An evolutionary algorithm for A-optimal incomplete block designs

Evolutionary algorithms are heuristic stochastic search and optimization techniques with principles taken from natural genetics. They are procedures mimicking the evolution process of an initial population through genetic transformations. This paper is concerned with the problem of finding A-optimal incomplete block designs for multiple treatment comparisons represented by a matrix of contrasts. An evolutionary algorithm for searching optimal, or nearly optimal, incomplete block designs is described in detail. Various examples regarding the application of the algorithm to some well-known problems illustrate the good performance of the algorithm     

D-optimal minimax design criterion for two-level fractional factorial designs

A D-optimal minimax design criterion is proposed to construct two-level fractional factorial designs, which can be used to estimate a linear model with main effects and some specified interactions. D-optimal minimax designs are robust against model misspecification and have small biases if the linear model contains more interaction terms. When the D-optimal minimax criterion is compared with the D-optimal design criterion, we find that the D-optimal design criterion is quite robust against model misspecification. Lower and upper bounds derived for the loss functions of optimal designs can be used to estimate the efficiencies of any design and evaluate the effectiveness of a search algorithm. Four algorithms to search for optimal designs for any run size are discussed and compared through several examples. An annealing algorithm and a sequential algorithm are particularly effective to search for optimal designs.     

Application of genetic algorithms to the construction of exact D-optimal designs

This paper studies the application of genetic algorithms to the construction of exact D-optimal experimental designs. The concept of genetic algorithms is introduced in the general context of the problem of finding optimal designs. The algorithm is then applied specifically to finding exact D-optimal designs for three different types of model. The performance of genetic algorithms is compared with that of the modified Fedorov algorithm in terms of computing time and relative efficiency. Finally, potential applications of genetic algorithms to other optimality criteria and to other types of model are discussed, along with some open problems for possible future research.     

Linear Integer Programming Approach to Construction of Balanced Incomplete Block Designs

This article proposes a linear integer programming-based algorithm to construct balanced incomplete block designs. Working of the algorithm is illustrated with the help of an example. The algorithm is able to generate balanced incomplete block designs very fast in most of the cases. The performance of the proposed algorithm is compared with other algorithms proposed in the literature. It is demonstrated that the proposed algorithm is competitive with the existing algorithms.     

Constructing Efficient Experimental Designs for Generalized Linear Models

Exchange algorithms are popular for finding optimal or efficient designs for linear models, but there are few discussions of this type of algorithm for generalized linear models (GLMs) in literature. A new algorithm, generalized Coordinate Exchange Algorithm (gCEA), is developed in this article to construct efficient designs for GLMs. We compare the performance of the proposed algorithm with other optimization algorithms, including point exchange algorithm, columnwise-pairwise algorithm, simulated annealing and generic algorithm, and demonstrate the superior performance of this new algorithm.     

On algorithmic construction of maximin distance designs

Maximin distance designs are useful for conducting expensive computer experiments. In this article, we compare some global optimization algorithms for constructing such designs. We also introduce several related space-filling designs, including nested maximin distance designs, sliced maximin distance designs, and general maximin distance designs with better projection properties. These designs possess more flexible structures than their analogs in the literature. Examples of these designs constructed by the algorithms are presented.     

A clustering-based coordinate exchange algorithm for generating G-optimal experimental designs

In the optimal experimental design literature, the G-optimality is defined as minimizing the maximum prediction variance over the entire experimental design space. Although the G-optimality is a highly desirable property in many applications, there are few computer algorithms developed for constructing G-optimal designs. Some existing methods employ an exhaustive search over all candidate designs, which is time-consuming and inefficient. In this paper, a new algorithm for constructing G-optimal experimental designs is developed for both linear and generalized linear models. The new algorithm is made based on the clustering of candidate or evaluation points over the design space and it is a combination of point exchange algorithm and coordinate exchange algorithm. In addition, a robust design algorithm is proposed for generalized linear models with modification of an existing method. The proposed algorithm are compared with the methods proposed by Rodriguez et al. [Generating and assessing exact G-optimal designs. J. Qual. Technol. 2010;42(1):3–20] and Borkowski [Using a genetic algorithm to generate small exact response surface designs. J. Prob. Stat. Sci. 2003;1(1):65–88] for linear models and with the simulated annealing method and the genetic algorithm for generalized linear models through several examples in terms of the G-efficiency and computation time. The result shows that the proposed algorithm can obtain a design with higher G-efficiency in a much shorter time. Moreover, the computation time of the proposed algorithm only increases polynomially when the size of model increases.     

