Global Optimization on Funneling Landscapes

Molecular conformation problems arising in computational chemistry require the global minimization of a non-convex potential energy function representing the interactions of, for example, the component atoms in a molecular system. Typically the number of local minima on the potential energy surface grows exponentially with system size, and often becomes enormous even for relatively modestly sized systems. Thus the simple multistart strategy of randomly sampling local minima becomes impractical. However, for many molecular conformation potential energy surfaces the local minima can be organized by a simple adjacency relation into a single or at most a small number of funnels. A distinguished local minimum lies at the bottom of each funnel and a monotonically descending sequence of adjacent local minima connects every local minimum in the funnel with the funnel bottom. Thus the global minimum can be found among the comparatively small number of funnel bottoms, and a multistart strategy based on sampling funnel bottoms becomes viable. In this paper we present such an algorithm of the basin-hopping type and apply it to the Lennard–Jones cluster problem, an intensely studied molecular conformation problem which has become a benchmark for global optimization algorithms. Results of numerical experiments are presented which confirm both the multifunneling character of the Lennard–Jones potential surface as well as the efficiency of the algorithm. The algorithm has found all of the current putative global minima in the literature up to 110 atoms, as well as discovered a new global minimum for the 98-atom cluster of a novel geometrical class.     

Test Functions with Variable Attraction Regions for Global Optimization Problems

Functions with local minima and size of their region of attraction known a priori, are often needed for testing the performance of algorithms that solve global optimization problems. In this paper we investigate a technique for constructing test functions for global optimization problems for which we fix a priori: (i) the problem dimension, (ii) the number of local minima, (iii) the local minima points, (iv) the function values of the local minima. Further, the size of the region of attraction of each local minimum may be made large or small. The technique consists of first constructing a convex quadratic function and then systematically distorting selected parts of this function so as to introduce local minima.     

Global Optimization of a Quadratic Functional with Quadratic Equality Constraints, Part 2

In this paper, we investigate a constrained optimization problem with a quadratic cost functional and two quadratic equality constraints. It is assumed that the cost functional is positive definite and that the constraints are both feasible and regular (but otherwise they are unrestricted quadratic functions). Thus, the existence of a global constrained minimum is assured. We develop a necessary and sufficient condition that completely characterizes the global minimum cost. Such a condition is of essential importance in iterative numerical methods for solving the constrained minimization problem, because it readily distinguishes between local minima and global minima and thus provides a stopping criterion for the computation. The result is similar to one obtained previously by the authors. In the previous result, we gave a characterization of the global minimum of a constrained quadratic minimization problem in which the cost functional was an arbitrary quadratic functional (as opposed to positive-definite here) and the constraints were at least positive-semidefinite quadratic functions (as opposed to essentially unrestricted here).     

A search technique for global optimization in a chaotic environment

We describe a new algorithm which uses the trajectories of a discrete dynamical system to sample the domain of an unconstrained objective function in search of global minima. The algorithm is unusually adept at avoiding nonoptimal local minima and successfully converging to a global minimum. Trajectories generated by the algorithm for objective functions with many local minima exhibit chaotic behavior, in the sense that they are extremely sensitive to changes in initial conditions and system parameters. In this context, chaos seems to have a beneficial effect: failure to converge to a global minimum from a given initial point can often be rectified by making arbitrarily small changes in the system parameters.     

Improvement on the northby algorithm for molecular conformation: Better solutions

In 1987, Northby presented an efficient lattice based search and optimization procedure to compute ground states ofn-atom Lennard-Jones clusters and reported putative global minima for 13n150. In this paper, we introduce simple data structures which reduce the time complexity of the Northby algorithm for lattice search fromO(n^5/3) per move toO(n^2/3) per move for ann-atom cluster involving full Lennard-Jones potential function. If nearest neighbor potential function is used, the time complexity can be further reduced toO(logn) per move for ann-atom cluster. The lattice local minimizers with lowest potential function values are relaxed by a powerful Truncated Newton algorithm. We are able to reproduce the minima reported by Northby. The improved algorithm is so efficient that less than 3 minutes of CPU time on the Cray-XMP is required for each cluster size in the above range. We then further improve the Northby algorithm by relaxingevery lattice local minimizer found in the process. This certainly requires more time. However, lower energy configurations were found with this improved algorithm forn=65, 66, 75, 76, 77 and 134. These findings also show that in some cases, the relaxation of a lattice local minimizer with a worse potential function value may lead to a local minimizer with a better potential function value.     

