Support faster Cholesky Decomposition of Toeplitz matrices
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- C++
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Description
I recently discovered that cholesky decomposition of toeplitz matrices (useful for GPs evaluated on a grid) can be done with O(n^2) rather than the standard cholesky O(n^3). I found an implementation here, where an academic has posted C, C++, Fortran, MATLAB & Python code (also mirrored in separate repositories here). I took a look at the python and it wasn't particularly optimized (used loops instead of vectorized alternatives), so in case it's useful here's the vectorized version I came up with:
import numpy as np
def cholesky_toeplitz(r):
"""
Cholesky decomposition of a Toeplitz matrix.
:param r: the first row of the Toeplitz matrix
:return: the lower triangular matrix L
"""
n = len(r)
l = np.zeros([n, n])
l[:, 0] = r
g = np.zeros([2, n])
g[0, 1:] = r[0:(n-1)]
g[1, 1:] = r[1:]
for i in range ( 1, n ):
rho = - g[1,i] / g[0,i]
gam = np.sqrt ( ( 1.0 - rho ) * ( 1.0 + rho ) )
alf = g[0, i:n]
bet = g[1, i:n]
temp_g_0 = (alf + rho * bet) / gam
temp_g_1 = (rho * alf + bet) / gam
g[0, i:n] = temp_g_0
g[1, i:n] = temp_g_1
l[i:n, i] = g[0, i:n]
g[0, i+1:n] = g[0, i:n-1]
g[0,i] = 0.0
return(l)
And in some light testing, it does seem to outperform scipy.linalg.cholesky() when n is large (& n.b. scipy uses LAPACK, so my comparison was native python vs compiled fortran).
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the linked Toeplitz Cholesky implementation and the provided cholesky_toeplitz function; compare its assumptions and numerical behavior with scipy.linalg.cholesky(). Identify the appropriate Stan Math entry point and tests, then verify that the supported Toeplitz decomposition has the intended performance and correctness.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- cpp, numpy, python
- Domain
- backend
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100