Using graphs to find the best block designs
Using graphs to find the best block designs
Contents
1 What makes an incomplete-block design good for experi-
ments? 3
3 Statistical issues 10
3.1 Estimation and variance . . . . . . . . . . . . . . . . . . . . . 10
3.2 Optimality criteria . . . . . . . . . . . . . . . . . . . . . . . . 11
3.3 Questions and an example . . . . . . . . . . . . . . . . . . . . 12
1
4 Highly patterned block designs 13
4.1 Balanced incomplete-block designs . . . . . . . . . . . . . . . 13
4.2 Other special designs . . . . . . . . . . . . . . . . . . . . . . . 14
8 Some history 26
11 Further reading 38
Abstract
A statistician designing an experiment wants to get as much infor-
mation as possible from the data gathered. Often this means the most
precise estimate possible (that is, an estimate with minimum possible
variance) of the unknown parameters. If there are several parame-
ters, this can be interpreted in many ways: do we want to minimize
the average variance, or the maximum variance, or the volume of a
confidence region for the parameters?
2
In the case of block designs, these optimality criteria can be cal-
culated from the concurrence graph of the design, and in many cases
from its Laplacian eigenvalues. The Levi graph can also be used. The
various criteria turn out to be closely connected with other proper-
ties of the graph as a network, such as number of spanning trees,
isoperimetric number, and the sum of the resistances between pairs of
vertices when the graph is regarded as an electrical network.
In this chapter, we discuss the notions of optimality for incomplete-
block designs, explain the graph-theoretic connections, and prove some
old and new results about optimality.
3
1 1 2 3 4 5 6 1 1 1 1 1 1 1
2 4 5 6 10 11 12 2 4 6 8 10 12 14
3 7 8 9 13 14 15 3 5 7 9 11 13 15
(a) (b)
1 1 1 1 2 2 2 1 1 1 1 2 2 2
2 3 3 4 3 3 4 1 3 3 4 3 3 4
3 4 5 5 4 5 5 2 4 5 5 4 5 5
(a) (b)
4
1 2 3 4 5 6 7 1 2 3 4 5 6 7
2 3 4 5 6 7 1 2 3 4 5 6 7 1
4 5 6 7 1 2 3 3 4 5 6 7 1 2
(a) (b)
5
Γ1 Γ2 Γ3 Γ4 Γ5 Γ6 Γ7
❍
❍
① P
❍
①
❍PP P
①
PP ✟ ❅❍❍
①
✟
① ✏① ✘✘✘
✟
✏✟ ✟✘
✟
①
❅
❅❅❍❍ ❍❍PP❅❅✟ PP ❅❍
✟ ✟ ✏✏✟ ✘ ✟
❅ ✟❍ ✏✏ ✟ ✘✘ ✟
❅ ❍❍ ❍✟ P
❍✟P❅PP✟✏
P
✟P✏ ✏❍
❅P ✘✘✟
❍
✟ ✘✘ ✟✟
❅ ❍❍ ✘PP❍ ✟
❅
❅ ✟✟ ❍❍ ✟❅
✏
✟✏
✏ P✘✘✟❅
✘✘ P PP
✟ PP❍✟
❅ ✟ ❍ ✟
✏
✘ ✘❍ ✟ ①✟ P ❍P
❅✟
① ✟
❍✘
✏
① ❅✟
❍ ① ❅✟
P ❍①
1 2 3 4 5
matrix N whose entries are the nij is the incidence matrix of the block design.
If the rows and columns of N are labelled, we can recover the block design
from its incidence matrix.
Figs. 5 and 6 show the concurrence graphs of the designs in Figs. 1 and 2,
respectively.
If k = 2, then the concurrence graph is effectively the same as the block
design. Although the block design cannot be recovered from the concurrence
graph for larger values of k, we shall see in Section 3.2 that the concurrence
graphs contain enough information to decide between two block designs on
any of the usual statistical criteria. They were introduced as variety concur-
rence graphs in [44], but are so useful that they may have been considered
earlier.
