Journal of Machine Learning Research 6 (2005) 1939–1959

Submitted 10/05; Published 12/05

A Unifying View of Sparse
Approximate Gaussian Process Regression
Joaquin Quiñonero-Candela
Carl Edward Rasmussen

JQC @ TUEBINGEN . MPG . DE
CARL @ TUEBINGEN . MPG . DE

Max Planck Institute for Biological Cybernetics
Spemannstraße 38
72076 Tübingen, Germany

Editor: Ralf Herbrich

Abstract
We provide a new unifying view, including all existing proper probabilistic sparse approximations
for Gaussian process regression. Our approach relies on expressing the effective prior which themethods are using. This allows new insights to be gained, and highlights the relationship between
existing methods. It also allows for a clear theoretically justified ranking of the closeness of the
known approximations to the corresponding full GPs. Finally we point directly to designs of new
better sparse approximations, combining the best of the existing strategies, within attractive computational constraints.
Keywords: Gaussian process, probabilistic regression, sparse approximation, Bayesian committee
machineRegression models based on Gaussian processes (GPs) are simple to implement, flexible, fully
probabilistic models, and thus a powerful tool in many areas of application. Their main limitationis that memory requirements and computational demands grow as the square and cube respectively,of the number of training cases n, effectively limiting a direct implementation to problems withat most a few thousand cases. To overcome the computational limitations numerous authors haverecently suggested a wealth of sparse approximations. Common to all these approximation schemesis that only a subset of the latent variables are treated exactly, and the remaining variables are given
some approximate, but computationally cheaper treatment. However, the published algorithms havewidely different motivations, emphasis and exposition, so it is difficult to get an overview (seeRasmussen and Williams, 2006, chapter 8) of how they relate to each other, and which can be
expected to give rise to the best algorithms.
In this paper we provide a unifying view of sparse approximations for GP regression. Our
approach is simple, but powerful: for each algorithm we analyze the posterior, and compute theeffective prior which it is using. Thus, we reinterpret the algorithms as “exact inference with anapproximated prior”, rather than the existing (ubiquitous) interpretation “approximate inferencewith the exact prior”. This approach has the advantage of directly expressing the approximations interms of prior assumptions about the function, which makes the consequences of the approximations
much easier to understand. While our view of the approximations is not the only one possible, it has
the advantage of putting all existing probabilistic sparse approximations under one umbrella, thus
enabling direct comparison and revealing the relation between them.
In Section 1 we briefly introduce GP models for regression. In Section 2 we present our unifying framework and write out the key equations in preparation for the unifying analysis of sparsec 2005 Joaquin Quiñonero-Candela and Carl Edward Rasmussen.

Q UI ÑONERO -C ANDELA AND R ASMUSSEN

algorithms in Sections 4-7. The relation of transduction and augmentation to our sparse framework
is covered in Section 8. All our approximations are written in terms of a new set of inducing variables. The choice of these variables is itself a challenging problem, and is discussed in Section
9. We comment on a few special approximations outside our general scheme in Section 10 andconclusions are drawn at the end.

1. Gaussian Processes for Regression
Probabilistic regression is usually formulated as follows: given a training set D = {(xi , yi ), i =1, . . . , n} of n pairs of (vectorial) inputs xi and noisy (real, scalar) outputs yi , compute the predictive
distribution of the function values f∗ (or noisy y∗ ) at test locations x∗ . In the simplest case (which
we deal with here) we assume that the noise is additive, independent and Gaussian, such that therelationship between the (latent) function f (x) and the observed noisy targets y are given byyi = f (xi ) + εi ,where

εi ∼ N (0, σ2noise ) ,(1)

where σ2noise is the variance of the noise.
Definition 1 A Gaussian process (GP) is a collection of random variables, any finite number ofwhich have consistent1 joint Gaussian distributions.
Gaussian process (GP) regression is a Bayesian approach which assumes a GP prior2 over functions,i.e. assumes a priori that function values behave according top(f|x1 , x2 , . . . , xn ) = N (0, K) ,(2)

where f = [ f1 , f2 , . . . , fn ]> is a vector of latent function values, fi = f (xi ) and K is a covariance matrix, whose entries are given by the covariance function, Ki j = k(xi , x j ). Note that the GP treats thelatent function values fi as random variables, indexed by the corresponding input. In the following,
for simplicity we will always neglect the explicit conditioning on the inputs; the GP model and all
expressions are always conditional on the corresponding inputs. The GP model is concerned onlywith the conditional of the outputs given the inputs; we do not model anything about the inputs
themselves.
Remark 2 Note, that to adhere to a strict Bayesian formalism, the GP covariance function,3 which
defines the prior, should not depend on the data (although it can depend on additional parameters).
As we will see in later sections, some approximations are strictly equivalent to GPs, while others
are not. That is, the implied prior may still be multivariate Gaussian, but the covariance function
may be different for training and test cases.
Definition 3 A Gaussian process is called degenerate iff the covariance function has a finite numberof non-zero eigenvalues.
1. By consistency is meant simply that the random variables obey the usual rules of marginalization, etc.
2. For notational simplicity we exclusively use zero-mean priors.
3. The covariance function itself shouldn’t depend on the data, though its value at a specific pair of inputs of course will.

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Degenerate GPs (such as e.g. with polynomial covariance function) correspond to finite linear(-in-the-parameters) models, whereas non-degenerate GPs (such as e.g. with squared exponential
or RBF covariance function) do not. The prior for a finite m dimensional linear model only considers a universe of at most m linearly independent functions; this may often be too restrictive whenn  m. Note however, that non-degeneracy on its own doesn’t guarantee the existence of the “rightkind” of flexibility for a given particular modelling task. For a more detailed background on GP
models, see for example that of Rasmussen and Williams (2006).
Inference in the GP model is simple: we put a joint GP prior on training and test latent values, f
and f∗ 4 , and combine it with the likelihood5 p(y|f) using Bayes rule, to obtain the joint posteriorp(f, f∗ |y) =p(f, f∗ )p(y|f)
.
p(y)

(3)

The final step needed to produce the desired posterior predictive distribution is to marginalize out
the unwanted training set latent variables:p(f∗ |y) =

Z

1
p(y)

p(f, f∗ |y)df =Zp(y|f) p(f, f∗ ) df ,(4)

or in words: the predictive distribution is the marginal of the renormalized joint prior times thelikelihood. The joint GP prior and the independent likelihood are both Gaussian
 hKi
f,f K∗,fp(f, f∗ ) = N 0,,
Kf,∗ K∗,∗andp(y|f) = N (f, σ2noise I) ,(5)

where K is subscript by the variables between which the covariance is computed (and we use theasterisk ∗ as shorthand for f∗ ) and I is the identity matrix. Since both factors in the integral are
Gaussian, the integral can be evaluated in closed form to give the Gaussian predictive distributionp(f∗ |y) = N K∗,f (Kf,f + σ2noise I)−1 y, K∗,∗ − K∗,f (Kf,f + σ2noise I)−1 Kf,∗ ,(6)

see the relevant Gaussian identity in appendix A. The problem with the above expression is that it
requires inversion of a matrix of size n × n which requires O (n3 ) operations, where n is the numberof training cases. Thus, the simple exact implementation can handle problems with at most a few
thousand training cases.

