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README.md

GLRM

GLRM is a python package for exploratory data analysis using Generalized Low Rank Models (GLRMs).

A GLRM seeks factors X and Y such that XY approximates data table A using an arbitrary error metric (i.e. loss function) for each column of A. This framework allows for the generalization of principal components analysis (PCA) to a heterogenous dataset A, where columns of A contain data with different data types (e.g., Boolean, ordinal, interval). GLRM easily handles missing data by choosing a loss of zero for the missing entries of A.

For more information on GLRMs, see our paper.

This project provides a GLRM object for automatically computing factors X and Y, decoding XY back into the appropriate domain, and imputing missing entries.

Installation

python setup.py install

Basic usage

The source code for similar problems can be found in the 'examples' folder.

A GLRM model is specified by data table A, loss functions L, regularizers for X and Y, rank k, and an (optional) list of missing entries.

from glrm import GLRM

Consider a data table A that is approximately rank k, where the first n1 columns contain Boolean data, and the next n2 columns contain numerical data.

m, n1, n2, k = 50, 25, 25, 5
eta = 0.1 # noise
A = randn(m,k).dot(randn(k,n1+n2)) + eta*randn(m,n1+n2)
A_bool = sign(A[:,:n1]) # Boolean data must be labeled as -1, 1
A_real = A[:,n1:]

We decide to use hinge loss for the Boolean data, and quadratic loss for the numerical data. The scaling of each loss function is handled automatically during the intialization of the GLRM object.

from glrm.loss import QuadraticLoss, HingeLoss

Data A is stored as a list of submatrices, where each submatrix is associated with a data type. The loss functions associated with each submatrix are stored similarly.

A_list      = [A_bool, A_real]
loss_list   = [HingeLoss, QuadraticLoss]

To improve generalization error, we choose to use quadratic regularization on both factors X and Y with weight 0.1. (For no regularization on X and Y, use ZeroReg.)

from glrm.reg import QuadraticReg
regX, regY = QuadraticReg(0.1), QuadraticReg(0.1)

If any entries are corrupted or missing, we store indices of the missing entries for each submatrix in the list format shown above. For example, if a 4x4 block of data is missing from the center of A, this corresponds to rows 24-27 and columns 49-50 of submatrix 1, and rows 24-27 and columns 1-2 of submatrix 2. (Python is 0-indexed.)

missing1     = [(23, 48), (23, 49), (24, 48), (24, 49), \
                (25, 48), (25, 49), (26, 48), (26, 49)]
missing2     = [(23, 0), (23, 1), (24, 0), (24, 1), \
                (25, 0), (25, 1), (26, 0), (26, 1)]
missing_list = [missing1, missing2]

If a GLRM object is not provided a list of missing entries, then it is assumed that no entries are missing.

[Optional] To specify the tolerance and maximum number of iterations of the alternating minimization algorithm, create a Convergence object to pass to the model. The default parameter values are shown below.

from glrm.util import Convergence
c = Convergence(TOL = 1e-3, max_iters = 1000)

All that remains is to initialize the GLRM model and call fit().

model = GLRM(A_list, loss_list, regX, regY, k, missing = missing_list, converge = c)
model.fit()

To extract the factors X, Y and impute missing values,

X, Y = model.factors()
A_hat = model.predict() # a horizontally concatenated matrix, not a list

To compare our prediction error,

norm(A_hat - hstack(A_list)) # by hand

To view convergence history,

ch = model.convergence() # grab convergence history of alt min problem
ch.plot() # view convergence of objective

Supported loss functions and regularizers

  • QuadraticLoss
  • HuberLoss
  • HingeLoss
  • OrdinalLoss
  • ZeroReg
  • LinearReg
  • QuadraticReg

Developing loss functions and regularizers (not guaranteed to work yet)

  • FractionalLoss
  • NonnegativeReg

To use NonnegativeReg on either X or Y, you must specify to use proximal gradient descent on the corresponding subproblem.

# given A_list, loss_list, k from above
from glrm.reg import NonnegativeReg
from glrm.algs import ProxGD

regX, regY = NonnegativeReg(1.0), NonnegativeReg(1.0)
model = GLRM(A_list, loss_list, regX, regY, k, algX = ProxGD, algY = ProxGD)
model.fit()

Questions/concerns/feedback

Please send messages to Corinne Horn (cehorn at stanford.edu).

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