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Center for Uncertainty
Quantification
Hierarchical matrix approximation of
large covariance matrices
A. Litvinenko1
, M. Genton2
, Ying Sun2
, R. Tempone
1
SRI-UQ Center and 2
Spatio-Temporal Statistics & Data Analysis Group
at KAUST
alexander.litvinenko@kaust.edu.sa
Center for Uncertainty
Quantification
Center for Uncertainty
Quantification
Abstract
We approximate large non-structured covariance ma-
trices in the H-matrix format with a log-linear com-
putational cost and storage O(n log n). We compute
inverse, Cholesky decomposition and determinant in
H-format. As an example we consider the class of
Matern covariance functions, which are very popu-
lar in spatial statistics, geostatistics, machine learning
and image analysis. Applications are: kriging and op-
timal design
1. Matern covariance
C(x, y) = C(|x−y|) = σ2 1
Γ(ν)2ν−1
√
2ν
r
L
ν
Kν
√
2ν
r
L
,
where Γ is the gamma function, Kν is the modified
Bessel function of the second kind, r = |x − y| and
ν, L are non-negative parameters of the covariance.
−2 −1.5 −1 −0.5 0 0.5 1 1.5 2
0
0.05
0.1
0.15
0.2
0.25
Matern covariance (nu=1)
σ=0.5, l=0.5
σ=0.5, l=0.3
σ=0.5, l=0.2
σ=0.5, l=0.1
−2 −1.5 −1 −0.5 0 0.5 1 1.5 2
0
0.05
0.1
0.15
0.2
0.25
nu=0.15
nu=0.3
nu=0.5
nu=1
nu=2
nu=30
As ν → ∞ [4],
C(r) = σ2
exp(−r2
/2L2
).
When ν = 0.5, the Matern covariance is identical to
the exponential covariance function.
Cν=3/2(r) = 1 +
√
3r
L
exp −
√
3r
L
Cν=5/2(r) = 1 +
√
5r
L
+
5r2
3L2
exp −
√
5r
L
.
Note: no need to assume neither C(x, y) = C(|x − y|) nor tensor
grid.
2. H-matrix approximation
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Figure 2: Two approximation strategies [1]: fixed rank (left) and
flexible rank (right) approximations, C ∈ Rn×n, n = 652.
I
I
I I
I
I
I I I I1
1
2
2
11 12 21 22
I11
I12
I21
I22
Q
Qt
S
dist
H=
t
s
1. Build cluster tree TI, I = {1, 2, ..., n}
2. Build block cluster tree TI×I
3. For each (t × s) ∈ TI×I, t, s ∈ TI, check admissibility
condition min{diam(Qt), diam(Qs)} ≤ η·dist(Qt, Qs).
if(adm=true) then M|t×s is a rank-k matrix block
if(adm=false) then divide M|t×s further or define as a
dense matrix block, if small enough.
Grid → cluster tree (TI) + admissibility condition →
block cluster tree (TI×I) → H-matrix → H-matrix arith-
metics.
Operation Sequential Complexity Parallel Complexity
(Hackbusch et al. ’99-’06) (Kriemann ’05)
storage(M) N = O(kn log n) N
P
Mx N = O(kn log n) N
P
M1 ⊕ M2 N = O(k2n log n) N
P
M1 M2, M−1 N = O(k2n log2 n) N
P + O(n)
H-LU N = O(k2n log2 n) N
P + O(k2
n log2
n
n1/d )
Table 1: Computational cost of H-matrix arithmetics, sequential
and parallel.
Let ε =
(C−CH
)z 2
C 2 z 2
, where z is a random vector.
n rank k size, MB t, sec. ε max
i=1..10
|λi − ˜λi|, i ε2
for ˜C C ˜C C ˜C
4.0 · 103
10 48 3 0.8 0.08 7 · 10−3
7.0 · 10−2
, 9 2.0 · 10−4
1.05 · 104
18 439 19 7.0 0.4 7 · 10−4
5.5 · 10−2
, 2 1.0 · 10−4
2.1 · 104
25 2054 64 45.0 1.4 1 · 10−5
5.0 · 10−2
, 9 4.4 · 10−6
Table 2: Accuracy of the H-matrix approx. exp. covariance function, l1 = l3 =
0.1, l2 = 0.5.
l1 l2 ε
0.01 0.02 3 · 10−2
0.1 0.2 8 · 10−3
0.5 1 2.8 · 10−5
Table 3: Dependence of the H-matrix accuracy on the covari-
ance lengths l1 and l2, n = 1292. The smaller cov. length the less
accurate is H-approximation.
