[Simsalabim-communicate] Design issues
lukas.gudmundsson at geo.uio.no
lukas.gudmundsson at geo.uio.no
Wed Nov 5 17:32:19 CET 2008
(@all others: this is a reply to a previous mail from Anton. You find it
at the end of this mail.)
thank you very much for the detailed descriptions on your ideas for
improving SSA in R. In the following I try to go through some of your last
mail and try to comment as good as possible on this.
As far as I understand, you are mostly concerned about performance and
numerical stability. As you already found out I have been ignoring both
important issues in some way, but had always the wish of these things
being tackled. I guess that you have already found out that I am solving
the problem of negative eigenvalues in a naive way by setting them
artificially to a small positive value. Some of the inefficiencies come
from certain design decisions, related to application patterns.
As you probably know I am a geoscientist, using SSA for identification and
extraction of low frequency patterns. Here I follow the tradition of using
eigenvectors and eigenvalues to identify signals (based i.e. on
significance testing or dominant frequencies of eigenvectors). This
approach is somewhat different from the w-correlation approach, but has
the advantage of full automation and less computations (for the RC's). In
addition it is often of interest only to consider signals with certain
time scales (based on spectra of eigenvectors). Any changes in
architecture should either still enable the usage of the according methods
or adopt them to new object structures.
One goal was to make the usage of SSA and SSA with missings as close as
possible. I tried to keep the object structure of decompSSA and decompSSAM
as close as possible. With the usage of svd in the complete case this
was not very straightforward. The reason is that the factor vectors do
not appear naturally in some of the algorithms for SSA with missing values
(and if they can be calculated that is numerically inefficient if one uses
only R [ * - operator]). However one could easily think about putting an
optional slot in the output of decompSSA that enables us to include the
factor vectors (this would also imply additional methods for reconSSA,
depending on the availability of the factor vectors.
Finally I think it is worth to think about how much one gains from certain
improvements (relative vs. absolute speedup). The thing that is
computationally by far most expensive in the current implementation is the
diagonal averaging procedure as this is fully implemented in R and I have
found no way to vectorize that. If I have it right in mind this accounts
for more than 80% of the system time. I do not want to say that other
approaches are not worth considering, but changing this (porting to C or
vectorize) absolute computation time (for large datasets) could drop from
hours to minutes.
I am as well sorry for that long and messy mail and the late reply, but I
hope I made some of my design decisions (based on usage patterns) clear. I
am looking forward to improve SSA in R together with you and other people
interested in this method.
---------------------------- Original Message ----------------------------
Subject: Re: [Simsalabim-communicate] test
From: "Anton Korobeynikov" <asl at math.spbu.ru>
Date: Wed, October 29, 2008 23:35
To: "Lukas Gudmundsson" <lukas.gudmundsson at geo.uio.no>
> I am looking forward to here about the outcome of your meeting
We discussed thoroughly possible problems & bottlenecks of the
(possible) R implementation of basic SSA algorithms having in mind all
known to us users & problems being solved with SSA.
Currently we're interested only in 'basic SSA', since it forms the base
for huge amount of other methods. Also, this allows us to have hands
clean and think about all possible solutions without dealing with
backward compatibility problems, etc.
One can easily consider all steps of algorithm either time consuming or
memory consuming (or both), thus flexible approach should be
As an example, let us consider the mentioned problem with factor
I. Singular decomposition.
There are different approaches here:
1. Compute eigevalues and eigenvectors of covariance matrix. But:
- This is known to be numericaly unstable , especially if
trajectory matrix is rank-deficient (you can easily obtain, for example,
negative eigenvalues even with standard LAPACK routines, and thus - R's
eigen() routine) or if there are some noticable amount of small
eigenvalues (this is exactly the case of SSA!).
- You need to compute covariance matrix. The complexity for this is
O(L*K^2) for naive approach (series => hankel => covariance matrix) and
O(L*K) for direct approach (seris => covariance matrix).
- You will need to compute factor vectos separately, or implicitely
later, with O(L*K^2) complexity.
2. Use singular value decomposition. But:
- Fast methods are usually numerically unstable due to finite
precision of computer arithmetics and special care should be made for
keeping set of singular vectors orthogonal.
- Stable & robust methods (Jacobi method, or Householder
bidiagonalization) are slow.
- We obtain set of factor vectors for free as a side effect of the
Fortunately, here have only 1 clear usage patter and shouldn't think
about how users will invoke singular decomposition routine, thus we can
end with some sane solution (or combination of different approaches
depending on size of input, etc).
Reconstruction itself in general costs alot, since we need to multiply 2
matrices here if factor vectors are known, or construct again trajectory
matrix and compute factor vectors implicitely (which will add to
One typical reconstruction usage pattern when we're looking for best
grouping for eigentriples usually involves construction of w-correlation
matrix, which costs O(N*M^2) (M - number of reconstructed series), if we
already have reconstructed series and... much more if we only have sets
of eigentriples. Add to this the need of computation of factor vectors
and you'll end with rather computation hog thing.
Surely, we have another problem, when factor vectors are big enough not
to keep them all in memory. Thus, we've ended with classical time/memory
There also other patterns, with similar results. I won't mention it here
to save your and my time :)
After studying of the problems we decided, that computations should be
as lazy as possible: for example, factor vectors need to be computed
only, when needed, BUT: saved for later use.
Lazyness should be also flexible: user should have ability to control,
how much data is saved & reused.
Functions need to provide some sane interface to specify, how much data
user wants to be precomputed (for example, "compute only first 20
eigentriples", or "compute series reconstructions based on first 5
I'm currently working on proof-of-concept implementation of our ideas.
Some of them are pretty straightforward, but others look tricky to
implement within R.
We plan to use simsalabim as 'reference implementation' and after
complete of proof-of-concept project start to port current simsalabim
algorithms to new base. This WILL break backward compatibility, but it
seems, that user-visible benefits will provide much more.
Sorry for such long and a bit messy e-mail, but I tried to nail down
problems and possible ways to solve them :)
I'm open to any comments, suggestions & questions.
 Bau III, David; Trefethen, Lloyd N. Numerical linear algebra,
Philadelphia: Society for Industrial and Applied Mathematics. 1997.
With best regards, Anton Korobeynikov.
Faculty of Mathematics & Mechanics, Saint Petersburg State University.
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