ArticleBMC bioinformatics2018
Data integration by multi-tuning parameter elastic net regression.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- The Evolving Landscape of Clinical Aging Clocks: From Epigenetic to Multi-Omics Integration.Aging cell · 2026Review
- Decoding Multi-Omics Signatures in Lower-Grade Glioma Using Protein-Protein Interaction-Informed Graph Attention Networks and Ensemble Learning.Diagnostics (Basel, Switzerland) · 2025Article
- Establishing the utility of multi-platform liquid biopsy by integrating the CSF methylome and proteome in CNS tumours.Journal of neuro-oncology · 2024Article
- Application of Metabolomics across the Spectrum of Pulmonary and Critical Care Medicine.American journal of respiratory cell and molecular biology · 2024Review
- Methods for multi-omic data integration in cancer research.Frontiers in genetics · 2024Review
- Spatial and temporal resolution of metabolic dysregulation in the Sugen hypoxia model of pulmonary hypertension.Pulmonary circulation · 2023Article
- Article
- An epigenome-wide study of DNA methylation profiles and lung function among American Indians in the Strong Heart Study.Clinical epigenetics · 2022Article
- Transcriptional, epigenetic and metabolic signatures in cardiometabolic syndrome defined by extreme phenotypes.Clinical epigenetics · 2022Article
- Functional impact of multi-omic interactions in breast cancer subtypes.Frontiers in genetics · 2022Article
- Hierarchical Ridge Regression for Incorporating Prior Information in Genomic Studies.Journal of data science : JDS · 2022Article
- Multidimensional analysis of immune responses identified biomarkers of recent Mycobacterium tuberculosis infection.PLoS computational biology · 2021Article
- Incorporating prior knowledge into regularized regression.Bioinformatics (Oxford, England) · 2021Article
- Development of a novel risk score for the prediction of critical illness amongst COVID-19 patients.International journal of clinical practice · 2021Article
- Multi-Omic Regulation of the PAM50 Gene Signature in Breast Cancer Molecular Subtypes.Frontiers in oncology · 2020Article
- Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundTo integrate molecular features from multiple high-throughput platforms in prediction, a regression model that penalizes features from all platforms equally is commonly used. However, data from different platforms are likely to differ in effect sizes, the proportion of predictive features, and correlations structures. Subtle but important features may be missed by shrinking all features equally.
resultsWe propose an Elastic net (EN) model with separate tuning parameter penalties for each platform that is fit using standard software. In a comprehensive simulation study, we evaluated the performance of EN logistic regression with multiple tuning penalties. We found that when the number of informative features differs among the platforms, and when there is no notable correlation between the features from different platforms, the multi-tuning parameter EN yields more predictive models. Moreover, the multi-tuning parameter EN is robust, in the sense that there is no loss of predictivity relative to a single tuning parameter EN when features across all platforms have similar effects. We also investigated the performance of multi-tuning parameter EN using real cancer datasets.
conclusionThe proposed multi-tuning parameter EN model, fit using standard penalized regression software, can achieve better prediction in sample classification when integrating multiple genomic platforms, compared to the traditional method where a single penalty parameter is used for all features in different platforms.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.