2. A New Unifying View
We now seek to modify the joint prior p(f∗ , f) from (5) in ways which will reduce the computational
requirements from (6). Let us first rewrite that prior by introducing an additional set of m latentvariables u = [u1 , . . . , um ]> , which we call the inducing variables. These latent variables are valuesof the Gaussian process (as also f and f∗ ), corresponding to a set of input locations Xu , which wecall the inducing inputs. Whereas the additional latent variables u are always marginalized out inthe predictive distribution, the choice of inducing inputs does leave an imprint on the final solution.
4. We will mostly consider a vector of test cases f∗ (rather than a single f∗ ).
5. You may have been expecting the likelihood written as p(y|f∗ , f) but since the likelihood is conditionally independentof everything else given f, this makes no difference.

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Q UI ÑONERO -C ANDELA AND R ASMUSSEN

The inducing variables will turn out to be generalizations of variables which other authors have referred to variously as “support points”, “active set” or “pseudo-inputs”. Particular sparse algorithms
choose the inducing variables in various different ways; some algorithms chose the inducing inputs
to be a subset of the training set, others not, as we will discuss in Section 9. For now consider any
arbitrary inducing variables.
Due to the consistency of Gaussian processes, we know that we can recover p(f∗ , f) by simply
integrating (marginalizing) out u from the joint GP prior p(f∗ , f, u)p(f∗ , f) =Z

p(f∗ , f, u) du =Zp(f∗ , f|u) p(u) du,

where

p(u) = N (0, Ku,u ) .

(7)This is an exact expression. Now, we introduce the fundamental approximation which gives riseto almost all sparse approximations. We approximate the joint prior by assuming that f∗ and f areconditionally independent given u, see Figure 1, such thatp(f∗ , f) ' q(f∗ , f) =Z

q(f∗ |u) q(f|u) p(u) du .

(8)

The name inducing variable is motivated by the fact that f and f∗ can only communicate thoughu, and u therefore induces the dependencies between training and test cases. As we shall detail in
the following sections, the different computationally efficient algorithms proposed in the literaturecorrespond to different additional assumptions about the two approximate inducing conditionals
q(f|u), q(f∗ |u) of the integral in (8). It will be useful for future reference to specify here the exact
expressions for the two conditionals
training conditional:
test conditional:−1p(f|u) = N (Kf,u Ku,uu, Kf,f − Qf,f ) ,−1
p(f∗ |u) = N (K∗,u Ku,uu, K∗,∗ − Q∗,∗ ) ,

(9a)
(9b)

−1 K . We can readily identify thewhere we have introduced the shorthand notation6 Qa,b , Ka,u Ku,uu,bexpressions in (9) as special (noise free) cases of the standard predictive equation (6) with u playing
the role of (noise free) observations. Note that the (positive semi-definite) covariance matrices in (9)have the form K − Q with the following interpretation: the prior covariance K minus a (non-negative
definite) matrix Q quantifying how much information u provides about the variables in question (f orf∗ ). We emphasize that all the sparse methods discussed in the paper correspond simply to different
approximations to the conditionals in (9), and throughout we use the exact likelihood and inducing
priorp(y|f) = N (f, σ2noise I) , and p(u) = N (0, Ku,u ) .
(10)

3. The Subset of Data (SoD) Approximation
Before we get started with the more sophisticated approximations, we mention as a baseline method
the simplest possible sparse approximation (which doesn’t fall inside our general scheme): use
only a subset of the data (SoD). The computational complexity is reduced to O (m3 ), where m < n.
We would not generally expect SoD to be a competitive method, since it would seem impossible(even with fairly redundant data and a good choice of the subset) to get a realistic picture of the
6. Note, that Qa,b depends on u although this is not explicit in the notation.

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u

u

f1

Q
Q
 AA Q
A QQ

Q
A

Q
A

Q
Q
A

r
r
r
r
r
f2
fn
f∗

f1

Q
Q
 AA Q
A QQ

Q
A

Q
A

Q
Q
A

r
r
r
r
r
f2
fn
f∗

Figure 1: Graphical model of the relation between the inducing variables u, the training latent functions values f = [ f1 , . . . , fn ]> and the test function value f∗ . The thick horizontal line represents a set of fully connected nodes. The observations y1 , . . . , yn , y∗ (not shown) would
dangle individually from the corresponding latent values, by way of the exact (factored)
likelihood (5). Left graph: the fully connected graph corresponds to the case where
no approximation is made to the full joint Gaussian process distribution between thesevariables. The inducing variables u are superfluous in this case, since all latent function values can communicate with all others. Right graph: assumption of conditional
independence between training and test function values given u. This gives rise to theseparation between training and test conditionals from (8). Notice that having cut thecommunication path between training and test latent function values, information from f
can only be transmitted to f∗ via the inducing variables u.

uncertainties, when only a part of the training data is even considered. We include it here mostly asa baseline against which to compare better sparse approximations.
In Figure 5 top, left we see how the SoD method produces wide predictive distributions, whentraining on a randomly selected subset of 10 cases. A fair comparison to other methods would
take into account that the computational complexity is independent of n as opposed to other moreadvanced methods. These extra computational resources could be spent in a number of ways,
e.g. larger m, or an active (rather than random) selection of the m points. In this paper we willconcentrate on understanding the theoretical foundations of the various approximations rather thaninvestigating the necessary heuristics needed to turn the approximation schemes into actually practical algorithms.