6
8 9
13 7 8 11 ① ① 10
7
① ① ① ① ① ❉ ☎ ①
❜❜ 4 ✧✧ ❜❜ 5 ✧✧ ❏ ❉ ☎ ✡❅
❜✧ ✧
❜ ❅①
◗ ❏ ❉ ☎ ✡ ✑ 11
① ①
✧ ❜ ✧ ❜ 6 ①
✧
① ❜① ✧
① ❜① ◗ ❏ ❉ ☎ ✡ ✑
10 1 ❚❚ ✔✔ 2 14 5 ❵❵❵◗◗❏ ❉ ☎ ✡✑✑✥✥✥①12
①
❵❵◗❵ ✥
✑
☎✡
❏❉❵ ✥✥
✥✥✥
①❵
❚✔①3 ✥ ✥ ✑ ✡ ◗
❏ ❵❵❵
✔ ✥ ✑ 1 ◗ ❵①13
✔✔ ❚ 4 ①
✑ ✡ ❏ ◗
12 ① ✔
✔
① ❚①9 ✑ ✡ ❏ ◗◗①
❚❚ ✔ 6 3 ✑① 14
❅ ✡ ❏
❚①
✔ ❅✡
① ❏①
15 2 15
(a) (b)
3 3
✟✟ ✟ ❍
①❍❍ ✟✟❍ ① ❍❍
✟
✟ ✟ ✟✟
✟ ✂❍❇
✂ ❇❍❍❍
❍❍ ✟ ✟✟ ✂❇✂❇❍ ❍❍
✟
✟
✟✟ ✂✂❇❇ ❍ ❍❍
❍① ✟
✟✟
✟ ✂ ✂ ❇ ❇ ❍❍ ❍①
1 ✟✟
◗ ✂ ❇ ❍
✑❍ ✟
◗ ✂ ❇ ❍
✑
✁✁ 2 1 ✁✁ 2
① ①
◗❆ ◗ ✂
❆ ❆◗ ✂ ❇ ✑ ✑ ❆❆❆◗
◗ ◗ ✂ ✂ ❇ ❇ ✑ ✑
◗
❆ ◗ ✂ ❇ ✑ ✁ ❇✑ ✑ ✁ ◗
❆ ◗ ✂ ❇ ✑ ✁ ✑ ✑ ✁
❆❆ ◗ ✂◗
✂ ✑ ◗
✑ ✑❇ ❇ ✁✁ ❆❆ ◗ ✂◗
✂ ✑ ◗
✑✑❇ ❇ ✁✁
❆ ✂ ✑ ◗ ❇ ❇ ✁✁
❆ ✂ ✑ ◗ ✑ ◗ ❆ ✂ ✑ ◗ ❇ ❇ ✁✁
❆ ✂ ✑ ◗ ✑ ◗
❆✑
✂ ✂✑ ❇✁❇①
◗ ❆✂✑ ◗❇✁❇①
4❆ ① ◗ ✁5 4❆ ① ✂✑ ◗ ✁5
(a) (b)
8 −1 −3 −2 −2 8 −2 −2 −2 −2
−1 8 −3 −2 −2
−2 8 −2 −2 −2
−3 −3 10 −2 −2
−2 −2 8 −2 −2
−2 −2 −2 8 −2 −2 −2 −2 8 −2
−2 −2 −2 −2 8 −2 −2 −2 −2 8
(a) (b)
7
2.3 The Laplacian matrix of a graph
Let H be an arbitrary graph with n vertices: it may have multiple edges, but
no loops. The Laplacian matrix L of H is defined to be the square matrix
with rows and columns indexed by the vertices of H whose (i, i)-entry Lii
is the valency of vertex i and whose (i, j)-entry Lij is the negativeP of the
number of edges between vertices i and j if i 6= j. Then Lii = j6=i Lij for
1 ≤ i ≤ n, and so the row sums of L are all zero. It follows that L has
eigenvalue 0 on the all-1 vector; this is called the trivial eigenvalue of L. We
show below that the multiplicity of the zero eigenvalue is equal to the number
of connected components of H. Thus the multiplicity is 1 if and only if H is
connected.
Call the remaining eigenvalues of L non-trivial. They are all non-negative,
as we show in the following theorem (see [7]).
(c) If L1 and L2 are the Laplacian matrices of graphs H1 and H2 with the
same vertices, and if H2 is obtained from H1 by inserting one extra
edge, then L2 − L1 is positive semi-definite.
(d) If L is the Laplacian matrix of the graph H, then the multiplicity of the
zero eigenvalue of L is equal to the number of connected components
of H.
i j
i 1 −1
j −1 1 .
The Laplacian is the sum of these matrices, which are all positive semi-
definite. This proves (a), (b) and (c).
From (b), the vector x is in the null space of the Laplacian if and only
if x takes the same value on both vertices of each edge, which happens if
and only if it takes a constant value on each connected component. This
proves (d).
8
Theorem 1 shows that the smallest non-trivial eigenvalue of a connected
graph is positive. This eigenvalue is sometimes called the algebraic connec-
tivity of the graph. The statistical importance of this is shown in Section 3.2.
In Section 3.1 we shall need the Moore–Penrose generalized inverse of L−
of L (see [45]). Put P0 = n−1 Jn , where Jn is the n × n matrix whose entries
are all 1, so that P0 is the matrix of orthogonal projection onto the space
spanned by the all-1 vector. If H is connected then L + P0 is invertible, and
L− = (L + P0 )−1 − P0 ,
The Levi graph is connected if and only if the concurrence graph is con-
nected; thus 0 is a simple eigenvalue of L̃ if and only if it is a simple eigenvalue
of L, which in turn occurs if and only if all contrasts between treatment pa-
rameters are estimable (see Section 3.1). A block design with this property
is itself called connected : we consider only connected block designs.
