Author ElOceanografo
Popularity
2 Stars
Updated Last
1 Year Ago
Started In
January 2021 This is a lightweight package to construct loading matrices for probabilistic factor analysis and dimensionality reduction. If you just need traditional factor analysis, that's available in MultivariateStats.jl. However, if you are doing factor analysis in a Bayesian or probabilistic context, or as part of a more complex statistical model, the utilities in this package may be useful.

Factor analysis is a statistical method where n-dimensional vector-valued variables x are represented as linear combination m-dimensional vectors of "factors" f. This linear combination is specified by an n × m loading matrix L,

where i indexes each observation. If we collect all observations of x and f in the columns of matrices X and F, we can write the system as

Factor analysis is useful when the elements of x are correlated with each other, so most of their variability can be captured using a small number of factors. That means we can set m < n, and that L will be a rectangular matrix with more rows than columns. Factor analysis is thus related to other dimensionality-reduction methods, like principle-component analysis/empirical orthogonal functions (PCA/EOF).

There is no unique way to do this decomposition, but we want all the columns of L to be linearly independent. A simple way to enforce this requirement is to set all entries above the diagonal to zero. FactorLoadingMatrices exports two functions for constructing matrices with this property:

• nnz_loading(nx, nfactor) calculates the number of nonzero entries in a lower-triangular matrix with size (nx, nfactor).
• loading_matrix(values, nx, nfactor) arranges the numers in the vector values in the lower triangle of the matrix with the specified size.

The following example shows how to use them.

julia> using FactorLoadingMatrices

julia> nx = 5;

julia> nfactor = 3;

12

5×3 Array{Float64,2}:
-1.3836     0.0         0.0
-1.6667     0.436374    0.0
0.285922  -0.0585805  -1.0485
0.512425  -0.457097   -1.43772
-2.74867   -0.128697    0.301587

This package also exports a function varimax (modified from the implementation by Haotian Li in NGWP.jl) to perform the varimax rotation on loading matrices.

## Bayesian factor analysis using Turing

The next example shows how the utility functions in FactorLoadingMatrices.jl make it easy to perform Bayesian probabilistic factor analysis in Turing.

using FactorLoadingMatrices
using Random
using Plots
using Turing
# using Memoization and reverse-mode autodiff speeds up MCMC sampling
# *a lot* when fitting high-dimensional models
using Memoization
using ReverseDiff

Random.seed!(1)

nx = 50
nfactor = 3
nobs = 300
σ = 0.5

F = randn(nfactor, nobs)
X = L * F .+ σ*randn()

@model function FactorModel(X, nfactor)
nx, nobs = size(X)
F ~ filldist(Normal(0, 1), nfactor, nobs)
σ ~ Exponential(1.0)
# observation likelihood
X ~ arraydist(Normal.(L * F, σ))
end

mod = FactorModel(X, nfactor)
chn = sample(mod, NUTS(), 100)

Once the sampler finishes running, we can extract the posterior for L. Note that the matrix is sampled inside the model as a flat vector of its nonzero entries, so we have to reconstruct the loading matrices from those.

vals_post = Array(group(chn, :vals))
L_post = [loading_matrix(v, nx, nfactor) for v in eachrow(vals_post)]

Before comparing the matrices in L_post to the true L, we'll apply varimax to each one. There's no guarantee that the model will converge on the same L and F we started with, but they should be the same (approximately) after applying a variance-maximizing rotation.

L_post_vm = varimax.(L_post)

plot(mean(L_post_vm), 1:nx, xerror=2std(L_post_vm), markerstrokecolor=1,
layout=(1, 3), label="Model", title=["L[:, 1]" "L[:, 2]" "L[:, 3]"])
plot!(varimax(L), 1:nx, layout=(1, 3), label="Truth") Columns 1 and 3 of the rotated matrix were recovered quite well by the model, though it struggled a bit with column 2.

This is a relatively simple use case, but it would be straightforward to add other layers and processes to the model (e.g. covariates, non-Gaussian observations, etc.).