convPCA 0.0.1

Convolutional version of PCA using Power Iteration, FastICA and Autoencoders.

convPCA

Various approaches to performing a convolutional analogue of PCA. The basic idea is to adapt power iteration (PI). PI finds the eigenvectors of A by initializing a random h and then iteratively setting h = norm(Ah) where norm(g)=g/sum(g^2) to have unit length.
In the PCA context, A is the empirical covariance, A=(X'X)/N. So we can equivalently update h = X'(Xh) [with the divide by N coming out in the wash when we normalize h]. The idea in convolutional PCA is to replace matrix multiplication with convolution operations. For 1D sequence data

• X is [N x P x L]
• h is [H x P x K]

where

• N is the number of sample sequences,
• P is the number of observed channels,
• L is the sequence length,
• H is the number of hidden channels/factors (1 for standard PI), and
• K is the PC/PWM/factor size/filter width.

The basic PI algorithm iterates

1. b = F.conv_transpose1d(x,h.transpose(0,1)) gives a [N x H x L+K-1] tensor (think of this as hidden node activations in an AE).
2. h = F.conv1d(b.transpose(0,1),x.transpose(0,1)) gives an updated h with the correct dimensions (this is like correlating the activations and the observed data).

There are two approaches to extending to H>1:

1. Orthonormalizing h at every iteration using QR decomposition or SVD.
2. "Deflating" X, i.e. removing signal explained by the previous PCs. For PCA these approaches are equivalent, not clear if this is true for convPCA (and it's certainly not for the sparse variant).

Other implemented features:

• sparse version, where all but the largest element in windows of b are zeroed out
• shift version, where we attempt to center the PWM to avoid cutting off a position at the edge
• batch version ala AdaOja

A couple of other approaches to fitting are implemented:

• A novel convolutional version of FastICA very analogous to ConvPCA. This includes a L1-penalty/lasso inspired nonlinearity (soft thresholding).
• A (shallow, linear) convolutional autoencoder, fit using SGD/Adam.