter;
private final double alpha;
private final double beta;
private final double temperature;

public BoqaPrioritiser(PriorityService priorityService, Counter counter) {
// TODO: add getCounter(): Counter to Priority Service, then initialise the Counter @Lazy in the exomiser-config
Expand All @@ -36,8 +37,9 @@ public BoqaPrioritiser(PriorityService priorityService, Counter counter) {
// it. The Counter now takes ~ 300ms to create, but still, it would be best to move it's creation into the config code.
this.priorityService = priorityService;
this.counter = counter;
this.alpha = 1.0/19077; // TODO: Make alpha and beta constructor parameters
this.alpha = 1.0/19077; // TODO: Make alpha, beta and temperature constructor parameters
this.beta = 0.9;
this.temperature = 1.0; // default
}

@Override
Expand All @@ -50,11 +52,20 @@ public Stream<BoqaPriorityResult> prioritise(List<String> hpoIds, List<Gene> gen
logger.info("Running BOQA prioritiser...XXX");
var observedHpoIds = hpoIds.stream().map(TermId::of).collect(toUnmodifiableSet());
PatientData patientData = new ExomiserPatientData(observedHpoIds, Collections.emptySet());
AlgorithmParameters params = AlgorithmParameters.create(alpha, beta);
BoqaAnalysisResult boqaAnalysisResult = BoqaPatientAnalyzer.computeBoqaResultsRawLog(patientData, counter, params);
List<BoqaResult> rescaledBoqaResults = reScaledRawLogBoqaExomiserScores(boqaAnalysisResult.boqaResults());
logger.debug("Top 10 BOQA results:");
rescaledBoqaResults.stream().sorted(Comparator.comparing(BoqaResult::boqaScore)).limit(10).forEach(b -> logger.debug("BOQA score: {} {} {}", b.counts().diseaseId(), b.boqaScore(), b.counts().diseaseLabel()));
AlgorithmParameters params = AlgorithmParameters.create(alpha, beta, temperature);
double epsilon = 0.000001d;
List<BoqaResult> rescaledBoqaResults;
BoqaAnalysisResult boqaAnalysisResult;
if((Math.abs(1.0 - temperature) < epsilon)) {
boqaAnalysisResult = BoqaPatientAnalyzer.computeBoqaResultsRawLog(patientData, counter, params);
rescaledBoqaResults = reScaledRawLogBoqaExomiserScores(boqaAnalysisResult.boqaResults());
logger.debug("Top 10 BOQA results:");
rescaledBoqaResults.stream().sorted(Comparator.comparing(BoqaResult::boqaScore)).limit(10).forEach(b -> logger.debug("BOQA score: {} {} {}", b.counts().diseaseId(), b.boqaScore(), b.counts().diseaseLabel()));
} else {
boqaAnalysisResult = BoqaPatientAnalyzer.computeBoqaResults(
patientData, counter, Integer.MAX_VALUE, params);
rescaledBoqaResults = boqaAnalysisResult.boqaResults().stream().toList();
}
Map<String, BoqaResult> boqaResultsByDiseaseId = rescaledBoqaResults.stream()
.collect(toUnmodifiableMap(boqaResult -> boqaResult.counts().diseaseId(), Function.identity()));
return genes.stream().map(prioritiseGene(boqaResultsByDiseaseId));
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