Description Usage Arguments Details Value Author(s) References See Also Examples
Fit generative latent variable model (see vignette for model specification) on two data sets. Regularize the solutions with priors, including constraints on marginal covariance structures, the structure of W, latent dimensionality etc. Probabilistic versions of PCA, factor analysis and CCA are available as special cases.
1 2 3 4 5 6 7  fit.dependency.model(X, Y, zDimension = 1, marginalCovariances = "full",
epsilon = 1e3,
priors = list(), matched = TRUE,
includeData = TRUE, calculateZ = TRUE, verbose = FALSE)
ppca(X, Y = NULL, zDimension = NULL, includeData = TRUE, calculateZ = TRUE)
pfa(X, Y = NULL, zDimension = NULL, includeData = TRUE, calculateZ = TRUE, priors = NULL)
pcca(X, Y, zDimension = NULL, includeData = TRUE, calculateZ = TRUE)

X, Y 
Data set/s X and Y. 'Variables x samples'. The second data set ( 
zDimension 
Dimensionality of the shared latent variable. 
marginalCovariances 
Structure of marginal covariances,
assuming multivariate Gaussian distributions for the datasetspecific
effects. Options: 
epsilon 
Convergence limit. 
priors 
Prior parameters for the model. A list, which can contain some of the following elements:

matched 
Logical indicating if the variables (dimensions) are matched between X and Y. Applicable only when dimX = dimY. Affects the results only when prior on the relationship Wx ~ Wy is set, i.e. when priors$Nm.wx.wy.sigma < Inf. 
includeData 
Logical indicating whether the original data is
included to the model output. Using 
calculateZ 
Logical indicating whether an expectation of the
latent variable Z is included in the model output. Otherwise the
expectation can be calculated with 
verbose 
Follow procedure by intermediate messages. 
The fit.dependency.model
function fits the dependency
model X = N(W$X * Z, phi$X); Y = N(W$Y * Z, phi$Y) with the
possibility to tune the model structure and parameter priors.
In particular, the datasetspecific covariance structure phi can be defined; nonnegative priors for W are possible; the relation between W$X and W$Y can be tuned. For a comprehensive set of examples, see the example scripts in the tests/ directory of this package.
Special cases of the model, obtained with particular prior
assumptions, include probabilistic canonical correlation analysis
(pcca
; Bach & Jordan 2005), probabilistic principal
component analysis (ppca
; Tipping & Bishop 1999),
probabilistic factor analysis (pfa
; Rubin & Thayer
1982), and a regularized version of canonical correlation analysis
(pSimCCA; Lahti et al. 2009).
The standard probabilistic PCA and factor analysis are methods for a single data set (X ~ N(WZ, phi)), with isotropic and diagonal covariance (phi) for pPCA and pFA, respectively. Analogous models for two data sets are obtained by concatenating the two data sets, and performing pPCA or pFA.
Such special cases are obtained with the following choices in the
fit.dependency.model
function:
marginalCovariances = "identical isotropic"
(Tipping & Bishop 1999)
marginalCovariances = "diagonal"
(Rubin & Thayer 1982)
marginalCovariances = "full"
(Bach & Jordan 2005)
marginaCovariances = "full", priors =
list(Nm.wxwy.mean = I, Nm.wxwy.sigma = 0)
. This is the default
method, corresponds to the case with W$X = W$Y. (Lahti et al.
2009)
marginalCovariances = "isotropic",
priors = list(Nm.wxwy.mean = 1, Nm.wx.wy.sigma = 1
(Lahti et al. 2009)
To avoid computational singularities, the covariance matrix phi is regularised by adding a small constant to the diagonal.
DependencyModel
OlliPekka Huovilainen ohuovila@gmail.com and Leo Lahti leo.lahti@iki.fi
Dependency Detection with Similarity Constraints, Lahti et al., 2009 Proc. MLSP'09 IEEE International Workshop on Machine Learning for Signal Processing, http://arxiv.org/abs/1101.5919
A Probabilistic Interpretation of Canonical Correlation Analysis, Bach Francis R. and Jordan Michael I. 2005 Technical Report 688. Department of Statistics, University of California, Berkley. http://www.di.ens.fr/~fbach/probacca.pdf
Probabilistic Principal Component Analysis, Tipping Michael E. and Bishop Christopher M. 1999. Journal of the Royal Statistical Society, Series B, 61, Part 3, pp. 611–622. http://research.microsoft.com/enus/um/people/cmbishop/downloads/BishopPPCAJRSS.pdf
EM Algorithms for ML Factorial Analysis, Rubin D. and Thayer D. 1982. Psychometrika, vol. 47, no. 1.
Output class for this function:
DependencyModel. Special cases: ppca
, pfa
, pcca
1 2 3 4 5 6 7 8 9 10 11 12  data(modelData) # Load example data X, Y
# probabilistic CCA
model < pcca(X, Y)
# dependency model with priors (W>=0; Wx = Wy; full marginal covariances)
model < fit.dependency.model(X, Y, zDimension = 1,
priors = list(W = 1e3, Nm.wx.wy.sigma = 0),
marginalCovariances = "full")
# Getting the latent variable Z when it has been calculated with the model
#getZ(model)

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