2024
Deep learning analysis of fMRI data for predicting Alzheimer’s Disease: A focus on convolutional neural networks and model interpretability
Zhou X, Kedia S, Meng R, Gerstein M. Deep learning analysis of fMRI data for predicting Alzheimer’s Disease: A focus on convolutional neural networks and model interpretability. PLOS ONE 2024, 19: e0312848. PMID: 39630834, PMCID: PMC11616848, DOI: 10.1371/journal.pone.0312848.Peer-Reviewed Original ResearchConceptsConvolutional neural networkNeural networkAlzheimer's diseaseConvolutional neural network modelMultimodal medical datasetsDeep learning methodsPotential of deep learningGenetic risk factorsMedical datasetsAlzheimer's Disease Neuroimaging InitiativeAD predictionDeep learningDeep learning analysisLearning methodsMedical imagesPredicting Alzheimer's diseaseDetection of Alzheimer's diseaseModel interpretationEarly detection of Alzheimer's diseaseAccuracy levelGenetic factorsDatasetEarly detection of ADNetworkDetection of ADBioCoder: a benchmark for bioinformatics code generation with large language models
Tang X, Qian B, Gao R, Chen J, Chen X, Gerstein M. BioCoder: a benchmark for bioinformatics code generation with large language models. Bioinformatics 2024, 40: i266-i276. PMID: 38940140, PMCID: PMC11211839, DOI: 10.1093/bioinformatics/btae230.Peer-Reviewed Original ResearchConceptsCode generationLanguage modelAmount of domain knowledgeDomain-specific knowledgeJava methodsDomain knowledgeClass declarationsPerformance gainsData operationsPython functionsTraining datasetSuccess modelIntricate taskTest benchmarksDocker imageBenchmarksCodeSmall modelsDatasetGlobal variablesBioCodeFunctional dependenceEvaluate various modelsIncreasing needCodeGen
2011
Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
Greenbaum D, Sboner A, Mu XJ, Gerstein M. Genomics and Privacy: Implications of the New Reality of Closed Data for the Field. PLOS Computational Biology 2011, 7: e1002278. PMID: 22144881, PMCID: PMC3228779, DOI: 10.1371/journal.pcbi.1002278.Peer-Reviewed Original ResearchConceptsPrivacy issuesGenomic privacySecure cloud computing environmentCloud computing environmentPersonal genomic dataComputing environmentPrivacy problemsPrivate dataData securityPrivacy concernsOpen sourceOpen dataPrivacyLarge datasetsImportant data setsVariant informationClosed dataData setsFuture accessSmall labsDatasetGenome CenterGenomic dataComputational strategyLarge scale