The Construction of Efficient Two-replicate Row–Column Designs for Use in Field Trials

Two-replicate row–column designs are often used for field trials in multisite tree or plant breeding programmes. With only two replicates for each trial, it is important to use designs with optimal or near optimal efficiency factors. This paper presents an algorithm for generating such designs. The method extends the contraction approach of Bailey and Patterson to any set of parameters and uses the factorial design construction algorithm of Williams and John to generate designs. Our experience with the algorithm is that it produces designs that are at least as good as, and often much better and more quickly generated than, those obtained by other recent computer algorithms.     

An algorithm for optimal designs on a design space

Two variations of a simple monotunic algorithm for computing optimal designs on a finite design space are presented. Various properties are listed. Comparisons witn other algorithms are made.     

Algorithmic construction of optimal block designs for two-colour cDNA microarray experiments using the linear mixed effects model

ABSTRACT

In this study, methods for efficient construction of A-, MV-, D- and E-optimal or near-optimal block designs for two-colour cDNA microarray experiments with array as the block effect are considered. Two algorithms, namely the array exchange and treatment exchange algorithms together with the complete enumeration technique are introduced. For large numbers of arrays or treatments or both, the complete enumeration method is highly computer intensive. The treatment exchange algorithm computes the optimal or near-optimal designs faster than the array exchange algorithm. The two methods however produce optimal or near-optimal designs with the same efficiency under the four optimality criteria.     

Experimental designs for detecting synergy and antagonism between two drugs in a pre‐clinical study

The identification of synergistic interactions between combinations of drugs is an important area within drug discovery and development. Pre‐clinically, large numbers of screening studies to identify synergistic pairs of compounds can often be ran, necessitating efficient and robust experimental designs. We consider experimental designs for detecting interaction between two drugs in a pre‐clinical in vitro assay in the presence of uncertainty of the monotherapy response. The monotherapies are assumed to follow the Hill equation with common lower and upper asymptotes, and a common variance. The optimality criterion used is the variance of the interaction parameter. We focus on ray designs and investigate two algorithms for selecting the optimum set of dose combinations. The first is a forward algorithm in which design points are added sequentially. This is found to give useful solutions in simple cases but can lack robustness when knowledge about the monotherapy parameters is insufficient. The second algorithm is a more pragmatic approach where the design points are constrained to be distributed log‐normally along the rays and monotherapy doses. We find that the pragmatic algorithm is more stable than the forward algorithm, and even when the forward algorithm has converged, the pragmatic algorithm can still out‐perform it. Practically, we find that good designs for detecting an interaction have equal numbers of points on monotherapies and combination therapies, with those points typically placed in positions where a 50% response is expected. More uncertainty in monotherapy parameters leads to an optimal design with design points that are more spread out. Copyright © 2015 John Wiley & Sons, Ltd.     

A multi-objective coordinate-exchange two-phase local search algorithm for multi-stratum experiments

A multi-stratum design is a useful tool for industrial experimentation, where factors that have levels which are harder to set than others, due to time or cost constraints, are frequently included. The number of different levels of hardness to set defines the number of strata that should be used. The simplest case is the split-plot design, which includes two strata and two sets of factors defined by their level of hardness-to-set. In this paper, we propose a novel computational algorithm which can be used to construct optimal multi-stratum designs for any number of strata and up to six optimality criteria simultaneously. Our algorithm allows the study of the entire Pareto front of the optimization problem and the selection of the designs representing the desired trade-off between the competing objectives. We apply our algorithm to several real case scenarios and we show that the efficiencies of the designs obtained present experimenters with several good options according to their objectives.     

Optimal and efficient crossover designs for comparing test treatments to a control treatment under various models

We study the optimality, efficiency, and robustness of crossover designs for comparing several test treatments to a control treatment. Since A-optimality is a natural criterion in this context, we establish lower bounds for the trace of the inverse of the information matrix for the test treatments versus control comparisons under various models. These bounds are then used to obtain lower bounds for efficiencies of a design under these models. Two algorithms, both guided by these efficiencies and results from optimal design theory, are proposed for obtaining efficient designs under the various models.     

