2025
Unveiling fine-scale spatial structures and amplifying gene expression signals in ultra-large ST slices with HERGAST
Gong Y, Yuan X, Jiao Q, Yu Z. Unveiling fine-scale spatial structures and amplifying gene expression signals in ultra-large ST slices with HERGAST. Nature Communications 2025, 16: 3977. PMID: 40295488, PMCID: PMC12037780, DOI: 10.1038/s41467-025-59139-w.Peer-Reviewed Original ResearchConceptsGene expression signalsSpatial transcriptomics data analysisExpression signalsTranscriptome data analysisHeterogeneous graph networkReal-world datasetsSpatial expression patternsOver-smoothing problemSpatial transcriptomics dataGlobal spatial relationshipsST data analysisTranscriptome dataUltra-large-scaleConquer strategyExpression patternsGraph networkData splittingGenes
2023
Reproducibility of Deep Learning Algorithms Developed for Medical Imaging Analysis: A Systematic Review
Moassefi M, Rouzrokh P, Conte G, Vahdati S, Fu T, Tahmasebi A, Younis M, Farahani K, Gentili A, Kline T, Kitamura F, Huo Y, Kuanar S, Younis K, Erickson B, Faghani S. Reproducibility of Deep Learning Algorithms Developed for Medical Imaging Analysis: A Systematic Review. Journal Of Imaging Informatics In Medicine 2023, 36: 2306-2312. PMID: 37407841, PMCID: PMC10501962, DOI: 10.1007/s10278-023-00870-5.Peer-Reviewed Original ResearchConceptsMedical image analysisDeep learningArtificial intelligenceMedical imagesDeep learning algorithm developmentAI breakthroughsDL modelsRetraction of scientific papersData splittingPerformance metricsDL toolsComplex taskAlgorithm codeDigital imagesAlgorithm developmentImage analysisHuman capabilitiesImaging existDatasetPublished papersScientific papersCodeLearningImagesReproducibility crisis
2022
Mitigating Bias in Radiology Machine Learning: 1. Data Handling
Rouzrokh P, Khosravi B, Faghani S, Moassefi M, Vera Garcia D, Singh Y, Zhang K, Conte G, Erickson B. Mitigating Bias in Radiology Machine Learning: 1. Data Handling. Radiology Artificial Intelligence 2022, 4: e210290. PMID: 36204544, PMCID: PMC9533091, DOI: 10.1148/ryai.210290.Peer-Reviewed Original Research
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