4. The Subset of Regressors (SoR) Approximation
The Subset of Regressors (SoR) algorithm was given by Silverman (1985), and mentioned again by
Wahba et al. (1999). It was then adapted by Smola and Bartlett (2001) to propose a sparse greedy
approximation to Gaussian process regression. SoR models are finite linear-in-the-parameters models with a particular prior on the weights. For any input x∗ , the corresponding function value f∗ isgiven by:f∗ = K∗,u wu ,

with

−1
p(wu ) = N (0, Ku,u
),

(11)

where there is one weight associated to each inducing input in Xu . Note that the covariance matrix
for the prior on the weights is the inverse of that on u, such that we recover the exact GP prior on u,1943

Q UI ÑONERO -C ANDELA AND R ASMUSSEN

which is Gaussian with zero mean and covarianceu = Ku,u wu ⇒ hu u> i = Ku,u hwu w>
u iKu,u = Ku,u .

(12)−1 u we can redefine the SoR model in an
Using the effective prior on u and the fact that wu = Ku,uequivalent, more intuitive way:−1u,f∗ = K∗,u Ku,uwith u ∼ N (0, Ku,u ) .

(13)

We are now ready to integrate the SoR model in our unifying framework. Given that there is adeterministic relation between any f∗ and u, the approximate conditional distributions in the integral
in eq. (8) are given by:−1
qSoR (f|u) = N (Kf,u Ku,uu, 0) ,

and−1
qSoR (f∗ |u) = N (K∗,u Ku,uu, 0) ,

(14)

with zero conditional covariance, compare to (9). The effective prior implied by the SoR approximation is easily obtained from (8), giving
 hQif,f Qf,∗qSoR (f, f∗ ) = N 0,,
Q∗,f Q∗,∗(15)−1 K . A more descriptive name for this method, would be thewhere we recall Qa,b , Ka,u Ku,uu,bDeterministic Inducing Conditional (DIC) approximation. We see that this approximate prior isdegenerate. There are only m degrees of freedom in the model, which implies that only m linearly
independent functions can be drawn from the prior. The m + 1-th one is a linear combination of theprevious. For example, in a very low noise regime, the posterior could be severely constrained byonly m training cases.
The degeneracy of the prior causes unreasonable predictive distributions. Indeed, the approximate prior over functions is so restrictive, that given enough data only a very limited family offunctions will be plausible under the posterior, leading to overconfident predictive variances. Thisis a general problem of finite linear models with small numbers of weights (for more details see
Rasmussen and Quiñonero-Candela, 2005). Figure 5, top, right panel, illustrates the unreasonablepredictive uncertainties of the SoR approximation on a toy dataset.7
The predictive distribution is obtained by using the SoR approximate prior (15) instead of thetrue prior in (4). For each algorithm we give two forms of the predictive distribution, one which iseasy to interpret, and the other which is economical to compute with:
qSoR (f∗ |y) = N Q∗,f (Qf,f + σ2noise I)−1 y, Q∗,∗ − Q∗,f (Qf,f + σ2noise I)−1 Qf,∗ ,
(16a)

−2
(16b)
= N σ K∗,u Σ Ku,f y, K∗,u ΣKu,∗ ,where we have defined Σ = (σ−2 Ku,f Kf,u + Ku,u )−1 . Equation (16a) is readily recognized as theregular prediction equation (6), except that the covariance K has everywhere been replaced by Q,
which was already suggested by (15). This corresponds to replacing the covariance function k with
−1 k(u, x ). The new covariance function has rank (at most) m. Thus we havekSoR (xi , x j ) = k(xi , u)Ku,uj
the following
7. Wary of this fact, Smola and Bartlett (2001) propose using the predictive variances of the SoD, or a more accuratecomputationally costly alternative (more details are given by Quiñonero-Candela, 2004, Chapter 3).

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Remark 4 The SoR approximation is equivalent to exact inference in the degenerate Gaussian−1 k(u, x ).
process with covariance function kSoR (xi , x j ) = k(xi , u)Ku,uj
The equivalent (16b) is computationally cheaper, and with (11) in mind, Σ is the covariance of theposterior on the weights wu . Note that as opposed to the subset of data method, all training cases
are taken into account. The computational complexity is O (nm2 ) initially, and O (m) and O (m2 ) per
test case for the predictive mean and variance respectively.

5. The Deterministic Training Conditional (DTC) Approximation
Taking up ideas already contained in the work of Csató and Opper (2002), Seeger et al. (2003)
recently proposed another sparse approximation to Gaussian process regression, which does not
suffer from the nonsensical predictive uncertainties of the SoR approximation, but that interestingly
leads to exactly the same predictive mean. Seeger et al. (2003), who called the method Projected
Latent Variables (PLV), presented the method as relying on a likelihood approximation, based on−1 u:
the projection f = Kf,u Ku,u−1p(y|f) ' q(y|u) = N (Kf,u Ku,uu, σ2noise I) .

(17)

The method has also been called the Projected Process Approximation (PPA) by Rasmussen andWilliams (2006, Chapter 8). One way of obtaining an equivalent model is to retain the usual likelihood, but to impose a deterministic training conditional and the exact test conditional from eq. (9b)−1qDTC (f|u) = N (Kf,u Ku,uu, 0),

andqDTC (f∗ |u) = p(f∗ |u) .

(18)

This reformulation has the advantage of allowing us to stick to our view of exact inference (withexact likelihood) with approximate priors. Indeed, under this model the conditional distributionof f given u is identical to that of the SoR, given in the left of (14). A systematic name for thisapproximation is the Deterministic Training Conditional (DTC).
The fundamental difference with SoR is that DTC uses the exact test conditional (9b) instead ofthe deterministic relation between f∗ and u of SoR. The joint prior implied by DTC is given by: hQi
f,f Qf,∗qDTC (f, f∗ ) = N 0,,
(19)
Q∗,f K∗,∗
which is surprisingly similar to the effective prior implied by the SoR approximation (15). The
fundamental difference is that under the DTC approximation f∗ has a prior variance of its own,
given by K∗,∗ . This prior variance reverses the behaviour of the predictive uncertainties, and turns
them into sensible ones, see Figure 5 for an illustration.
The predictive distribution is now given by:
qDTC (f∗ |y) = N (Q∗,f (Qf,f + σ2noise I)−1 y, K∗,∗ − Q∗,f (Qf,f + σ2noise I)−1 Qf,∗>,
= N σ−2 K∗,u Σ Ku,f y, K∗,∗ − Q∗,∗ + K∗,u ΣK∗,u

