An Algorithm for Generating Good Mixed Level Factorial Designs

Ulrike Grömping

based on joint work with Roberto Fontana

The setting

Situation


GWLP / GMA and strength / resolution


Design representation via counting vector r




                n=3 runs
                m=2 factors with s1=2 and s2=3 levels \[ d=\left (\begin{smallmatrix} 0 & 2\\ 0 & 0\\ 1 & 1 \end{smallmatrix}\right ) \]

n x m factorial design d:

Representation by N x 1 counting vector r:

Formula for Aj


Mj the N x df(j) model matrix of all j-factor interactions

Mℱ,j the n x df(j) sub matrix of Mj

n2Aj = 1nTMℱ,jMℱ,jT1n = rTMjMjTr

Minimizing Aj in terms of r


Thus: Aj can be minimized

Overview of GMA algorithm


Mixed integer optimization

Ingredients


Simple example


\[ D= \begin{pmatrix} 0\\ 1\\ 2 \end{pmatrix}, \mathbf r= \begin{pmatrix} r_1\\ r_2\\ r_3 \end{pmatrix} \] r1, r2, r3 ≥ 0 (integers) with sum n = 10

Main effects model matrix M1 (3x2)
in normalized orthogonal coding:
\[ \mathbf M_1= \begin{pmatrix} -\sqrt{3/2} & -\sqrt{1/2}\\ 0 & \sqrt 2 \\ \sqrt{3/2} & -\sqrt{1/2} \end{pmatrix} \]

a single qualitative 3-level factor
N = 3 (unreplicated full factorial)
n = 10 runs to be assigned

Simple example


r1, r2, r3 ≥ 0 (integers) with sum n = 10
M1 model matrix in norm. orthog. coding



Minimize
            102A1 = rTM1M1Tr = rTH1r     with

\[ \mathbf H_1= \begin{pmatrix} 2 & -1 & -1\\ -1 & 2 & -1 \\ -1 & -1 & 2 \end{pmatrix} \]

a single qualitative 3-level factor
N = 3 (unreplicated full factorial)
n = 10 runs to be assigned

Conic quadratic representation


r1, r2, r3 ≥ 0 (integers) with sum n = 10
M1 model matrix in norm. orthog. coding


add free variables y1 and y2 to the problem, with

\[ \mathbf y = \begin{pmatrix} y_1 \\ y_2 \end{pmatrix} = \mathbf M_1^\top \mathbf r = \frac{1}{\sqrt 2}\begin{pmatrix} \sqrt 3 (r_3-r_1)\\ 2r_2-r_1+r_3 \end{pmatrix} \]
The objective function in terms of y: \[ \mathbf {rM}_1\mathbf M_1^\top \mathbf r = \mathbf{y^\top y}=y_1^2+y_2^2 \]


Conic quadratic representation


r1, r2, r3 ≥ 0 (integers) with sum n = 10
y=M1r

minimize quadratic objective
    rTM1M1Tr = y12 + y22

quadratic \(\rightarrow\) linear:
    add variable t1, constrained by t12y12 + y22

minimize linear objective t1, subject to

Vocabulary of mixed integer optimization


Example: Relaxing


minimize t1 subject to
    r1, r2, r3 ≥ 0 (integrality not required),
    y = M1Tr,
    and
    t12y12 + y22

relaxed optimum:
    r1 = r2 = r3 = 10/3
    objective value: 0 (lower bound)

Example: Branching


relaxed optimum: r1 = r2 = r3 = 10/3 objective value: 0 (lower bound)

branch 1 with r1 ≥ 4:
    relaxed problem has integer optimum
    r1 = 4, r2 = r3 = 3
    incumbent
    objective value: 2 (upper bound)

branch 2 with r1 ≤ 3
    relaxed problem has non-integer optimum
    r1 = 3, r2 = r3 = 3.5
    objective value: 0.5 (lower bound)

Example: Further branching


branch 2 with r1 ≤ 3

branch 2.1 with r2 ≥ 4
    relaxed problem has integer optimum
    r1 = 3, r2 = 4, r3 = 3
    objective value: 2

branch 2.2 with r2 ≤ 3
    relaxed problem has integer optimum
    r1 = r2 = 3, r3 = 4
    objective value: 2

two branch solutions, objective values equal to those of previous incumbent

Example: Optimum reached


Thus: upper bound = lower bound, gap=0.

