2024
A simple but tough-to-beat baseline for fMRI time-series classification
Popov P, Mahmood U, Fu Z, Yang C, Calhoun V, Plis S. A simple but tough-to-beat baseline for fMRI time-series classification. NeuroImage 2024, 303: 120909. PMID: 39515403, PMCID: PMC11625415, DOI: 10.1016/j.neuroimage.2024.120909.Peer-Reviewed Original ResearchConceptsComplex machine learning modelsBlack-box natureMulti-layer perceptronMachine learning modelsPrediction accuracyBlack-box modelsFMRI classificationComplex classifiersClassification accuracySequential informationHuman fMRI dataLearning modelsBlack-boxRich modelsSuperior performanceComplex model developmentFMRI dataTime-series fMRI dataTime series dataClassifierStand-alone pieceClassificationAccuracyDesign modelSeries dataT-cell receptor binding prediction: A machine learning revolution
Weber A, Pélissier A, Martínez M. T-cell receptor binding prediction: A machine learning revolution. ImmunoInformatics 2024, 15: 100040. DOI: 10.1016/j.immuno.2024.100040.Peer-Reviewed Original ResearchProtein language modelsT cell receptorExtract biological insightsUnlabeled protein sequencesProtein sequencesBinding specificityBiological insightsProtein modelsRepertoire dataDeep learning modelsSequenceBlack-box modelsUnsupervised clustering approachDataset biasEvolution of computational modelsLack of generalityLanguage modelImmunizing sequencesMachine learning effortsCompetitive performanceOpaque modelsBiological propertiesLearning modelsClustering approachSupervised models
2022
DECODE: a computational pipeline to discover T cell receptor binding rules
Papadopoulou I, Nguyen A, Weber A, Martínez M. DECODE: a computational pipeline to discover T cell receptor binding rules. Bioinformatics 2022, 38: i246-i254. PMID: 35758821, PMCID: PMC9235487, DOI: 10.1093/bioinformatics/btac257.Peer-Reviewed Original ResearchConceptsT cell receptor bindingT cell receptorComputational pipelineTCR-epitope bindingBlack-box natureSequence motifsSequencing technologiesSupplementary dataBlack-box modelsBiochemical rulesMachine learningVisualization toolsComputational rulesDecodingData abundanceSequenceBioinformaticsEasy-to-useAdaptive immune responsesBindingBinding propertiesT cell-based therapiesT-cell receptor sequencingTCR bindingTCR specificity
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