{"title":"Graph-guided Bayesian Factor Model for Integrative Analysis of Multi-modal Data with Noisy Network Information.","authors":"Wenrui Li, Qiyiwen Zhang, Kewen Qu, Qi Long","doi":"10.1007/s12561-024-09452-7","DOIUrl":"10.1007/s12561-024-09452-7","url":null,"abstract":"<p><p>There is a growing body of literature on factor analysis that can capture individual and shared structures in multi-modal data. However, few of these approaches incorporate biological knowledge such as functional genomics and functional metabolomics. Graph-guided statistical learning methods that can incorporate knowledge of underlying networks have been shown to improve predication and classification accuracy, and yield more interpretable results. Moreover, these methods typically use graphs extracted from existing databases or rely on subject matter expertise which are known to be incomplete and may contain false edges. To address this gap, we propose a graph-guided Bayesian factor model that can account for network noise and identify globally shared, partially shared and modality-specific latent factors in multimodal data. Specifically, we use two sources of network information, including the noisy graph extracted from existing databases and the estimated graph from observed features in the dataset at hand, to inform the model for the true underlying network via a latent scale modeling framework. This model is coupled with the Bayesian factor analysis model with shrinkage priors to encourage feature-wise and modal-wise sparsity, thereby allowing feature selection and identification of factors of each type. We develop an efficient Markov chain Monte Carlo algorithm for posterior sampling. We demonstrate the advantages of our method over existing methods in simulations, and through analyses of gene expression and metabolomics datasets for Alzheimer's disease.</p>","PeriodicalId":45094,"journal":{"name":"Statistics in Biosciences","volume":" ","pages":""},"PeriodicalIF":0.4,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12221265/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144691908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chenguang Zhang, Masayuki Nigo, Shivani Patel, Duo Yu, Edward Septimus, Hulin Wu
{"title":"Use of Real-World EMR Data to Rapidly Evaluate Treatment Effects of Existing Drugs for Emerging Infectious Diseases: Remdesivir for COVID-19 Treatment as an Example","authors":"Chenguang Zhang, Masayuki Nigo, Shivani Patel, Duo Yu, Edward Septimus, Hulin Wu","doi":"10.1007/s12561-023-09411-8","DOIUrl":"https://doi.org/10.1007/s12561-023-09411-8","url":null,"abstract":"","PeriodicalId":45094,"journal":{"name":"Statistics in Biosciences","volume":"112 45","pages":"1-30"},"PeriodicalIF":1.0,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139391299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Joseph Boyle, Mary H. Ward, Stella Koutros, M. Karagas, M. Schwenn, Alison T. Johnson, Debra T. Silverman, David C. Wheeler
{"title":"Modeling Historic Arsenic Exposures and Spatial Risk for Bladder Cancer","authors":"Joseph Boyle, Mary H. Ward, Stella Koutros, M. Karagas, M. Schwenn, Alison T. Johnson, Debra T. Silverman, David C. Wheeler","doi":"10.1007/s12561-023-09404-7","DOIUrl":"https://doi.org/10.1007/s12561-023-09404-7","url":null,"abstract":"","PeriodicalId":45094,"journal":{"name":"Statistics in Biosciences","volume":"5 11","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138966433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Considerations and Targeted Approaches to Identifying Bad Actors in Exposure Mixtures","authors":"Alexander P. Keil, Katie M. O’Brien","doi":"10.1007/s12561-023-09409-2","DOIUrl":"https://doi.org/10.1007/s12561-023-09409-2","url":null,"abstract":"","PeriodicalId":45094,"journal":{"name":"Statistics in Biosciences","volume":"6 13","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139006657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Causal Mediation Tree Model for Feature Identification on High-Dimensional Mediators","authors":"Yao Li, Wei Xu","doi":"10.1007/s12561-023-09402-9","DOIUrl":"https://doi.org/10.1007/s12561-023-09402-9","url":null,"abstract":"","PeriodicalId":45094,"journal":{"name":"Statistics in Biosciences","volume":"79 8","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138606084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Evaluating Effects of Various Exposures on Mortality Risk of Opioid Use Disorders with Linked Administrative Databases","authors":"Trevor J. Thomson, X. Joan Hu, Bohdan Nosyk","doi":"10.1007/s12561-023-09407-4","DOIUrl":"https://doi.org/10.1007/s12561-023-09407-4","url":null,"abstract":"","PeriodicalId":45094,"journal":{"name":"Statistics in Biosciences","volume":" 32","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138616782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kecheng Li, Tugba Akkaya Hocagil, Richard J. Cook, Louise M. Ryan, R. C. Carter, Khue-Dung Dang, J. Jacobson, S. Jacobson
{"title":"Use of Generalized Propensity Scores for Assessing Effects of Multiple Exposures","authors":"Kecheng Li, Tugba Akkaya Hocagil, Richard J. Cook, Louise M. Ryan, R. C. Carter, Khue-Dung Dang, J. Jacobson, S. Jacobson","doi":"10.1007/s12561-023-09403-8","DOIUrl":"https://doi.org/10.1007/s12561-023-09403-8","url":null,"abstract":"","PeriodicalId":45094,"journal":{"name":"Statistics in Biosciences","volume":" 6","pages":""},"PeriodicalIF":1.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138617119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"On Estimation of the Effect Lag of Predictors and Prediction in a Functional Linear Model","authors":"Haiyan Liu, Georgios Aivaliotis, Vijay Kumar, Jeanine Houwing-Duistermaat","doi":"10.1007/s12561-023-09393-7","DOIUrl":"https://doi.org/10.1007/s12561-023-09393-7","url":null,"abstract":"Abstract We propose a functional linear model to predict a functional response using multiple functional and longitudinal predictors and to estimate the effect lags of predictors. The coefficient functions are written as the expansion of a basis system (e.g. functional principal components, splines), and the coefficients of the basis functions are estimated via optimizing a penalization criterion. Then effect lags are determined by simultaneously searching on a prior designed grid mesh based on minimization of a proposed prediction error criterion. Mathematical properties of the estimated regression functions and predicted responses are studied. The performance of the method is evaluated by extensive simulations and a real data analysis application on chronic obstructive pulmonary disease (COPD).","PeriodicalId":45094,"journal":{"name":"Statistics in Biosciences","volume":"205 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135341192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bayesian Inference for High Dimensional Cox Models with Gaussian and Diffused-Gamma Priors: A Case Study of Mortality in COVID-19 Patients Admitted to the ICU","authors":"Jiyeon Song, Subharup Guha, Yi Li","doi":"10.1007/s12561-023-09395-5","DOIUrl":"https://doi.org/10.1007/s12561-023-09395-5","url":null,"abstract":"","PeriodicalId":45094,"journal":{"name":"Statistics in Biosciences","volume":"87 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135774370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Phillip Shreeves, Jeffrey L. Andrews, Xinchen Deng, Ramie Ali-Adeeb, Andrew Jirasek
{"title":"Nonnegative Matrix Factorization with Group and Basis Restrictions","authors":"Phillip Shreeves, Jeffrey L. Andrews, Xinchen Deng, Ramie Ali-Adeeb, Andrew Jirasek","doi":"10.1007/s12561-023-09398-2","DOIUrl":"https://doi.org/10.1007/s12561-023-09398-2","url":null,"abstract":"","PeriodicalId":45094,"journal":{"name":"Statistics in Biosciences","volume":"16 12","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135726760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}