2016
Reconstructing Causal Biological Networks through Active Learning
Cho H, Berger B, Peng J. Reconstructing Causal Biological Networks through Active Learning. PLOS ONE 2016, 11: e0150611. PMID: 26930205, PMCID: PMC4773135, DOI: 10.1371/journal.pone.0150611.Peer-Reviewed Original ResearchConceptsGaussian Bayesian networksBayesian networkContinuous Bayesian networksDiscrete Bayesian networksBiological networksFast convergenceGreat practical interestGene regulatory networksGraph structurePractical interestQuantitative propertiesSignificant runtime improvementsComplex biological systemsRuntime improvementCausal biological networksSystems biologyCentral problemFinal distributionPrevious approachesNetwork structureResource constraintsData setsLearning algorithmImportant modelActive learning algorithm
2015
Exploiting ontology graph for predicting sparsely annotated gene function
Wang S, Cho H, Zhai C, Berger B, Peng J. Exploiting ontology graph for predicting sparsely annotated gene function. Bioinformatics 2015, 31: i357-i364. PMID: 26072504, PMCID: PMC4542782, DOI: 10.1093/bioinformatics/btv260.Peer-Reviewed Original ResearchConceptsFunction prediction algorithmsPrediction algorithmVariety of algorithmsFunctional labelsOntology graphCross-validation experimentsOverfitting problemGraph structurePrevious stateGene functionAlgorithmAnnotation catalogsTens of thousandsMolecular interaction networksFunction predictionOntology databasePoor predictive performanceAnnotationLabelsPredictive performanceGene Ontology databaseInformationLarge numberGO termsInteraction networks