A hybrid elitist pareto-based coordinate exchange algorithm for constructing multi-criteria optimal experimental designs

This paper presents a new Pareto-based coordinate exchange algorithm for populating or approximating the true Pareto front for multi-criteria optimal experimental design problems that arise naturally in a range of industrial applications. This heuristic combines an elitist-like operator inspired by evolutionary multi-objective optimization algorithms with a coordinate exchange operator that is commonly used to construct optimal designs. Benchmarking results from both a two-dimensional and three-dimensional example demonstrate that the proposed hybrid algorithm can generate highly reliable Pareto fronts with less computational effort than existing procedures in the statistics literature. The proposed algorithm also utilizes a multi-start operator, which makes it readily parallelizable for high performance computing infrastructures.     

The construction of optimal designs for dose-escalation studies

Methods for the construction of A-, MV-, D- and E-optimal designs for dose-escalation studies are presented. Algebraic results proved elusive and explicit expressions for the requisite optimal designs are only given for a restricted class of traditional designs. Recourse to numerical procedures and heuristics is therefore made. Complete enumeration of all possible designs is discussed but is, as expected, highly computer intensive. Two exchange algorithms, one based on block exchanges and termed the Block Exchange Algorithm and the other a candidate-set-free algorithm based on individual exchanges and termed the Best Move Algorithm, are therefore introduced. Of these the latter is the most computationally effective. The methodology is illustrated by means of a range of carefully selected examples.     

RANDOMIZED SEARCH STRATEGIES FOR FINDING OPTIMAL OR NEAR OPTIMAL BLOCK AND ROW-COLUMN DESIGNS

We consider a family of effective and efficient strategies for generating experimental designs of several types with high efficiency. These strategies employ randomized search directions and at some stages allow the possibility of taking steps in a direction of decreasing efficiency in an effort to avoid local optima. Hence our strategies have some affinity with the simulated annealing algorithm of combinatorial optimization. The methods work well and compare favourably with other search strategies. We have implemented them for incomplete block designs, optionally resolvable, and for row-column designs.     

Exchange algorithms for constructing large spatial designs

Exchange algorithms are widely used for optimizing design criteria and have proven to be highly effective. However, application of these algorithms can be computationally prohibitive for very large design problems, and in situations for which the design criterion is sufficiently complex so as to prevent efficient evaluation strategies. This paper reports on several modifications to exchange algorithms that lead to large reductions in the computational burden associated with optimizing any given design criterion. A small study indicates that these modifications do not significantly impact the quality of designs, while reductions in effort of over 90% can be achieved.     

Optimal parametric design with applications to pharmacokinetic and pharmacodynamic trials

This paper considers optimal parametric designs, i.e. designs represented by probability measures determined by a set of parameters, for nonlinear models and illustrates their use in designs for pharmacokinetic (PK) and pharmacokinetic/pharmacodynamic (PK/PD) trials. For some practical problems, such as designs for modelling PK/PD relationship, this is often the only feasible type of design, as the design points follow a PK model and cannot be directly controlled. Even for ordinary design problems the parametric designs have some advantages over the traditional designs, which often have too few design points for model checking and may not be robust to model and parameter misspecifications. We first describe methods and algorithms to construct the parametric design for ordinary nonlinear design problems and show that the parametric designs are robust to parameter misspecification and have good power for model discrimination. Then we extend this design method to construct optimal repeated measurement designs for nonlinear mixed models. We also use this parametric design for modelling a PK/PD relationship and propose a simulation based algorithm. The application of parametric designs is illustrated with a three-parameter open one-compartment PK model for the ordinary design and repeated measurement design, and an Emax model for the phamacokinetic/pharmacodynamic trial design.     

基于块状bootstrap技术的Bagging Trees集成算法研究

集成算法已经成为机器学习研究的一大热点,已有许多改进的集成算法,但对"病态"数据的集成研究并不常见。本文通过对一海藻繁殖案例的研究,提出了一种基于块状bootstrap技术的集成算法,并将其与几种常用的集成算法比较研究得出,在对于一些"病态"数据而言,该算法往往比其它算法具有更小的模型推广误差和更高的预测精度的优点。     

Combinatorial Equivalence of Fractional Factorial Designs

Two symmetrical fractional factorial designs are said to be combinatorially equivalent if one design can be obtained from another by reordering the runs, relabeling the factors and relabeling the levels of one or more factors. This article presents concepts of ordered distance frequency matrix, distance frequency vector, and reduced distance frequency vector for a design. Necessary conditions for two designs to be combinatorial equivalent based on these concepts are presented. A new algorithm based on the results obtained is proposed to check combinatorial non-equivalence of two factorial designs and several illustrating examples are provided.