(20a)
(20b)

where again we have defined Σ = (σ−2 Ku,f Kf,u + Ku,u )−1 as in (16). The predictive mean for the
DTC is identical to that of the SoR approximation (16), but the predictive variance replaces the Q∗,∗
from SoR with K∗,∗ (which is larger, since K∗,∗ − Q∗,∗ is positive definite). This added term is thepredictive variance of the posterior of f∗ conditioned on u. It grows to the prior variance K∗,∗ as x∗
moves far from the inducing inputs in Xu .
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Q UI ÑONERO -C ANDELA AND R ASMUSSEN

u

f1

Q
Q
 AA Q
A QQ

Q
A

Q
A

Q
Q
A

r
r
r
f2
fn
f∗

Figure 2: Graphical model for the FITC approximation. Compared to those in Figure 1, all edges
between latent function values have been removed: the latent function values are conditionally fully independent given the inducing variables u. Although strictly speaking
the SoR and DTC approximations could also be represented by this graph, note that bothfurther assume a deterministic relation between f and u.

Remark 5 The only difference between the predictive distribution of DTC and SoR is the variance.
The predictive variance of DTC is never smaller than that of SoR.
Note, that since the covariances for training cases and test cases are computed differently, see (19),
it follows that
Remark 6 The DTC approximation does not correspond exactly to a Gaussian process,as the covariance between latent values depends on whether they are considered training or test
cases, violating consistency, see Definition 1. The computational complexity has the same order asfor SoR.

6. The Fully Independent Training Conditional (FITC) Approximation
Recently Snelson and Ghahramani (2006) proposed another likelihood approximation to speed up
Gaussian process regression, which they called Sparse Gaussian Processes using Pseudo-inputs(SGPP). While the DTC is based on the likelihood approximation given by (17), the SGPP proposesa more sophisticated likelihood approximation with a richer covariance−1p(y|f) ' q(y|u) = N (Kf,u Ku,uu, diag[Kf,f − Qf,f ] + σ2noise I) ,(21)

where diag[A] is a diagonal matrix whose elements match the diagonal of A. As we did in (18)for the DTC, we provide an alternative equivalent formulation called Fully Independent Training
Conditional (FITC) based on the inducing conditionals:n
−1
qFITC (f|u) = ∏ p( fi |u) = N Kf,u Ku,uu, diag[Kf,f −Qf,f ] , and qFITC ( f∗ |u) = p( f∗ |u) . (22)i=1

We see that as opposed to SoR and DTC, FITC does not impose a deterministic relation between fand u. Instead of ignoring the variance, FITC proposes an approximation to the training conditional
distribution of f given u as a further independence assumption. In addition, the exact test conditionalfrom (9b) is used in (22), although for reasons which will become clear towards the end of this1946

S PARSE A PPROXIMATE G AUSSIAN P ROCESS R EGRESSION

section, we initially consider only a single test case, f∗ . The corresponding graphical model is given
in Figure 2. The effective prior implied by the FITC is given by h Q − diag[Q − K ] Q i
f,f
f,f
f,f
f,∗
.
qFITC (f, f∗ ) = N 0,
Q∗,f
K∗,∗

(23)

Note, that the sole difference between the DTC and FITC is that in the top left corner of the impliedprior covariance, FITC replaces the approximate covariances of DTC by the exact ones on the
diagonal. The predictive distribution is
qFITC ( f∗ |y) = N Q∗,f (Qf,f + Λ)−1 y, K∗,∗ − Q∗,f (Qf,f + Λ)−1 Qf,∗
(24a)

(24b)
= N K∗,u ΣKu,f Λ−1 y, K∗,∗ − Q∗,∗ + K∗,u ΣKu,∗ ,where we have defined Σ = (Ku,u + Ku,f Λ−1 Kf,u )−1 and Λ = diag[Kf,f − Qf,f + σ2noise I ]. The computational complexity is identical to that of SoR and DTC.
So far we have only considered a single test case. There are two options for joint predictions,either 1) use the exact full test conditional from (9b), or 2) extend the additional factorizing assumption to the test conditional. Although Snelson and Ghahramani (2006) don’t explicitly discuss
joint predictions, it would seem that they probably intend the second option. Whereas the additional independence assumption for the test cases is not really necessary for computational reasons,it does affect the nature of the approximation. Under option 1) the training and test covariance arecomputed differently, and thus this does not correspond to our strict definition of a GP model, but
Remark 7 Iff the assumption of full independence is extended to the test conditional, the FITC approximation is equivalent to exact inference in a non-degenerate Gaussian process with covariancefunction kFIC (xi , x j ) = kSoR (xi , x j ) + δi, j [k(xi , x j ) − kSoR (xi , x j )],where δi, j is Kronecker’s delta. A logical name for the method where the conditionals (training andtest) are always forced to be fully independent would be the Fully Independent Conditional (FIC)
approximation. The effective prior implied by FIC is:i h Q − diag[Q − K ]
Qf,∗
f,f
f,f
f,f
.
qFIC (f, f∗ ) = N 0,Q∗,fQ∗,∗ − diag[Q∗,∗ − K∗,∗ ](25)

7. The Partially Independent Training Conditional (PITC) Approximation
In the previous section we saw how to improve the DTC approximation by approximating the training conditional with an independent distribution, i.e. one with a diagonal covariance matrix. In thissection we will further improve the approximation (while remaining computationally attractive) byextending the training conditional to have a block diagonal covariance:
−1
qPITC (f|u) = N Kf,u Ku,uu, blockdiag[Kf,f − Qf,f ] , and qPITC (f∗ |u) = p(f∗ |u) .
(26)

where blockdiag[A] is a block diagonal matrix (where the blocking structure is not explicitly stated).
We represent graphically the PITC approximation in Figure 3. Developing this analogously to the
FITC approximation from the previous section, we get the joint prior h Q − blockdiag[Q − K ] Q i
f,f
f,f
f,f
f,∗
qPITC (f, f∗ ) = N 0,
,
Q∗,f
K∗,∗
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Q UI ÑONERO -C ANDELA AND R ASMUSSEN

u

fI1

Q
Q
 AA Q
A QQ

Q
A

Q
A

Q
Q
A

r
r
r
fI
fI
f∗
2

k

Figure 3: Graphical representation of the PITC approximation. The set of latent function values fIi
indexed by the the set of indices Ii is fully connected. The PITC differs from FITC (seegraph in Fig. 2) in that conditional independence is now between the k groups of training
latent function values. This corresponds to the block diagonal approximation to the true
training conditional given in (26).