In the equireplicate case, the above expressions for L and L̃ give a relation-
ship between their Laplacian eigenvalues, as follows. Let x be an eigenvector
of L with eigenvalue φ 6= rk. Then, for each of the two solutions θ of the
quadratic equation
rk − φ = (r − θ)(k − θ),
there is a unique vector z in Rb such that [ x⊤ z⊤ ]⊤ is an eigenvector of L̃
with eigenvalue θ. Conversely, any eigenvalue θ 6= k of L̃ arises in this way.
The Laplacian matrices of the concurrence graphs in Fig. 6 are shown in
Table 1.
9
3 Statistical issues
3.1 Estimation and variance
As part of the experiment, we measure the response Yω on each experimental
unit ω. If ω is in block Γ, then we assume that
Yω = τf (ω) + βΓ + εω ; (2)
10
xi τi is equal to (x⊤ L− x)kσ 2 . In particular, the variance Vij of the BLUE
P
i
of the simple difference τi − τj is given by Vij = L− − −
ii + Ljj − 2Lij kσ .
2
because the row sums and column sums of L are all 0. It follows that V̄ =
2kσ 2 Tr(L− )/(v − 1).
Let θ1 , . . . , θv−1 be the non-trivial eigenvalues of L, now listed according
to multiplicity and in non-decreasing order. Then
1 1
Tr(L− ) = +···+ ,
θ1 θv−1
and so
1
V̄ = 2kσ 2 × .
harmonic mean of θ1 , . . . , θv−1
A block design is defined to be A-optimal (in some given class of designs
with the same values of b, k and v) if it minimizes the value of V̄ ; here ‘A’
stands for ‘average’. Thus a design is A-optimal if and only if it maximizes
the harmonic mean of θ1 , . . . , θv−1 .
For v > 2, the generalization of a confidence interval is a confidence
ellipsoid centered at the point (τ̂1 , . . . , τ̂v ) which gives the estimated
P value of
(τ1 , . . . , τv ) in the (v − 1)-dimensional subspace of Rv for which τi = 0. A
block design is called D-optimal if it minimizes the p volume of this confidence
ellipsoid. Since this volume is proportional to det(L− + P0 ), a design is
D-optimal if and only if it maximizes the geometric mean of θ1 , . . . , θv−1 .
Here ‘D’ stands for ‘determinant’.
Rather than looking at averages, we might consider the worst case. If all
the entries in the vector P x are multiplied by2 a constant c, then the variance
of the estimator of xi τi is multiplied by c . Thus, those contrast vectors x
which give the largest variance relative to their own length are those which
maximize x⊤ L− x/x⊤ x; these are precisely the eigenvectors of L with eigen-
value θ1 . A design is defined to be E-optimal if it maximizes the value of θ1 ;
here ‘E’ stands for ‘extreme’.
11
More generally, for p in (0, ∞), a design is called Φp -optimal if it minimizes
Pv−1 !1/p
−p
i=1 θi
.
v−1
Example 1 Fig. 7 shows the values of the A- and D-criteria for all equi-
replicate block designs with v = 8, b = 12 and k = 2: of course, these are
just regular graphs with 8 vertices and degree 3. The harmonic mean is
shown on the A-axis, and the geometric mean on the D-axis. (Note that this
figure includes some designs that were omitted from Figure 3 of [4].) The
rankings on these two criteria are not exactly the same, but they do agree
at the top end, where it matters. The second-best graph on both criteria
is the cube; the best is the Möbius ladder, whose vertices are the elements
of Z8 and whose edges are {i, i + 1} and {i, i + 4} for i in Z8 . These two
graphs are so close on both criteria that, for practical purposes, they can be
regarded as equally good.
The plotting symbols show the edge-connectivity of the graphs: edge-
connectivity 3, 2, 1 is shown as ×, +, ◦ respectively. This does suggest that
the higher the edge-connectivity the better is the design on the A- and D-
12
D
Möbius ladder
× ×
×
× cube
3.0 ++
++
++ s
K2,6
++
◦ +
◦ +
◦
2.4 ◦
1.8
0.6 1.2 1.8 2.4 3.0 A
Figure 7: Values of two optimality criteria for all equireplicate block designs
with v = 8, b = 12, and k = 2, and for K2,6
13
by Yates in [54].
In [38], Kshirsagar proved that, if there exists a BIBD for given values
of v, b and k, then it is A-optimal. Kiefer generalized this in [35] to cover
Φp -optimality for all p in (0, ∞), including the limiting cases of D- and E-
optimality. The core of Kiefer’s
Pv−1 proof is as follows: binary designs maximize
Tr(L), which
P is−pequal to i=1 θi ; for any fixed −p
value T of this sum of positive
numbers, θi is minimized at [T /(v − 1)] when θ1 = · · · = θv−1 =
T /(v − 1); and T −p is minimized when T is maximized.
14
5 Graph concepts linked to D-optimality
5.1 Spanning trees of the concurrence graph
Let G be the concurrence graph of a connected block design, and let L be
its Laplacian matrix. A spanning tree for G is a spanning subgraph which is
a tree. Kirchhoff’s famous Matrix-tree theorem in [36] states the following:
Note that Theorem 3 gives an easy proof of Cayley’s theorem on the num-
ber of spanning trees for the complete graph Kv . The non-trivial eigenvalues
of its Laplacian matrix are all equal to v, so Theorem 3 shows that it has
v v−2 spanning trees.
