2023
Computational modelling of immunological mechanisms: From statistical approaches to interpretable machine learning
MartÃnez M, Barberis M, Niarakis A. Computational modelling of immunological mechanisms: From statistical approaches to interpretable machine learning. ImmunoInformatics 2023, 12: 100029. DOI: 10.1016/j.immuno.2023.100029.Peer-Reviewed Original ResearchHigh-throughput experimental technologiesComputational biologyDevelopment of high-throughput experimental technologiesImmune systemHigh-throughput data analysisImmunological mechanismsMolecular functionsSystems biologyImmune-related diseasesOptimal immunotherapyTherapeutic optionsAutoimmune diseasesComplex disorderInterpretable machine learningMachine learning modelsCellular interactionsGeneration of computational modelsBiologyComputer scienceMachine learningMachine-learning modelsDiverse domainsLearning modelsExperimental technologyInterpretable machineIs Attention Interpretation? A Quantitative Assessment on Sets
Haab J, Deutschmann N, MartÃnez M. Is Attention Interpretation? A Quantitative Assessment on Sets. Communications In Computer And Information Science 2023, 1752: 303-321. DOI: 10.1007/978-3-031-23618-1_21.Peer-Reviewed Original ResearchBinary classification problemInterpretation of attentionClassification problemAttention mechanismSynthetic datasetsUnordered collectionClassification performanceSilent failuresMachine learningGlobal labelsData modalitiesIndividual instancesAttention distributionAttention scoresAttention patternsData pointsSub-componentsInstancesDataset
2022
DECODE: a computational pipeline to discover T cell receptor binding rules
Papadopoulou I, Nguyen A, Weber A, MartÃnez 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
2021
The Multiple Dimensions of Networks in Cancer: A Perspective
Axenie C, Bauer R, MartÃnez M. The Multiple Dimensions of Networks in Cancer: A Perspective. Symmetry 2021, 13: 1559. DOI: 10.3390/sym13091559.Peer-Reviewed Original Research
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