and the predictive distribution is identical to (24), except for the alternative definition of Λ =blockdiag[Kf,f − Qf,f + σ2noise I ]. An identical expression was obtained by Schwaighofer and Tresp(2003, Sect. 3), developing from the original Bayesian committee machine (BCM) by Tresp (2000).
The relationship to the FITC was pointed out by Lehel Csató. The BCM was originally proposed asa transductive learner (i.e. where the test inputs have to be known before training), and the inducing
inputs Xu were chosen to be the test inputs. We discuss transduction in detail in the next section.
It is important to realize that the BCM proposes two orthogonal ideas: first, the block diagonal
structure of the partially independent training conditional, and second setting the inducing inputs tobe the test inputs. These two ideas can be used independently and in Section 8 we propose using
the first without the second.
The computational complexity of the PITC approximation depends on the blocking structure
imposed in (26). A reasonable choice, also recommended by Tresp (2000) may be to choosek = n/m blocks, each of size m × m. The computational complexity remains O (nm2 ). Since in
the PITC model the covariance is computed differently for training and test cases
Remark 8 The PITC approximation does not correspond exactly to a Gaussian process.
This is because computing covariances requires knowing whether points are from the training- or
test-set, (27). One can obtain a Gaussian process from the PITC by extending the partial conditional
independence assumption to the test conditional, as we did in Remark 7 for the FITC.

8. Transduction and Augmentation
The idea of transduction is that one should restrict the goal of learning to prediction on a prespecified set of test cases, rather than trying to learn an entire function (induction) and then evaluate
it at the test inputs. There may be no universally agreed upon definition of transduction. In thispaper we use
Definition 9 Transduction occurs only if the predictive distribution depends on other test inputs.
This operational definition excludes models for which there exist an equivalent inductive counterpart. According to this definition, it is irrelevant when the bulk of the computation takes place.
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u

f∗



 AA
A


A

A
 

A

r r r
fI
fI
fI
1

2

k

Figure 4: Two views on Augmentation. One view is to see that the test latent function value f∗
is now part of the inducing variables u and therefore has access to the training latentfunction values. An equivalent view is to consider that we have dropped the assumptionof conditional independence between f∗ and the training latent function values. Even iff∗ has now direct access to each of the training fi , these still need to go through u totalk to each other if they fall in conditionally independent blocks. We have in this figure
decided to recycle the graph for PITC from Figure 3 to show that all approximations wehave presented can be augmented, irrespective of what the approximation for the training
conditional is.

There are several different possible motivations for transduction: 1) transduction is somehow
easier than induction (Vapnik, 1995), 2) the test inputs may reveal important information, whichshould be used during training. This motivation drives models in semi-supervised learning (studied
mostly in the context of classification) and 3) for approximate algorithms one may be able to limit
the discrepancies of the approximation at the test points.
For exact GP models it seems that the first reason doesn’t really apply. If you make predictions
at the test points that are consistent with a GP, then it is trivial inside the GP framework to extend
these to any other input points, and in effect we have done induction.
The second reason seems more interesting. However, in a standard GP setting, it is a consequence of the consistency property, see Remark 2, that predictions at one test input are independentof the location of any other test inputs. Therefore transduction can not be married with exact GPs:
Remark 10 Transduction can not occur in exact Gaussian process models.
Whereas this holds for the usual setting of GPs, it could be different in non-standard situations
where e.g. the covariance function depends on the empirical input densities.
Transduction can occur in the sparse approximation to GPs, by making the choice of inducing
variables depend on the test inputs. The BCM from the previous section, where Xu = X∗ (whereX∗ are the test inputs) is an example of this. Since the inducing variables are connected to all othernodes (see Figure 3) we would expect the approximation to be good at u = f∗ , which is what we careabout for predictions, relating to reason 3) above. While this reasoning is sound, it is not necessarily
a sufficient consideration for getting a good model. The model has to be able to simultaneously
explain the training targets as well and if the choice of u makes this difficult, the posterior at the
points of interest may be distorted. Thus, the choice of u should be governed by the ability to model
the conditional of the latents given the inputs, and not solely by the density of the (test) inputs.
The main drawback of transduction is that by its nature it doesn’t provide a predictive modelin the way inductive models do. In the usual GP model one can do the bulk of the computation
1949

Q UI ÑONERO -C ANDELA AND R ASMUSSEN

involved in the predictive distributions (e.g. matrix inversion) before seeing the test cases, enabling
fast computation of test predictions.
It is interesting that whereas other methods spend much effort trying to optimize the inducing
variables, the BCM simply uses the test set. The quality of the BCM approximation depends thenon the particular location of the test inputs, upon which one usually does not have any control. We
now see that there may be a better method, eliminating the drawback of transduction, namely use
the PITC approximation, but choose the u’s carefully (see Section 9), don’t just use the test set.
8.1 Augmentation
An idea closely related to transduction, but not covered by our definition, is augmentation, whichin contrast to transduction is done individually for each test case. Since in the previous sections,
we haven’t assumed anything about u, we can simply augment the set of inducing variables by f∗(i.e. have one additional inducing variable equal to the current test latent), and see what happensin the predictive distributions for the different methods. Let’s first investigate the consequences
for the test conditional from (9b). Note, the interpretation of the covariance matrix K∗,∗ − Q∗,∗was “the prior covariance minus the information which u provides about f∗ ”. It is clear that theaugmented u (with f∗ ) provides all possible information about f∗ , and consequently Q∗,∗ = K∗,∗ .
An equivalent view on augmentation is that the assumption of conditional independence betweenf∗ and f is dropped. This is seen trivially by adding edges between f∗ and the fi in the graphicalmodel, Figure 4.
Augmentation was originally proposed by Rasmussen (2002), and applied in detail to the SoR
with RBF covariance by Quiñonero-Candela (2004). Because the SoR is a finite linear model, andthe basis functions are local (Gaussian bumps), the predictive distributions can be very misleading.
For example, when making predictions far away from the center of any basis function, all basis
functions have insignificant magnitudes, and the prediction (averaged over the posterior) will beclose to zero, with very small error-bars; this is the opposite of the desired behaviour, where wewould expect the error-bars to grow as we move away from the training cases. Here augmentation
makes a particularly big difference turning the nonsensical predictive distribution into a reasonable
one, by ensuring that there is always a basis function centered on the test case. Compare the nonaugmented to the augmented SoR in Figure 5. An analogous Gaussian process based finite linear
model that has recently been healed by augmentation is the relevance vector machine (Rasmussen
and Quiñonero-Candela, 2005).
Although augmentation was initially proposed for a narrow set of circumstances, it is easily
applied to any of the approximations discussed. Of course, augmentation doesn’t make any sense
for an exact, non-degenerate Gaussian process model (a GP with a covariance function that has afeature-space which is infinite dimensional, i.e. with basis functions everywhere).
Remark 11 A full non-degenerate Gaussian process cannot be augmented,
since the corresponding f∗ would already be connected to all other variables in the graphical model.
But augmentation does make sense for sparse approximations to GPs.
The more general process view on augmentation has several advantages over the basis function
view. It is not completely clear from the basis function view, which basis function should be used
for augmentation. For example, Rasmussen and Quiñonero-Candela (2005) successfully apply augmentation using basis functions that have a zero contribution at the test location! In the process view1950