If G is sparse, it may be much easier to count the number of spanning
trees than to compute the eigenvalues of L. For example, if G has a single
cycle, which has length s, then the number of spanning trees is s, irrespective
of the remaining edges in G.
In the context of optimal block designs, Gaffke discovered the importance
of Kirchhoff’s theorem in [26]. Cheng followed this up in papers such as
[16, 17, 19]. Particularly intriguing is the following theorem from [21].
15
5.2 Spanning trees of the Levi graph
In [27] Gaffke stated the following relationship between the numbers of span-
ning trees in the concurrence graph and the Levi graph.
Theorem 5 Let G and G̃ be the concurrence graph and Levi graph for a
connected incomplete-block design for v treatments in b blocks of size k. Then
the number of spanning trees for G̃ is equal to k b−v+1 times the number of
spanning trees for G.
Ohm’s Law: In every edge, the voltage drop is the product of the current
and the resistance.
Kirchhoff’s Voltage Law: The total voltage drop from one vertex to any
other vertex is the same no matter which path we take from one to the
other.
We find the total current from i to j, and then use Ohm’s Law to define
the effective resistance Rij between i and j as the reciprocal of this current.
It is a standard result of electrical network theory that the linear equations
implicitly defined above for the currents and voltage differences have a unique
solution.
Let T be the set of treatments and Ω the set of experimental units.
Current flows in each edge eαω , where α and ω are experimental units in the
same block which receive different treatments; let I(α, ω) be the current from
f (α) to f (ω) in this edge. Thus I is a function I: Ω × Ω 7→ R such that
16
(a) I(α, ω) = 0 if α = ω or if f (α) = f (ω) or if α and ω are in different
blocks.
(d) If l ∈
/ {i, j}, then Iout (l) = 0.
If G is connected and different voltages V (i) and V (j) are given for a
pair of distinct treatments i and j, then there are unique functions I and V
satisfying conditions (a)–(d). Moreover, Iout (j) = −Iout (i) 6= 0. Then Rij is
defined by
V (i) − V (j)
Rij = .
Iout (i)
It can be shown that the value of Rij does not depend on the choice of values
for V (i) and V (j), so long as these are different. In practical examples, it is
usually convenient to take V (i) = 0 and let I take integer values.
What has all of this got to do with block designs? The following theorem,
which is a standard result from electrical engineering, gives the answer.
Rij = L− − −
ii + Ljj − 2Lij .
17
[−25]
✈
✔
✔ ❚❚
5 ✔ ⑦ ❚ 5
❃✔ ❚
[−15] [−20] ✔ ❚ [−30] [−47]
✈ ✲ ✔
✈ ✲ ❚✈ ✲ ✈
❚ 5 ✔ 10 ❚ 17 j ✔
❚ ✔ ❚ ✔
5❚⑥ ❃✔10 2⑥❚
❃✔19
❚ ✔ ❚ ✔
❚ ✈✔ ❚ ✔
[−10] ✔❚ ✔ [−28]
❚✈
✔ ❚ ✔ ❚
5 ✔ ❚ 10 14 ✔ ❚ 7
❃✔ ❚⑥ ❃✔ ❚⑥
✔ ❚ ✔ ❚
✔
✈ 5✛ ❚✈i ✲14 ✔
✈ ✲7 ❚✈
[−5] [0] ❚ ✔
[−14] [−21]
❚ ✔
⑦❚ ✔7
7 ❚ ❃ ✔
❚ ✔
❚✔✈
[−7]
18
˜ Γ) flows in edge ẽα from vertex
the Levi graph G̃. In G̃, the current I(α,
f (α) to vertex Γ, where α ∈ Γ. Hence the pairwise variance Vij can also be
calculated from the effective resistance R̃ij in the Levi graph.
˜ Γ) = I(Γ,
if α ∈ Γ; otherwise, put I(α, ˜ α) = 0. Put Ṽ (i) = kV (i) for all i
in T , and X
Ṽ (Γ) = V (f (ω))
ω∈Γ
I˜out (Γ) = ˜ α) = −
X XX
I(Γ, I(α, ω) = 0,
α∈Γ α∈Γ ω∈Γ
I˜out (l) = ˜ Γ) =
X X X X
I(α, I(α, ω) = Iout (l).
α:f (α)=l Γ∈B α:f (α)=l ω∈Ω
In particular, I˜out (l) = 0 if l ∈ / {i, j}, which shows that the analogue of
˜ Ṽ ) is the current–voltage pair on
condition (d) is satisfied. It follows that (I,
G̃ defined by Ṽ (i) and Ṽ (j).
19
Now
Ṽ (i) − Ṽ (j) k(V (i) − V (j))
R̃ij = = = kRij .
˜
Iout (i) Iout (i)
Then Theorems 2 and 6 show that Vij = Rij σ 2 .
