R-package `mvs`

Methods for high-dimensional multi-view learning based on the multi-view stacking (MVS) framework. Data have a multi-view structure when features comprise different ‘views’ of the same observations. For example, the different views may comprise omics, imaging or electronic health records. Package mvs provides functions to fit stacked penalized logistic regression (StaPLR) models, which are a special case of multi-view stacking (MVS). Additionally, mvs generalizes the StaPLR model to settings with a Gaussian or Poisson outcome distribution, and to hierarchical multi-view structures with more than two levels. For more information about the StaPLR and MVS methods, see Van Loon, Fokkema, Szabo, & De Rooij (2020) and Van Loon et al. (2022).

Installation

The current stable release can be installed directly from CRAN:

utils::install.packages("mvs")

The current development version can be installed from GitLab using package devtools:

devtools::install_gitlab("wsvanloon/mvs@develop")

Using `mvs`

The two main functions are StaPLR() (alias staplr), which fits penalized and stacked penalized regression models models with up to two levels, and MVS() (alias mvs), which fits multi-view stacking models with >= 2 levels. Objects returned by either function have associated coef and predict methods.

Example: `StaPLR`

library("mvs")

Generate 1000 observations with four two-feature views with varying within- and between-view correlation:

set.seed(012)
n <- 1000
cors <- seq(0.1, 0.7, 0.1)
X <- matrix(NA, nrow=n, ncol=length(cors)+1)
X[ , 1] <- rnorm(n)
for (i in 1:length(cors)) {
  X[ , i+1] <- X[ , 1]*cors[i] + rnorm(n, 0, sqrt(1-cors[i]^2))
}
beta <- c(1, 0, 0, 0, 0, 0, 0, 0)
eta <- X %*% beta
p <- exp(eta)/(1+exp(eta))
y <- rbinom(n, 1, p)

Fit StaPLR:

view_index <- rep(1:(ncol(X)/2), each=2)
set.seed(012)
fit <- StaPLR(X, y, view_index)

Extract coefficients at the view level:

coefs <- coef(fit)
coefs$meta

## 5 x 1 sparse Matrix of class "dgCMatrix"
##                    s1
## (Intercept) -2.345398
## V1           4.693861
## V2           .       
## V3           .       
## V4           .

We see that the only the first view has been selected. The data was generated so that only the first feature (from the first view) was a true predictor, but it was also substantially correlated with features from other views (see cor(X)), most strongly with the features from the fourth view.

Extract coefficients at the base level:

coefs$base

## [[1]]
## 3 x 1 sparse Matrix of class "dgCMatrix"
##                      s1
## (Intercept) -0.05351035
## V1           0.86273113
## V2           0.09756006
## 
## [[2]]
## 3 x 1 sparse Matrix of class "dgCMatrix"
##                        s1
## (Intercept) -6.402186e-02
## V1           1.114585e-38
## V2           1.156060e-38
## 
## [[3]]
## 3 x 1 sparse Matrix of class "dgCMatrix"
##                      s1
## (Intercept) -0.06875322
## V1           0.26176566
## V2           0.35602028
## 
## [[4]]
## 3 x 1 sparse Matrix of class "dgCMatrix"
##                      s1
## (Intercept) -0.03101978
## V1           0.27605205
## V2           0.39234018

We see that the first feature has the strongest effect on the predicted outcome, with a base-level regression coefficient of 0.86. The features in views two, three and four all have zero effect, since the meta-level coefficients for these views are zero.

Compute predictions:

new_X <- matrix(rnorm(16), nrow=2)
predict(fit, new_X)

##      lambda.min
## [1,]  0.8698197
## [2,]  0.1819153

By default, the predictions are made using the values of the penalty parameters which minimize the cross-validation error (lambda.min).

Generalizations

As StaPLR was developed in the context of binary classification problems, the default outcome distribution is family = "binomial". Other outcome distributions (e.g., Gaussian, Poisson) can be modeled by specifying, e.g., family = "gaussian" or family = "poisson".
A generalization of stacked penalized (logistic) regression to three or more hierarchical levels is implemented in function MVS (alias mvs).

References

Van Loon, W., De Vos, F., Fokkema, M., Szabo, B., Koini, M., Schmidt, R., & De Rooij, M. (2022). Analyzing hierarchical multi-view MRI data with StaPLR: An application to Alzheimer’s disease classification. Frontiers in Neuroscience, 16, 830630. https://doi.org/10.3389/fnins.2022.830630

Van Loon, W., Fokkema, M., Szabo, B., & De Rooij, M. (2020). Stacked penalized logistic regression for selecting views in multi-view learning. Information Fusion, 61, 113–123. https://doi.org/10.1016/j.inffus.2020.03.007

R-package mvs