S PARSE A PPROXIMATE G AUSSIAN P ROCESS R EGRESSION

however, it seems clear that one would chose the additional inducing variable to be f∗ , to minimize
the effects of the approximations.
Let us compute the effective prior for the augmented SoR. Given that f∗ is in the inducing set,
the test conditional is not an approximation and we can rewrite the integral leading to the effective
prior:Z
qASoR (f∗ , f) =qSoR (f| f∗ , u) p( f∗ , u) du .

(28)

It is interesting to notice that this is also the effective prior that would result from augmenting the
DTC approximation, since qSoR (f| f∗ , u) = qDTC (f| f∗ , u).
Remark 12 Augmented SoR (ASoR) is equivalent to augmented DTC (ADTC).
Augmented DTC only differs from DTC in the additional presence of f∗ among the inducing variables in the training conditional. We can only expect augmented DTC to be a more accurate approximation than DTC, since adding an additional inducing variable can only help capture informationfrom y. Therefore
Remark 13 DTC is a less accurate (but cheaper) approximation than augmented SoR.
We saw previously in Section 5 that the DTC approximation does not suffer from the nonsensical predictive variances of the SoR. The equivalence between the augmented SoR and augmented
DTC is another way of seeing how augmentation reverses the misbehaviour of SoR. The predictive
distribution of the augmented SoR is obtained by adding f∗ to u in (20).
Prediction with an augmented sparse model comes at a higher computational cost, since now f∗
directly interacts with all of f and not just with u. For each new test case, updating the augmented Σin the predictive equation (for example (20b) for DTC) implies computing the vector matrix productK∗,f Kf,u with complexity O (nm). This is clearly higher than the O (m) for the mean, and O (m2 ) forthe predictive distribution of all the non-augmented methods we have discussed.
Augmentation seems to be only really necessary for methods that make a severe approximation to the test conditional, like the SoR. For methods that make little or no approximation to thetest conditional, it is difficult to predict the degree to which augmentation would help. However,
one can see by giving f∗ access to all of the training latent function values in f, one would expect
augmentation to give less under-confident predictive distributions near the training data. Figure 5
clearly shows that augmented DTC (equivalent to augmented SoR) has a superior predictive distribution (both mean and variance) than standard DTC. Note however that in the figure we have
purposely chosen a too short lengthscale to enhance visualization. Quantitatively, this superiority
was experimentally assessed by Quiñonero-Candela (2004, Table 3.1). Augmentation hasn’t been
compared to the more advanced approximations FITC and PITC, and the figure would change inthe more realistic scenario where the inducing inputs and hyperparameters are learnt (Snelson andGhahramani, 2006).
Transductive methods like the BCM can be seen as joint augmentation, and one could potentiallyuse it for any of the methods presented. It seems that the good performance of the BCM could
essentially stem from augmentation, the presence of the other test inputs in the inducing set being
probably of little benefit. Joint augmentation might bring some computational advantage, but won’tchange the scaling: note that augmenting m times at a cost of O (nm) apiece implies the same
O (nm2 ) total cost as the jointly augmented BCM.
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Q UI ÑONERO -C ANDELA AND R ASMUSSEN

SoD

SoR

1.5

1.5

1

1

0.5

0.5

0

0

−0.5

−0.5

−1

−1

−1.5
−15

−10

−5

0

5

10

15

−1.5
−15

−10

−5

DTC
1.5

1.5

1

1

0.5

0.5

0

0

−0.5

−0.5

−1

−1

−1.5
−15

−10

−5

0

5

10

15

−1.5
−15

−10

−5

FITC
1.5

1

1

0.5

0.5

0

0

−0.5

−0.5

−1

−1

−10

−5

0

5

10

15

0

5

10

15

5

10

15

PITC

1.5

−1.5
−15

0
ASoR/ADTC

5

10

15

−1.5
−15

−10

−5

0

Figure 5: Toy example with identical covariance function and hyperparameters. The squared exponential covariance function is used, and a slightly too short lengthscale is chosen on
purpose to emphasize the different behaviour of the predictive uncertainties. The dots
are the training points, the crosses are the targets corresponding to the inducing inputs,
randomly selected from the training set. The solid line is the mean of the predictive
distribution, and the dotted lines show the 95% confidence interval of the predictions.
Augmented DTC (ADTC) is equivalent to augmented SoR (ASoR), see Remark 12.