0
100
200
300
0
50
100
150
200
250
300
−1
0
1
2
−1
−0.5
0
0.5
1
1.5
2
2.5
3
0
100
200
300
0
50
100
150
200
250
300
−1
0
1
2
−3
−2
−1
0
1
2
Figure 4: Two realizations of random field generated via
Cholesky decomposition of Matern covariance matrix, ν = 0.4.
3. Kullback-Leibler divergence
Measure of the information lost when distribution Q is used to
approximate P.
DKL(P Q) =
i
P(i) ln
P(i)
Q(i)
, DKL(P Q) =
∞
−∞
p(x) ln
p(x)
q(x)
dx,
where p, q densities of P and Q. For miltivariate normal distribu-
tions (µ0, C) and (µ1, CH):
2DKL(N0 N1) = tr((CH
)−1
C) + (µ1 − µ0)T
(CH
)−1
(µ1 − µ0) − n − ln
det C
det CH
.
0 10 20 30 40 50 60 70 80 90 100
−16
−14
−12
−10
−8
−6
−4
−2
0
rank k
log(rel.error)
Spectral norm, L=0.1, nu=0.5
Frob. norm, L=0.1
Spectral norm, L=0.2
Frob. norm, L=0.2
Spectral norm, L=0.5
Frob. norm, L=0.5
0 10 20 30 40 50 60 70 80 90 100
−18
−16
−14
−12
−10
−8
−6
−4
−2
0
rank k
log(rel.error)
Spectral norm, L=0.1, ν=1.5
Frob. norm, L=0.1
Spectral norm, L=0.2
Frob. norm, L=0.2
Spectral norm, L=0.5
Frob. norm, L=0.5
Figure 5: Relative H-matrix approx. error C−CH
2 for different
cov. lengths L = {0.1, 0.2, 0.5} and ν = {0.5, 1.5}
k KLD(C, CH) C − CH
2 C(CH)−1 − I 2
L = 0.25 L = 0.75 L = 0.25 L = 0.75 L = 0.25 L = 0.75
5 0.51 2.3 4.0e-2 0.1 4.8 63
6 0.34 1.6 9.4e-3 0.02 3.4 22
8 5.3e-2 0.4 1.9e-3 0.003 1.2 8
10 2.6e-3 0.2 7.7e-4 7.0e-4 6.0e-2 3.1
12 5.0e-4 2e-2 9.7e-5 5.6e-5 1.6e-2 0.5
15 1.0e-5 9e-4 2.0e-5 1.1e-5 8.0e-4 0.02
20 4.5e-7 4.8e-5 6.5e-7 2.8e-7 2.1e-5 1.2e-3
50 3.4e-13 5e-12 2.0e-13 2.4e-13 4e-11 2.7e-9
Table 4: Dependence of KLD on H-matrix rank k, Matern co-
variance with L = {0.25, 0.75} and ν = 0.5, domain G = [0, 1]2,
C(L=0.25,0.75) 2 = {212, 568}.
For ν = 1.5 the KLD and the inverse (CH)−1 is hard to compute
numerically. Results in Table 4 are better since covariance ma-
trix with ν = 0.5 has smallest eigenvalues far enough from zero.
The case ν = 1.5 is more smooth, the eigenvalues decay faster,
but the smallest eigenvalues come much closer to zero than in
ν = 0.5 case.
4. Other applications
4.1 Low-rank approximation of Kriging and geo-
statistical optimal design
Let ˆs ∈ Rn to be estimated, Css covariance matrix, y ∈ Rm is
vector of measurements. The corresponding cross- and auto-
covariance matrices are denoted by Csy and Cyy, respectively,
sized n × m and m × m.
Kriging estimate ˆs = CsyC−1
yy y .
The estimation variance ˆσ is the diagonal of the cond. cov. ma-
trix Css|y: ˆσs = diag(Css|y) = diag Css − CsyC−1
yy Cys
Geostatistical optimal design:
φA = n−1 trace Css|y
φC = cT Css − CsyC−1
yy Cys c, c − a vector.
4.2 Weather forecast in Europa
180 240
30
60
Figure 6: Europa weather stations (≈ 2500). Collected data set
M ∈ R2500×365
.
0 50 100 150 200 250 300 350 400
−20
−15
−10
−5
0
5
10
15
20
Figure 7: Truth temperature forecast and its low-rank approxi-
mation (rank 50 approximation of matrix M) in one station, rel.
error=25%.
