Sandra E. Safo

Elise F. Palzer, Sandra E. Safo

The package mvlearnR and accompanying Shiny App is intended for integrating data from multiple sources or views or modalities (e.g. genomics, proteomics, clinical and demographic data). Most existing software packages for multiview learning are decentralized and offer limited capabilities, making it difficult for users to perform comprehensive integrative analysis. The new package wraps statistical and machine learning methods and graphical tools, providing a convenient and easy data integration workflow. For users with limited programming language, we provide a Shiny Application to facilitate data integration anywhere and on any device. The methods have potential to offer deeper insights into complex disease mechanisms. Availability and Implementation: mvlearnR is available from the following GitHub repository: https://github.com/lasandrall/mvlearnR. The web application is hosted on shinyapps.io and available at: https://multi-viewlearn.shinyapps.io/MultiView_Modeling/

Elise F. Palzer, Christine Wendt, Russell Bowler et al.

Analyzing multi-source data, which are multiple views of data on the same subjects, has become increasingly common in molecular biomedical research. Recent methods have sought to uncover underlying structure and relationships within and/or between the data sources, and other methods have sought to build a predictive model for an outcome using all sources. However, existing methods that do both are presently limited because they either (1) only consider data structure shared by all datasets while ignoring structures unique to each source, or (2) they extract underlying structures first without consideration to the outcome. We propose a method called supervised joint and individual variation explained (sJIVE) that can simultaneously (1) identify shared (joint) and source-specific (individual) underlying structure and (2) build a linear prediction model for an outcome using these structures. These two components are weighted to compromise between explaining variation in the multi-source data and in the outcome. Simulations show sJIVE to outperform existing methods when large amounts of noise are present in the multi-source data. An application to data from the COPDGene study reveals gene expression and proteomic patterns that are predictive of lung function. Functions to perform sJIVE are included in the R.JIVE package, available online at http://github.com/lockEF/r.jive .

Jiuzhou Wang, Sandra E. Safo

COVID-19 severity is due to complications from SARS-Cov-2 but the clinical course of the infection varies for individuals, emphasizing the need to better understand the disease at the molecular level. We use clinical and multiple molecular data (or views) obtained from patients with and without COVID-19 who were (or not) admitted to the intensive care unit to shed light on COVID-19 severity. Methods for jointly associating the views and separating the COVID-19 groups (i.e., one-step methods) have focused on linear relationships. The relationships between the views and COVID-19 patient groups, however, are too complex to be understood solely by linear methods. Existing nonlinear one-step methods cannot be used to identify signatures to aid in our understanding of the complexity of the disease. We propose Deep IDA (Integrative Discriminant Analysis) to address analytical challenges in our problem of interest. Deep IDA learns nonlinear projections of two or more views that maximally associate the views and separate the classes in each view, and permits feature ranking for interpretable findings. Our applications demonstrate that Deep IDA has competitive classification rates compared to other state-of-the-art methods and is able to identify molecular signatures that facilitate an understanding of COVID-19 severity.