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S PARSE A PPROXIMATE G AUSSIAN P ROCESS R EGRESSION

9. On the Choice of the Inducing Variables
We have until now assumed that the inducing inputs Xu were given. Traditionally, sparse models
have very often been built upon a carefully chosen subset of the training inputs. This concept isprobably best exemplified in the popular support vector machine (Cortes and Vapnik, 1995). In
sparse Gaussian processes it has also been suggested to select the inducing inputs Xu from among
the training inputs. Since this involves a prohibitive combinatorial optimization, greedy optimization approaches have been suggested using various selection criteria like online learning (Csató andOpper, 2002), greedy posterior maximization (Smola and Bartlett, 2001), maximum information
gain (Seeger et al., 2003), matching pursuit (Keerthi and Chu, 2006), and probably more. As discussed in the previous section, selecting the inducing inputs from among the test inputs has also
been considered in transductive settings. Recently, Snelson and Ghahramani (2006) have proposed
to relax the constraint that the inducing variables must be a subset of training/test cases, turning thediscrete selection problem into one of continuous optimization. One may hope that finding a goodsolution is easier in the continuous than the discrete case, although finding the global optimum is
intractable in both cases. And perhaps the less restrictive choice can lead to better performance invery sparse models.
Which optimality criterion should be used to set the inducing inputs? Departing from a fully
Bayesian treatment which would involve defining priors on Xu , one could maximize the marginal
likelihood (also called the evidence) with respect to Xu , an approach also followed by Snelson andGhahramani (2006). Each of the approximate methods proposed involves a different effective prior,and hence its own particular effective marginal likelihood conditioned on the inducing inputs
q(y|Xu ) =ZZp(y|f) q(f|u) p(u|Xu )du df =Zp(y|f) q(f|Xu )df ,(29)

which of course is independent of the test conditional. We have in the above equation explicitly
conditioned on the inducing inputs Xu . Using Gaussian identities, the effective marginal likelihood
is very easily obtained by adding a ridge σ2noise I (from the likelihood) to the covariance of effective
prior on f. Using the appropriate definitions of Λ, the log marginal likelihood becomeslog q(y|Xu ) = − 21 log |Qf,f + Λ| − 12 y> (Qf,f + Λ)−1 y − n2 log(2π) ,(30)

where ΛSoR = ΛDTC = σ2noise I, ΛFITC = diag[Kf,f − Qf,f ] + σ2noise I, and ΛPITC = blockdiag[Kf,f −Qf,f ] + σ2noise I. The computational cost of the marginal likelihood is O (nm2 ) for all methods, that ofits gradient with respect to one element of Xu is O (nm). This of course implies that the complexityof computing the gradient wrt. to the whole of Xu is O (dnm2 ), where d is the dimension of the input
space.
It has been proposed to maximize the effective posterior instead of the effective marginal likelihood (Smola and Bartlett, 2001). However this is potentially dangerous and can lead to overfitting.
Maximizing the whole evidence instead is sound and comes at an identical computational cost (fora deeper analysis see Quiñonero-Candela, 2004, Sect. 3.3.5 and Fig. 3.2).
The marginal likelihood has traditionally been used to learn the hyperparameters of GPs in thenon fully Bayesian treatment (see for example Williams and Rasmussen, 1996). For the sparse
approximations presented here, once you are learning Xu it is straightforward to allow for learning
hyperparameters (of the covariance function) during the same optimization, and there is no needto interleave optimization of u with learning of the hyperparameters as it has been proposed forexample by Seeger et al. (2003).
1953

Q UI ÑONERO -C ANDELA AND R ASMUSSEN

10. Other Methods
In this section we briefly mention two approximations which don’t fit in our unifying scheme,
since one doesn’t correspond to a proper probabilistic model, and the other one uses a particularconstruction for the covariance function, rather than allowing any general covariance function.
10.1 The Nyström Approximation
The Nyström Approximation for speeding up GP regression was originally proposed by Williams
and Seeger (2001), and then questioned by Williams et al. (2002). Like SoR and DTC, the Nyström
Approximation for GP regression approximates the prior covariance of f by Qf,f . However, unlike
these methods, the Nyström Approximation is not based on a generative probabilistic model. The
prior covariance between f∗ and f is taken to be exact, which is inconsistent with the prior covariance
on f:
i
 hQ
f,f Kf,∗.
(31)
q(f, f∗ ) = N 0,
K∗,f K∗,∗
As a result we cannot derive this method from our unifying framework, nor represent it with agraphical model. Worse, the resulting prior covariance matrix is not even guaranteed to be positive
definite, allowing the predictive variances to be negative. Notice that replacing Kf,∗ by Qf,∗ in (31)is enough to make the prior covariance positive definite, and one obtains the DTC approximation.
Remark 14 The Nyström Approximation does not correspond to a well-formed probabilistic model.
Ignoring any quibbles about positive definiteness, the predictive distribution of the Nyström Approximation is given by:>>p( f∗ |y) = N Kf,∗
[Qf,f + σ2noise I]−1 y, K∗,∗ − Kf,∗
[Qf,f + σ2noise I]−1 Kf,∗ ,(32)
but the predictive variance is not guaranteed to be positive. The computational cost is O (nm2 ).
10.2 The Relevance Vector Machine
The relevance vector machine, introduced by Tipping (2001), is a finite linear model with an independent Gaussian prior imposed on the weights. For any input x∗ , the corresponding function
output is given by:f∗ = φ∗ w , with p(w|A) = N (0, A) ,(33)

where φ∗ = [φ1 (x), . . . , φm (x)] is the (row) vector of responses of the m basis functions, and A =diag(α1 , . . . , αm ) is the diagonal matrix of joint prior precisions (inverse variances) of the weights.
The αi are learnt by maximizing the RVM evidence (obtained by also assuming Gaussian additiveiid. noise, see (1)), and for the typical case of rich enough sets of basis functions many of the
precisions go to infinity effectively pruning out the corresponding weights (for a very interesting
analysis see Wipf et al., 2004). The RVM is thus a sparse method and the surviving basis functions
are called relevance vectors.
Note that since the RVM is a finite linear model with Gaussian priors on the weights, it can beseen as a Gaussian process:Remark 15 The RVM is equivalent to a degenerate Gaussian process with covariance function−1
kRVM (xi , x j ) = φi A−1 φ>j = ∑m
k=1 αk φk (xi ) φk (x j ),1954

S PARSE A PPROXIMATE G AUSSIAN P ROCESS R EGRESSION

Methodq(f∗ |u)q(f|u)

GP

exact

exact

SoR

determ.

determ.

DTC

exact

determ.

FITC(exact)fully indep.