Figure 9: Current between i and j for the Levi graph corresponding to the
concurrence graph in Fig. 8
˜ Γ) =
X X X
0= I(α, [Ṽ (f (α)) − Ṽ (Γ)] = k V (f (α)) − k Ṽ (Γ),
α∈Γ α∈Γ α∈Γ
20
P
and so Ṽ (Γ) = V (f (α)). Also, if α ∈ Γ, then
α∈Γ
X X
I(α, ω) = [V (f (α)) − V (f (ω))]
ω∈Γ ω∈Γ
X
= kV (f (α)) − V (f (ω))
ω∈Γ
= Ṽ (f (α)) − Ṽ (Γ)
˜ Γ).
= I(α,
Therefore, this transformation reverses the one used in the proof of Theo-
rem 7.
There is yet another way of obtaining Theorem 7. If we use the re-
sponses Yω to estimate the block parameters βΓ in (2) as well as the treat-
ment parameters τi , then standard theory of linear models shows that, if the
design
Pv is connected,
Pb then we canPestimate
P linear combinations of the form
i=1 xi τi + j=1 zj βj so long as xi = zj . Moreover, the variance of the
BLUE of this linear combination is
− x 2 R N
[ x⊤ z⊤ ]C σ , where C=
z N⊤ kIb
21
This is also rather easy to calculate directly when the graph is sparse.
Summing all the Rij and using Theorem 8 gives the following result from
[49].
22
The random walk approach gives alternative proofs of some of the main
results about electrical networks. We discuss this further in the guide to the
literature.
Further extensions have been found, but require a stronger condition on the
graph. The sum of resistances between all pairs of vertices at distance at
most m can be written down explicitly if the graph is walk-regular up to
distance m; this means that the number of closed walks of length k starting
and finishing at a vertex i is independent of i, for k ≤ m. The formula was
discovered by Emil Vaughan, to whom this part of the chapter owes a debt.
In particular, if the graph is distance-regular (see [14]), then the value
of the A-criterion can be written down in terms of the so-called intersection
array of the graph.
6.6 Distance
At first sight it seems obvious that pairwise variance should decrease as con-
currence increases, but there are many counter-examples to this. However,
the following theorem is proved in [3].
It does appear that effective resistance, and hence pairwise variance, gen-
erally increases with distance in the concurrence graph. In [7, Question 5.1]
we pointed out that this is not always exactly so, and asked if it is nevertheless
true that the maximal value of Rij is achieved for some pair of vertices {i, j}
whose distance apart in the graph is maximal. Here is a counter-example.
Example 2 Let k = 2, so that the block design is the same as its concurrence
graph. Take v = 10 and b = 14. The graph consists of a cube, with two
extra vertices 1 and 2 attached as leaves to vertex 3. The vertex antipodal
23
to 3 in the cube is labelled 4. It is straightforward to check (either using an
electrical network, or by using the fact that the cube is distance-regular) that
the effective resistance between a pair of cube vertices is 7/12, 3/4 and 5/6
for vertices at distances 1, 2 and 3. Hence R1j ≤ 11/6 for all cube vertices j,
while R12 = 2. On the other hand, the distance between vertices 1 and 2 is
only 2, while that between either of them and vertex 4 is 4.
There are some ‘nice’ graphs where pairwise variance does indeed increase
with distance. The following result is proved in [6]. Biggs gave the equivalent
result for effective resistances in [12].
Theorem 12 Suppose that a block design has just two distinct concurrences,
and that the pairs of vertices corresponding to the larger concurrence form
the edges of a distance-regular graph H. Then pairwise variance increases
with distance in H.
The next result shows that the isoperimetric number is related to the E-
criterion. It is useful not so much for identifying the E-optimal designs as for
easily showing that large classes of designs cannot be E-optimal: any design
whose concurrence graph has low isoperimetric number performs poorly on
the E-criterion.
24
ProofP We know that θ1 is the minimum of x⊤ Lx/x⊤ x over real vectors x
with i xi = 0. Put
n if i ∈ S
xi =
−m otherwise.
Then x⊤ x = nm(m + n) and
X
x⊤ Lx = (xi − xj )2 = c(m + n)2 .
edges ij
Hence
x⊤ Lx c(m + n)2
1 1 2c 2 |∂S|
θ1 ≤ ⊤ = =c + ≤ = .
x x nm(m + n) m n m |S|
Corollary 1 Let θ1 be the smallest non-trivial eigenvalue of the Laplacian
matrix L of the connected graph G. Then θ1 ≤ 2ι(G).
There is also an upper bound for the isoperimetric number in terms of
θ1 , which is loosely referred to as a ‘Cheeger-type inequality’; for details, see
the further reading.
We also require a second cutset lemma, phrased in terms of vertex cutsets.
Cutset Lemma 2 Let G have a vertex-cutset C of size c whose removal
separates the graph into parts S and T with m, n vertices respectively (so
nm > 0). Let m′ and n′ be the number of edges from vertices in C to vertices
in S, T respectively. Then
m′ n2 + n′ m2
θ1 ≤ .
nm(m + n)
In particular, if there are no multiple edges at any vertex of C then θ1 ≤ c,
with equality if and only if every vertex in C is joined to every vertex in
S ∪ T.