5. Open question
1. Compute the whole spectrum of large covariance matrix
2. Compute KLD for large matrices (det Σ ?)
3. How sensible is KLD to H-matrix accuracy ?
4. Derive/estimate KLD for non-Gaussian distributions.
Acknowledgements
A. Litvinenko is a member of the KAUST SRI UQ Center.
References
1. B. N. Khoromskij, A. Litvinenko, H. G. Matthies, Application of
hierarchical matrices for computing the Karhunen?Lo´eve expan-
sion, Computing, Vol. 84, Issue 1-2, pp 49-67, 2008
2. R. Furrer, M. Genton, D. Nychka, Covariance tapering for in-
terpolation of large spatial datasets, J. Comp. & Graph. Stat.,
Vol.15, N3, pp502-523.
3. M. Stein, Limitations on low rank approximations for covari-
ance matrices of spatial data, Spat. Statistics, 2013
4. J. Castrillion-Candis, M. Genton, R. Yokota, Multi-Level Re-
stricted Maximum Likelihood Cov. Estim. and Kriging for Large
Non-Gridded Datasets, 2014.
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Hierarchical matrix approximation of large covariance matrices

  • 1. Center for Uncertainty Quantification Hierarchical matrix approximation of large covariance matrices A. Litvinenko1 , M. Genton2 , Ying Sun2 , R. Tempone 1 SRI-UQ Center and 2 Spatio-Temporal Statistics & Data Analysis Group at KAUST [email protected] Center for Uncertainty Quantification Center for Uncertainty Quantification Abstract We approximate large non-structured covariance ma- trices in the H-matrix format with a log-linear com- putational cost and storage O(n log n). We compute inverse, Cholesky decomposition and determinant in H-format. As an example we consider the class of Matern covariance functions, which are very popu- lar in spatial statistics, geostatistics, machine learning and image analysis. Applications are: kriging and op- timal design 1. Matern covariance C(x, y) = C(|x−y|) = σ2 1 Γ(ν)2ν−1 √ 2ν r L ν Kν √ 2ν r L , where Γ is the gamma function, Kν is the modified Bessel function of the second kind, r = |x − y| and ν, L are non-negative parameters of the covariance. −2 −1.5 −1 −0.5 0 0.5 1 1.5 2 0 0.05 0.1 0.15 0.2 0.25 Matern covariance (nu=1) σ=0.5, l=0.5 σ=0.5, l=0.3 σ=0.5, l=0.2 σ=0.5, l=0.1 −2 −1.5 −1 −0.5 0 0.5 1 1.5 2 0 0.05 0.1 0.15 0.2 0.25 nu=0.15 nu=0.3 nu=0.5 nu=1 nu=2 nu=30 As ν → ∞ [4], C(r) = σ2 exp(−r2 /2L2 ). When ν = 0.5, the Matern covariance is identical to the exponential covariance function. Cν=3/2(r) = 1 + √ 3r L exp − √ 3r L Cν=5/2(r) = 1 + √ 5r L + 5r2 3L2 exp − √ 5r L . Note: no need to assume neither C(x, y) = C(|x − y|) nor tensor grid. 2. H-matrix approximation 25 20 20 20 20 16 20 16 20 20 16 16 20 16 16 16 19 20 20 19 32 19 19 16 16 32 19 20 20 19 19 16 19 16 32 32 20 20 20 20 32 32 32 20 19 19 19 32 20 19 16 16 32 32 20 32 32 20 32 32 32 32 20 32 32 20 19 19 19 20 16 19 16 32 32 20 32 32 32 32 32 20 32 32 32 20 32 20 20 20 20 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 20 20 20 19 20 20 32 32 32 20 20 20 32 20 32 32 20 20 20 32 32 20 32 20 20 20 32 32 32 32 20 20 20 20 19 20 32 32 32 20 20 20 32 20 32 32 20 20 20 32 32 20 32 20 20 20 32 32 32 32 20 20 20 20 20 20 32 32 32 20 19 20 19 32 32 32 20 20 19 19 32 32 32 20 20 20 20 32 32 32 32 20 32 32 32 20 32 32 32 20 32 32 32 20 32 32 32 32 20 32 32 32 20 32 32 32 20 32 32 32 20 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 20 20 20 20 2019 20 20 20 32 32 32 32 20 32 32 20 32 32 32 32 20 32 32 