PITC

exact

partially indep.

joint prior covarianceKf,f Kf,∗
K
K∗,∗
 ∗,f

Qf,f Qf,∗
Q
Q∗,∗
 ∗,f

Qf,f Qf,∗
Q∗,f K∗,∗
Qf,f − diag[Qf,f − Kf,f ] Qf,∗
Q∗,f
K∗,∗


Qf,f − blokdiag[Qf,f − Kf,f ] Qf,∗
Q∗,f
K∗,∗

GP?
√
√

√
( )

Table 1: Summary of the way approximations are built. All these methods are detailed in the previous sections. The initial cost and that of the mean and variance per test case are respectively
n2 , n and n2 for the exact GP, and nm2 , m and m2 for all other methods. The “GP?” column
indicates whether the approximation is equivalent to a GP. For FITC see Remark 7.

as was also pointed out by Tipping (2001, eq. (59)). Whereas all sparse approximations we havepresented until now are totally independent of the choice of covariance function, for the RVM
this choice is restricted to covariance functions that can be expressed as finite expansions in termsof some basis functions. Being degenerate GPs in exactly the same way as the SoR (presented
in Section 4), the RVM does also suffer from unreasonable predictive variances. Rasmussen andQuiñonero-Candela (2005) show that the predictive distributions of RVMs can also be healed byaugmentation, see Section 8. Once the αi have been learnt, denoting by m the number of surviving
relevance vectors, the complexity of computing the predictive distribution of the RVM is O (m) for
mean and O (m2 ) for the variance.
RVMs are often used with radial basis functions centered on the training inputs. One potentiallyinteresting extension to the RVM would be to learn the locations of the centers of the basis functions,in the same way as proposed by Snelson and Ghahramani (2006) for the FITC approximation, see
Section 6. This is a curious reminiscence of learning the centers in RBF Networks.

11. Conclusions
We have provided a unifying framework for sparse approximations to Gaussian processes for regression. Our approach consists of two steps, first 1) we recast the approximation in terms of approximations to the prior, and second 2) we introduce inducing variables u and the idea of conditional
independence given u. We recover all existing sparse methods by making further simplifications of
the covariances of the training and test conditionals, see Table 1 for a summary.
Previous methods were presented based on different approximation paradigms (e.g. likelihood
approximations, projection methods, matrix approximations, minimization of Kullback-Leibler divergence, etc), making direct comparison difficult. Under our unifying view we deconstruct methods, making it clear which building blocks they are based upon. For example, the SGPP by Snelson
1955

Q UI ÑONERO -C ANDELA AND R ASMUSSEN

and Ghahramani (2006) contains two ideas, 1) a likelihood approximation and 2) the idea of varying
the inducing inputs continuously; these two ideas could easily be used independently, and incorporated in other methods. Similarly, the BCM by Tresp (2000) contains two independent ideas 1) a
block diagonal assumption, and 2) the (transductive) idea of choosing the test inputs as the inducing variables. Finally we note that although all three ideas of 1) transductively setting u = f∗ , 2)augmentation and 3) continuous optimization of Xu have been proposed in very specific settings, infact they are completely general ideas, which can be applied to any of the approximation schemes
considered.
We have ranked the approximation according to how close they are to the corresponding full
GP. However, the performance in practical situations may not always follow this theoretical ranking
since the approximations might exhibit properties (not present in the full GP) which may be particularly suitable for specific datasets. This may make the interpretation of empirical comparisonschallenging. A further complication arises when adding the necessary heuristics for turning thetheoretical constructs into practical algorithms. We have not described full algorithms in this paper,
but are currently working on a detailed empirical study (in preparation, see also Rasmussen andWilliams, 2006, chapter 8).
We note that the order of the computational complexity is identical for all the methods considered, O (nm2 ). This highlights that there is no computational excuse for using gross approximations,such as assuming deterministic relationships, in particular one should probably think twice before
using SoR or even DTC. Although augmentation has attractive predictive properties, it is computationally expensive. It remains unclear whether augmentation could be beneficial on a fixedcomputational budget.
We have only considered the simpler case of regression in this paper, but sparseness is also commonly sought in classification settings. It should not be difficult to cast probabilistic approximation
methods such as Expectation Propagation (EP) or the Laplace method (for a comparison, see Kussand Rasmussen, 2005) into our unifying framework.
Our analysis suggests that a new interesting approximation would come from combining the best
possible approximation (PITC) with the most powerful selection method for the inducing inputs.
This would correspond to a non-transductive version of the BCM. We would evade the necessity ofknowing the test set before doing the bulk of the computation, and we could hope to supersede thesuperior performance reported by Snelson and Ghahramani (2006) for very sparse approximations.

Acknowledgments
Thanks to Neil Lawrence for arranging the 2005 Gaussian Process Round Table meeting in Sheffield,
which provided much inspiration to this paper. Special thanks to Olivier Chapelle, Lehel Csató,Zoubin Ghahramani, Matthias Seeger, Ed Snelson and Chris Williams for helpful discussions, andto three anonymous reviewers. Both authors were supported by the German Research Council(DFG) through grant RA 1030/1. This work was supported in part by the IST Programme of theEuropean Community, under the PASCAL Network of Excellence, IST-2002-506778.
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S PARSE A PPROXIMATE G AUSSIAN P ROCESS R EGRESSION

Appendix A. Gaussian and Matrix Identities
In this appendix we provide identities used to manipulate matrices and Gaussian distributions
throughout the paper. Let x and y be jointly Gaussian
 

 

A C
x
µx
,
(34)
,
∼ N
y
µy
C> B
then the marginal and the conditional are given byx ∼ N (µx , A) ,and x|y ∼ N µx +C B−1 (y − µy ), A −C B−1C>



(35)

Also, the product of a Gaussian in x with a Gaussian in a linear projection P x is again a Gaussian,although unnormalized
N (x|a, A) N (P x|b, B) = zc N (x|c,C) ,
(36)
where
C = A−1 + P> B−1 P

−1c = C A−1 a + P> B−1 b .

,The normalizing constant zc is gaussian in the means a and b of the two Gaussians:


−1
1
m
zc = (2 π)− 2 |B + P A P> |− 2 exp − 21 (b − P a)> B + P A P> (b − P a) .

(37)

The matrix inversion lemma, also known as the Woodbury, Sherman & Morrison formula states
that:(Z +UWV > )−1 = Z −1 − Z −1U(W −1 +V > Z −1U)−1V > Z −1 ,(38)assuming the relevant inverses all exist. Here Z is n × n, W is m × m and U and V are both of sizen × m; consequently if Z −1 is known, and a low rank (ie. m < n) perturbation are made to Z as inleft hand side of eq. (38), considerable speedup can be achieved.

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