Proof Put
n if i ∈ S
xi = −m if i ∈ T
0 otherwise.
25
7.2 Variance balance
A block design is variance-balanced if all the concurrences λij are equal for
i 6= j. In such a design, all of the pairwise variances Vij are equal. Morgan
and Srivastav proved the following result in [43].
Table 1(b) shows that the design in Fig. 2(b) is variance-balanced. Block
Γ1 has defect 1, and each other block has defect 0, so the sum of the block
defects is certainly less than 5/2, and Theorem 14 shows that the design is E-
optimal. It is rather counter-intuitive that the non-binary design in Fig. 2(b)
can be better than the design in Fig. 2(a); in fact, in his contribution to the
discussion of Tocher’s paper [51], which introduced this design, David Cox
said
I suspect that . . . balanced ternary designs are of no practical
value.
Computation shows that the design in Fig. 2(a) is Φp -better than the one
in Fig. 2(b) if p < 5.327. In particular, it is A- and D-better.
8 Some history
As we have seen, if the experimental units form a single block and there are
only two treatments then it is best for their replications to be as equal as
possible. Statisticians know this so well that it is hard for us to imagine
that more information may be obtained, about all treatment comparisons, if
replications differ by more than 1.
In agriculture, or in any area with qualitative treatments, A-optimality
is the natural criterion. If treatments are quantities of different substances,
26
then D-optimality is preferable, as the ranking on this criterion is invariant
to change of measurement units. Thus industrial statisticians have tended
to prefer D-optimality, although E-optimality has become popular among
chemical process engineers. Perhaps the different camps have not talked to
each other as much as they should have.
For most of the 20th century, it was normal practice in field experiments
to have all treatments replicated three or four times. Where incomplete
blocks were used, they typically had size from 3 to 20. Yates introduced his
square lattice designs with v = k 2 in [55]. He used uniformity data and two
worked examples to show that these designs can give lower average pairwise
variance than a design using a highly replicated control treatment, but both
of his examples were equireplicate with r ∈ {3, 4}.
In the 1930s, 1940s and 1950s, analysis of the data from an experiment
involved inverting the Laplacian matrix without a computer: this is easy
for BIBDs, and only slightly harder if the Laplacian matrix has only two
distinct non-trivial eigenvalues. The results in [35] and [38] encouraged the
beliefs that the optimal designs, on all Φp -criteria, are as equireplicate as
possible, with concurrences as equal as possible, and that the same designs
are optimal, or nearly so, on all of these criteria.
Three short papers in the same journal in 1977–1982 demonstrate the
beliefs at that time. In [29], John and Mitchell did not even consider designs
with unequal replication. They conjectured that, if there exist any regular-
graph designs for given values of v, b and k, then the A- and D-optimal designs
are regular-graph designs. For the parameter sets which they had examined
by computer search, the same designs were optimal on the A- and D-criteria.
In [33], Jones and Eccleston reported the results of various computer searches
for A-optimal designs without the constraint of equal replication. For k = 2
and b = v ∈ {10, 11, 12} (but not v = 9) their A-optimal design is almost
a queen-bee design, and their designs are D-worse than those in [29]. The
belief in equal replication was so ingrained that some readers assumed that
there was an error in their program.
John and Williams followed this with the paper [30] on conjectures for
optimal block designs for given values of v, b and k. Their conjectures in-
cluded:
27
statement that they “are inefficient”, and declared that the three unequally
replicated A-optimal designs in [33] were “of academic rather than of prac-
tical interest”. These conjectures and opinions seemed quite reasonable to
people who had been finding good designs for the sizes needed in agricultural
experiments.
At the end of the 20th century, there was an explosion in the number of
experiments in genomics, using microarrays. Simplifying the story greatly,
these are effectively block designs with k = 2, and biologists wanted A-
optimal designs, but they did not know the vocabulary ‘block’ or ‘A-optimal’,
‘graph’ or ‘cycle’. Computers were now much more powerful than in 1980,
and researchers in genomics could simply undertake computer searches with-
out the benefit of any statistical theory. In 2001, Kerr and Churchill [34]
published the results of a computer search for A-optimal designs with k = 2
and v = b ≤ 11. For v ∈ {10, 11, 12}, their results were completely consistent
with those in [33], which they did not cite. They called cycles loop designs.
Mainstream statisticians began to get involved. In 2005, Wit, Nobile and
Khanin published the paper [53] giving the results of a computer search for
A- and D-optimal designs with k = 2 and v = b. The results are shown
in Fig. 10. The A-optimal designs differ from the D-optimal designs when
v ≥ 9, but are consistent with those found in [34].
What is going on here? Why are the designs so different when v ≥ 9?
Why is there such a sudden, large change in the A-optimal designs? We
explain this in the next section.