20 20 20 20 20 20 20 20 20 20 20 32 20 32 32 20 20 20 20 20 20 20 20 20 20 20 32 20 32 32 20 20 20 20 20 20 20 20 20 20 20 32 20 32 32 32 20 32 32 32 20 32 32 32 20 32 32 20 20 20 20 20 20 20 20 19 20 20 20 32 32 32 20 32 32 32 32 32 20 32 32 32 20 32 20 20 20 20 20 20 20 20 20 20 20 32 32 20 32 20 20 20 20 20 20 20 20 20 20 20 32 32 20 32 20 20 20 20 20 20 20 20 20 20 20 32 32 20 32 32 32 20 32 32 32 20 32 32 32 20 32 20 20 20 20 20 20 20 20 20 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 19 19 20 20 32 32 32 32 20 32 32 20 32 32 32 32 20 32 32 19 20 19 20 32 32 32 20 32 32 32 32 32 20 32 32 32 20 32 20 20 20 20 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 20 20 32 32 32 32 20 20 20 32 20 32 32 20 20 20 32 32 20 32 20 20 20 32 32 32 32 20 20 32 32 32 32 20 20 20 32 20 32 32 20 20 20 32 32 20 32 20 20 20 32 32 32 32 20 20 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 20 32 32 32 20 32 20 32 20 32 32 32 20 32 20 32 32 20 32 32 32 20 32 32 32 20 20 32 32 20 20 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 25 9 9 20 9 9 20 7 7 16 9 9 20 9 9 20 9 9 32 9 9 20 9 9 20 9 9 32 9 9 32 9 9 32 9 9 20 9 9 20 9 9 32 9 9 20 9 9 20 9 9 32 9 9 32 9 9 32 9 9 32 9 9 32 9 9 20 9 9 20 9 9 32 9 9 32 9 9 32 9 9 20 9 9 20 9 9 32 9 9 32 9 9 32 9 9 32 9 9 32 9 9 32 9 9 32 9 9 32 9 9 32 9 9 32 9 9 32 Figure 2: Two approximation strategies [1]: fixed rank (left) and flexible rank (right) approximations, C ∈ Rn×n, n = 652. I I I I I I I I I I1 1 2 2 11 12 21 22 I11 I12 I21 I22 Q Qt S dist H= t s 1. Build cluster tree TI, I = {1, 2, ..., n} 2. Build block cluster tree TI×I 3. For each (t × s) ∈ TI×I, t, s ∈ TI, check admissibility condition min{diam(Qt), diam(Qs)} ≤ η·dist(Qt, Qs). if(adm=true) then M|t×s is a rank-k matrix block if(adm=false) then divide M|t×s further or define as a dense matrix block, if small enough. Grid → cluster tree (TI) + admissibility condition → block cluster tree (TI×I) → H-matrix → H-matrix arith- metics. Operation Sequential Complexity Parallel Complexity (Hackbusch et al. ’99-’06) (Kriemann ’05) storage(M) N = O(kn log n) N P Mx N = O(kn log n) N P M1 ⊕ M2 N = O(k2n log n) N P M1 M2, M−1 N = O(k2n log2 n) N P + O(n) H-LU N = O(k2n log2 n) N P + O(k2 n log2 n n1/d ) Table 1: Computational cost of H-matrix arithmetics, sequential and parallel. Let ε = (C−CH )z 2 C 2 z 2 , where z is a random vector. n rank k size, MB t, sec. ε max i=1..10 |λi − ˜λi|, i ε2 for ˜C C ˜C C ˜C 4.0 · 103 10 48 3 0.8 0.08 7 · 10−3 7.0 · 10−2 , 9 2.0 · 10−4 1.05 · 104 18 439 19 7.0 0.4 7 · 10−4 5.5 · 10−2 , 2 1.0 · 10−4 2.1 · 104 25 2054 64 45.0 1.4 1 · 10−5 5.0 · 10−2 , 9 4.4 · 10−6 Table 2: Accuracy of the H-matrix approx. exp. covariance function, l1 = l3 = 0.1, l2 = 0.5. l1 l2 ε 0.01 0.02 3 · 10−2 0.1 0.2 8 · 10−3 0.5 1 2.8 · 10−5 Table 3: Dependence of the H-matrix accuracy on the covari- ance lengths l1 and l2, n = 1292. The smaller cov. length the less accurate is H-approximation. 0 100 200 300 0 50 100 150 200 250 300 −1 0 1 2 −1 −0.5 0 0.5 1 1.5 2 2.5 3 0 100 200 300 0 50 100 150 200 250 300 −1 0 1 2 −3 −2 −1 0 1 2 Figure 4: Two realizations of random field generated via Cholesky decomposition of Matern covariance matrix, ν = 0.4. 