In problems of realistic size,

Remarks on mixed integer optimization


Remarks on mixed integer optimization


GMA with mixed integer optimization

Efficiency considerations


Tuning possibilities


Biotechnological example

Example: Experimental setup


by Vasilev et al. (2014)

72 runs feasible

actual experiment (VSGFS in R package DoE.base):
constructed by column optimization from the OA(72, 243384161) provided by Kuhfeld (2009)

GWLP of the actual experiment: (A1, A2, A3, A4) = (0, 0, 0.451, 3.247)

Lower bound for A3 in a resolution III array: 2/27 = 0.074 < 0.451
our algorithm provides such an array

Example: worst case balance improved


Example: algorithm’s behavior


DoE.MIParray’s result strongly depends on the order of factor levels:

Final remarks

Final remarks


References

Theory


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Bailey, R.A.B. (1982). The decomposition of treatment degrees of freedom in quantitative factorial experiments. Journal of the Royal Statistical Society B 44, 63-70.

Butler, N.A. (2005). Generalised minimum aberration construction results for symmetrical orthogonal arrays. Biometrika 92, 485-491.

Cheng, S.-W. and Ye, K.Q. (2004). Geometric isomorphism and minimum aberration for factorial designs with quantitative factors. The Annals of Statistics 32, 2168-2185.

Fontana, R. (2013). Algebraic generation of minimum size orthogonal fractional factorial designs: an approach based on integer linear programming. Computational Statistics 28, 241-253.

Fontana, R. (2017). Generalized minimum aberration mixed-level orthogonal arrays: A general approach based on sequential integer quadratically constrained quadratic programming. Communications in Statistics Theory and Methods 46, 4275-4284.

Georgiou, S.D. (2014). Supersaturated designs: a review of their construction and analysis. Journal of Statistical Planning and Inference 144, 92 - 109.

Grömping, U. (2017). Frequency tables for the coding invariant quality assessment of factorial designs. IISE Transactions 49, 505-517.

Grömping, U. (2018). Coding Invariance in Factorial Linear Models and a New Tool for Assessing Combinatorial Equivalence of Factorial Designs. Journal of Statistical Planning and Inference 193, 1-14.

Grömping, U. and Bailey, R.A. (2016). Regular fractions of factorial arrays. In: Kunert, J., Müller, C.H., Atkinson, A.C. (Eds.), MODA11—Advances in Model-Oriented Design and Analysis. Springer, pp. 143–151.

Grömping, U. and Fontana, R. (2018). An Algorithm for Generating Good Mixed Level Factorial Designs. Report 1/2018, Reports in Mathematics, Physics and Chemistry, Department II, Beuth University of Applied Sciences Berlin.

Grömping, U. and Xu, H. (2014). Generalized resolution for orthogonal arrays. The Annals of Statistics 42, 918-939.

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Software, arrays and examples

Eendebak, P. T. and Schoen, E. D., (2010). Orthogonal Arrays Website. http://www.pietereendebak.nl/oapackage/series.html. Last accessed February 27, 2017.

Grömping, U. (in press). R Package DoE.base for Factorial Designs. Journal of Statistical Software. Preprint at http://www1.beuth-hochschule.de/FB_II/reports/Report-2016-001.pdf.

Grömping, U. (2017b). DoE.MIParray: Creation of Arrays by mixed integer optimization. R package version 0.10. In: R Core Team (2017).

Gupta, V.K., Parsad, R., Kole, B. and Bhar, L.M. (2011). Supersaturated Designs. http://www.iasri.res.in/design/Supersaturated_Design/SSD/Supersaturated.html. Indian Agricultural Statistics Research Institute (ICAR), New Delhi 110 012, India. Last accessed September 22, 2017.

Gurobi Optimization, Inc. (2017). Gurobi Optimizer Reference Manual. http://www.gurobi.com/documentation/current/refman.pdf.

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http://support.sas.com/techsup/technote/ts723.html. Last accessed September 25 2017.

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Schoen, E. D., Eendebak, P. T. and Nguyen, M. V. M. (2010). Complete enumeration of pure-level and mixed-level orthogonal arrays. Journal of Combinatorial Designs 18, 123–140. doi:10.1002/jcd.20236.

Vasilev, N., Schmitz, Ch., Grömping, U., Fischer, R. and Schillberg, S. (2014). Assessment of Cultivation Factors that Affect Biomass and Geraniol Production in Transgenic Tobacco Cell Suspension Cultures. PLoS ONE 9(8): e104620. DOI:10.1371/journal.pone.0104620.

Wheeler, B. (2014). AlgDesign: Algorithmic Experimental Design. R package version 1.1-7.3. In R Core Team (2017).