28
r r r r
r r r
r
r r r r r
r
r r r
r r r r
r r r r r
r r r
r r
r r r r
r r
r r r r
r r
r r r r
r r r r
r r r r
r r r
r
r r r r r
r
r r r
r r r r
r r r r r r r r
r r r r
r r r r r r r r r
r r r
r r r r r r
✟✉ ✉
✟
✉ ✟ ✉ ✉ ✉
❅ ❆ ❅
❅ ❆ ❅
✉ ❅✉ ❆✉ ✉ ❅✉ ✉
❆ ❅ ✁ ❅
❆ ❅ ✁ ❅
❆✉
❍❍ ✁
❅✉ ✉ ❅✉
❍✉ ✉
29
set Lemma 1 then shows that θ1 ≤ 5/6 < 1. The only other tree which is
not a star√ is the path of length 3, for which direct calculation shows that
θ1 = 2 − 2 < 1. Hence the E-optimal designs are also the stars.
10 ① 10 ①
①12 8 ① ① ① ①12 ①8 ① ①
❚ ✔ ❚ ❚ ✔
❚ ✔ 9 11 ❚ ❚ ✔9 11
❚ ✔ ❚ ❚ ✔
❚① ✔
① ①7 ❚① ❚①
✔ ①7
✔1 6 ❚ ✔1 6❚
✔ ❚ ✔ ❚
✔ ❚ ✔ ❚
✔
①2 5 ❚① ✔2
① 5 ❚①
❚ ✔ ❚ ✔
❚ ✔ ❚ ✔
❚ ✔ ❚ ✔
3
❚① 4 ✔
① 3
❚① 4①
✔
(a) (b)
For A-optimality, we first show that no graph like the one in Fig. 12(a)
can be optimal. If vertex 12 is moved so that it is joined to vertex 6, instead
of vertex 1, then the sum of the variances Vi,12 for i in the cycle is unchanged
and the variances Vi,12 for the remaining vertices i are all decreased. This
argument shows that all the trees must be attached to the same vertex of
the cycle.
30
V̄ /σ 2
5
+ v = 13
+ +
+ × v = 12
+ ×
+ × × ◦ v = 11
4 + ×
× ◦ ◦
◦ • v = 10
+
× ◦
+
× ◦ • • • ⋄ v=9
+
×
◦ + +
× ◦ •
•
⋄ +
×
◦ ×
◦ ◦
• • ⋄ ⋄ ⋄ ∗ v=8
∗ •
⋄ • ⋄ ⋄
⊙ ∗ ⋄ ∗ ⊙ v=7
3 ⋆ ⊙ ∗ ∗ ∗ ∗
⊙ ⊙ ⋆ v=6
⋆ ⊙
⋆ ⊙
⋆
⋆
2 s
3 6 9 12 15
Now V̄ /σ 2 = g(s)/[3v(v − 1)] and we seek the minimum of g(s) for integers
s in the interval [2, v].
Fig. 13 plots g(s)/[3v(v − 1)] for s in [2, v] and 6 ≤ v ≤ 13. When v ≤ 7,
the function g is monotonic decreasing, so it attains its minimum on [2, v]
at s = v. For all larger values of v, the function g has a local minimum in
the interval [3, 5]: when v ≥ 9, the value at this local minimum is less than
g(v). This change from the upper end of the interval to the local minimum
explains the sudden change in the A-optimal designs. Detailed examination
of the local minimum gives the following result.
31
Theorem 16 If k = 2 and b = v ≥ 3 then the A-optimal designs are:
• a cycle, if v ≤ 8;
• a cycle, if v ≤ 5;
32
9.3 More blocks
What happens when b is larger than v but still has the same order of mag-
nitude? The following theorems show that the A- and E-optimal designs are
very different from the D-optimal designs when v is large. The proofs of
Theorems 19 and 20 are in [4] and [7] respectively.
33
(in a suitable model) are close to A-optimal with high probability. On the
other hand if b ≤ Cv then a graph consisting of a large almost equireplicate
part (all degrees 3 and 4 with average degree close to Cv) together with a
suitable number of leaves joined to a single vertex is strictly better than any
queen-bee design.
34
10.1 Least replication
If b(k −1) = v −1 and the design is connected, then the Levi graph G̃ is a tree
and the concurrence graph G looks like those in Fig. 5. Hypergraph-theorists
do not seem to have an agreed name for such designs.
For both D- and A-optimality, it turns out to be convenient to use the
Levi graph. Since all the Levi graphs are trees, Theorem 5 shows that the
D-criterion does not distinguish among connected designs.
By Theorem 7, Vij = R̃ij σ 2 . When G̃ is a tree, R̃ij = 2 when i and j
are in the same block; otherwise, R̃ij = 4 if any block containing i has a
treatment in common with any block containing j; and otherwise, R̃ij ≥ 6.
The queen-bee designs are the only ones for which R̃ij ≤ 4 for all i and j,
and so they are the A-optimal designs.
