Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction 英文参考文献.docVIP

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Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction 英文参考文献.doc

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Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction 英文参考文献

GlobalDiscriminativeLearningforHigher- AccuracyComputationalGenePrediction Axel Bernal1*,Koby Crammer1,Artemis Hatzigeorgiou2,Fernando Pereira1 1DepartmentofComputerandInformationScience,UniversityofPennsylvania,Philadelphia,Pennsylvania,UnitedStatesofAmerica,2DepartmentofGenetics,University ofPennsylvania,Philadelphia,Pennsylvania,UnitedStatesofAmerica Most ab initio gene predictors use a probabilistic sequence model, typically a hidden Markov model, to combine separately trained models of genomic signals and content. By combining separate models of relevant genomic features,suchgenepredictorscanexploitsmalltrainingsets andincomplete annotations,andcanbetrainedfairly efficiently. However, that type of piecewise training does not optimize prediction accuracy and has difficulty in accounting for statistical dependencies among different parts of the gene model. With genomic information being createdatanever-increasingrate,itisworthinvestigatingalternativeapproachesinwhichmanydifferenttypesof genomicevidence, with complex statistical dependencies, canbe integratedby discriminative learningto maximize annotation accuracy. Among discriminative learning methods, large-margin classifiers have become prominent because of the success of support vector machines (SVM) in many classification tasks. We describe CRAIG, a new programforabinitiogenepredictionbasedonaconditionalrandomfieldmodelwithsemi-Markovstructurethatis trainedwithanonlinelarge-marginalgorithmrelatedtomulticlassSVMs.Ourexperimentsonbenchmarkvertebrate datasets and on regions from the ENCODE project show significant improvements in prediction accuracy over publishedgenepredictorsthatuseintrinsicfeaturesonly,particularlyatthegenelevelandongeneswithlongintrons. Citation:BernalA,CrammerK,HatzigeorgiouA,PereiraF(2007)Globaldiscriminativelearningforhigher-accuracycomputationalgeneprediction.PLoSComputBiol3(3): e54.doi:10.1371/journal.pcbi.0030054 regions represent more than 95% of the total number of genesinmos