2023
Chemical representation learning for toxicity prediction
Born J, Markert G, Janakarajan N, Kimber T, Volkamer A, Martínez M, Manica M. Chemical representation learning for toxicity prediction. Digital Discovery 2023, 2: 674-691. DOI: 10.1039/d2dd00099g.Peer-Reviewed Original ResearchChemical language modelsLanguage modelMolecular property prediction tasksMolecular property prediction modelProperty prediction tasksMolecular property predictionExplicit supervisionAttention weightsMultiscale convolutionData augmentationPrediction taskToxicity datasetMolecular representationsProperty prediction modelsImproved accuracyModel reliabilityDatasetProperty predictionChemical representationsToxicity predictionPrediction uncertaintyUncertainty estimationDrug discoveryRepresentationPrediction model
2021
TITAN: T-cell receptor specificity prediction with bimodal attention networks
Weber A, Born J, Martínez M. TITAN: T-cell receptor specificity prediction with bimodal attention networks. Bioinformatics 2021, 37: i237-i244. PMID: 34252922, PMCID: PMC8275323, DOI: 10.1093/bioinformatics/btab294.Peer-Reviewed Original ResearchConceptsK-nearest neighborAttention networkLeverage transfer learningState-of-the-artK-nearest-neighbor (KNN) classifierInput data spaceK-NN classifierBimodal neural networkSMILES sequencesTransfer learningData augmentationAttention heatmapsCompetitive performanceNeural networkData spaceT cell receptorBoost performanceT-cell receptor sequencingClassifierNetworkImproved performanceT cellsPrediction of specificityPerformanceSequencing of T-cell receptor