The non-trivial eigenvalues of a queen-bee design are 1, k and v, with
multiplicities b − 1, b(k − 2) and 1, respectively. If the design is not a queen-
bee design, then there is a treatment i that is in more than one block but
not in all blocks. Thus vertex i forms a cutset for the concurrence graph G
which is not joined to every other vertex of G. Cutset Lemma 2 shows that
θ1 < 1. Hence the E-optimal designs are also the queen-bee designs.
35
Proof The Levi graph G̃ is unicyclic, so its number of spanning trees is
maximized when the cycle has maximal length. Theorem 5 shows that the
D-optimal designs are precisely those with s = b.
Theorem 22 If b(k−1) = v then the A-optimal designs are those in C(b, k, s),
where the value of s is given in Table 2.
k b 2 3 4 5 6 7 8 9 10 11 12 13
2 2 3 4 5 6 7 8 4 4 4 3 or 4 3
3 2 3 4 5 6 3 3 3 3 3 2 2
4 2 3 4 5 3 2 2 2 2 2 2 2
5 2 3 4 5 2 2 2 2 2 2 2 2
6 2 3 4 2 2 2 2 2 2 2 2 2
Proof The Levi graph G̃ has one cycle, whose length is 2s, where 1 ≤ s ≤ b.
A similar argument to the one used at the start of the proof of Theorem 16
shows that this cannot be A-optimal unless the design is in C(b, k, s). If
s ≥ 2 or k ≥ 4, then each block-vertex in the cycle has k − 2 treatment-
vertices attached as leaves; all other block-vertices are joined to the same
single treatment-vertex in the cycle, and each has k − 1 treatment vertices
attached as leaves. In C(b, 3, 1) the first type of design has a Levi graph
like this, and the other type has the same multiset of effective resistances
between treatment-vertices, because their concurrence graphs are identical.
The following calculations use the first type.
Let V1 be the set of treatment-vertices in the cycle, V2 the set of other
treatment-vertices joined to blocks in the cycle, and V3 the set of remaining
treatment-vertices. For 1 ≤ i ≤ j ≤ 3, denote by Rij the sum of the pairwise
resistances between vertices in Vi and Vj .
Put
s−1
X 2d(2s − 2d) s2 − 1
R1 = =
d=1
2s 3
and
s−1
X (2d + 1)(2s − 2d − 1) 2s2 + 1
R2 = = .
2s 6
d=0
36
Then R11 = sR1 /2, R12 = s(k − 2)(R2 + s), R13 = (b − s)(k − 1)(R1 + 2s),
R22 = s(k − 2)(k − 3) + s(k − 2)2 [R1 + 2(s − 1)]/2, R23 = (b − s)(k − 1)(k −
2)(R2 +3s), and R33 = (b−s)(k −1)(k −2)+2(b−s)(b−s−1)(k −1)2. Hence
the sum of the pairwise effective resistances between treatment-vertices in the
Levi graph is g(s)/6, where
If g ′ (b) > 0 then g has a local minimum in the interval (1, b). If, in addition,
g(3) > g(2), then the minimal value for integer s occurs at s = 2. These
conditions are both satisfied if k = 3 and b ≥ 12, k = 4 and b ≥ 8, k ≥ 5 and
b ≥ 7, or k ≥ 9 and b ≥ 6.
Given Theorem 16, there remain only a finite number of pairs (b, k) to
be checked individually to find the smallest value of g(s). The results are in
Table 2.
Proof If 2 < s < b then the concurrence graph G has a vertex which forms
a vertex-cutset and which is not joined to all other vertices; moreover, G has
no multiple edges. Thus Cutset Lemma 2 shows that θ1 < 1.
Direct calculation shows that θ1 = 1 if s = 1 or s = 2. For k ≥ 4, all
contrasts between singly replicated treatments in the same block are eigen-
vectors of the Laplacian matrix L with eigenvalue k. When k ≥ 3 and s = b
37
the contrast between singly and doubly replicated treatments has eigenvalue
2(k − 1). For s = b, a straightforward calculation shows that the remaining
eigenvalues of L are
s
2πn 2 2πn
k − cos ± (k − 1)2 − sin
b b
11 Further reading
The Laplacian matrix of a graph, and its eigenvalues, are widely used, espe-
cially in connection with network properties such as connectivity, expansion,
and random walks. A good introduction to this material can be found in the
textbook by Bollobás [13], especially Chapters II (electrical networks) and
IX (random walks). Connection between the smallest non-zero eigenvalue
and connectivity is described in surveys by de Abreu [1] and by Mohar [42].
In this terminology, a version of Theorem 17 is in [24].
The basic properties of electrical networks can be found in textbooks of
electrical engineering, for example Balabanian and Bickart [9]. A treatment
connected to the multivariate Tutte polynomial appears in Sokal’s survey [50].
Bollobás describes several approaches to the theory, including the fact (which
we have not used) that the current flow minimises the power consumed in
the network, and explains the interactions between electrical networks and
random walks in the network. See also Deo [22].
The connection with optimal design theory was discussed in detail by the
authors in their survey [7]. Further reading on optimal design can be found
in John and Williams [31], Schwabe [47], or Shah and Sinha [48]. For general
principles of experimental design, see Bailey [5].
38
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43