3. Kullback-Leibler divergence Measure of the information lost when distribution Q is used to approximate P. DKL(P Q) = i P(i) ln P(i) Q(i) , DKL(P Q) = ∞ −∞ p(x) ln p(x) q(x) dx, where p, q densities of P and Q. For miltivariate normal distribu- tions (µ0, C) and (µ1, CH): 2DKL(N0 N1) = tr((CH )−1 C) + (µ1 − µ0)T (CH )−1 (µ1 − µ0) − n − ln det C det CH . 0 10 20 30 40 50 60 70 80 90 100 −16 −14 −12 −10 −8 −6 −4 −2 0 rank k log(rel.error) Spectral norm, L=0.1, nu=0.5 Frob. norm, L=0.1 Spectral norm, L=0.2 Frob. norm, L=0.2 Spectral norm, L=0.5 Frob. norm, L=0.5 0 10 20 30 40 50 60 70 80 90 100 −18 −16 −14 −12 −10 −8 −6 −4 −2 0 rank k log(rel.error) Spectral norm, L=0.1, ν=1.5 Frob. norm, L=0.1 Spectral norm, L=0.2 Frob. norm, L=0.2 Spectral norm, L=0.5 Frob. norm, L=0.5 Figure 5: Relative H-matrix approx. error C−CH 2 for different cov. lengths L = {0.1, 0.2, 0.5} and ν = {0.5, 1.5} k KLD(C, CH) C − CH 2 C(CH)−1 − I 2 L = 0.25 L = 0.75 L = 0.25 L = 0.75 L = 0.25 L = 0.75 5 0.51 2.3 4.0e-2 0.1 4.8 63 6 0.34 1.6 9.4e-3 0.02 3.4 22 8 5.3e-2 0.4 1.9e-3 0.003 1.2 8 10 2.6e-3 0.2 7.7e-4 7.0e-4 6.0e-2 3.1 12 5.0e-4 2e-2 9.7e-5 5.6e-5 1.6e-2 0.5 15 1.0e-5 9e-4 2.0e-5 1.1e-5 8.0e-4 0.02 20 4.5e-7 4.8e-5 6.5e-7 2.8e-7 2.1e-5 1.2e-3 50 3.4e-13 5e-12 2.0e-13 2.4e-13 4e-11 2.7e-9 Table 4: Dependence of KLD on H-matrix rank k, Matern co- variance with L = {0.25, 0.75} and ν = 0.5, domain G = [0, 1]2, C(L=0.25,0.75) 2 = {212, 568}. For ν = 1.5 the KLD and the inverse (CH)−1 is hard to compute numerically. Results in Table 4 are better since covariance ma- trix with ν = 0.5 has smallest eigenvalues far enough from zero. The case ν = 1.5 is more smooth, the eigenvalues decay faster, but the smallest eigenvalues come much closer to zero than in ν = 0.5 case. 4. Other applications 4.1 Low-rank approximation of Kriging and geo- statistical optimal design Let ˆs ∈ Rn to be estimated, Css covariance matrix, y ∈ Rm is vector of measurements. The corresponding cross- and auto- covariance matrices are denoted by Csy and Cyy, respectively, sized n × m and m × m. Kriging estimate ˆs = CsyC−1 yy y . The estimation variance ˆσ is the diagonal of the cond. cov. ma- trix Css|y: ˆσs = diag(Css|y) = diag Css − CsyC−1 yy Cys Geostatistical optimal design: φA = n−1 trace Css|y φC = cT Css − CsyC−1 yy Cys c, c − a vector. 4.2 Weather forecast in Europa 180 240 30 60 Figure 6: Europa weather stations (≈ 2500). Collected data set M ∈ R2500×365 . 0 50 100 150 200 250 300 350 400 −20 −15 −10 −5 0 5 10 15 20 Figure 7: Truth temperature forecast and its low-rank approxi- mation (rank 50 approximation of matrix M) in one station, rel. error=25%. 5. Open question 1. Compute the whole spectrum of large covariance matrix 2. Compute KLD for large matrices (det Σ ?) 3. How sensible is KLD to H-matrix accuracy ? 4. Derive/estimate KLD for non-Gaussian distributions. Acknowledgements A. Litvinenko is a member of the KAUST SRI UQ Center. References 1. B. N. Khoromskij, A. Litvinenko, H. G. Matthies, Application of hierarchical matrices for computing the Karhunen?Lo´eve expan- sion, Computing, Vol. 84, Issue 1-2, pp 49-67, 2008 2. R. Furrer, M. Genton, D. Nychka, Covariance tapering for in- terpolation of large spatial datasets, J. Comp. & Graph. Stat., Vol.15, N3, pp502-523. 3. M. Stein, Limitations on low rank approximations for covari- ance matrices of spatial data, Spat. Statistics, 2013 4. J. Castrillion-Candis, M. Genton, R. Yokota, Multi-Level Re- stricted Maximum Likelihood Cov. Estim. and Kriging for Large Non-Gridded Datasets, 2014.