Local Optimization Method with Global Multidimensional Search

This paper presents a new method for solving global optimization problems. We use a local technique based on the notion of discrete gradients for finding a cone of descent directions and then we use a global cutting angle algorithm for finding global minimum within the intersection of the cone and the feasible region. We present results of numerical experiments with well-known test problems and with the so-called cluster function. These results confirm that the proposed algorithms allows one to find a global minimizer or at least a deep local minimizer of a function with a huge amount of shallow local minima.     

Deterministic Global Optimization in Nonlinear Optimal Control Problems

The accurate solution of optimal control problems is crucial in many areas of engineering and applied science. For systems which are described by a nonlinear set of differential-algebraic equations, these problems have been shown to often contain multiple local minima. Methods exist which attempt to determine the global solution of these formulations. These algorithms are stochastic in nature and can still get trapped in local minima. There is currently no deterministic method which can solve, to global optimality, the nonlinear optimal control problem. In this paper a deterministic global optimization approach based on a branch and bound framework is introduced to address the nonlinear optimal control problem to global optimality. Only mild conditions on the differentiability of the dynamic system are required. The implementa-tion of the approach is discussed and computational studies are presented for four control problems which exhibit multiple local minima.     

GOSH: derivative-free global optimization using multi-dimensional space-filling curves

Global optimization is a field of mathematical programming dealing with finding global (absolute) minima of multi-dimensional multiextremal functions. Problems of this kind where the objective function is non-differentiable, satisfies the Lipschitz condition with an unknown Lipschitz constant, and is given as a “black-box” are very often encountered in engineering optimization applications. Due to the presence of multiple local minima and the absence of differentiability, traditional optimization techniques using gradients and working with problems having only one minimum cannot be applied in this case. These real-life applied problems are attacked here by employing one of the mostly abstract mathematical objects—space-filling curves. A practical derivative-free deterministic method reducing the dimensionality of the problem by using space-filling curves and working simultaneously with all possible estimates of Lipschitz and Hölder constants is proposed. A smart adaptive balancing of local and global information collected during the search is performed at each iteration. Conditions ensuring convergence of the new method to the global minima are established. Results of numerical experiments on 1000 randomly generated test functions show a clear superiority of the new method w.r.t. the popular method DIRECT and other competitors.     

Docking of Atomic Clusters Through Nonlinear Optimization

The problem of molecular docking is defined as that of finding a minimum energy configuration of a pair of molecular structures (usually consisting of proteins, DNA or RNA fragments). It is often assumed that the two interacting structures can be considered as rigid bodies and that it is of interest to researchers to develop methods which enable to discover the potential binding sites. Many different models have been proposed in the literature for the definition of the potential energy between two molecular structures, most of which contain at least a term (known as Van Der Waals interaction) which accounts for pairwise attraction between atoms, a repulsion term and a term which takes into account electrostatic forces (Coulomb interaction). Some well known models, and in particular those used in rigid docking, are based on the assumption that the only terms which are relevant in the process of docking are pairwise interactions between atoms belonging to the two different parts of the structure. In this paper the problem of finding the lowest energy configuration of a pair of biomolecular structures, considered as rigid bodies, is defined and formulated as a global optimization problem. In terms of dimension of the search space this formulation is not 'high-dimensional', as there are only six degrees of freedom: 3 translation and 3 rotation parameters. However the energy surface of the docking problem is characterized by a huge number of local minima; moreover each function evaluation is quite expensive (interesting structures usually possess a few thousand atoms each). So there is a strong need both of local and of global optimization procedures. In this paper a local optimization technique, based upon standard non linear programming software and a penalized objective function, is introduced and its potential usefulness in the context of global optimization is outlined.     

Iterative Convex Quadratic Approximation for Global Optimization in Protein Docking

An algorithm for finding an approximate global minimum of a funnel shaped function with many local minima is described. It is applied to compute the minimum energy docking position of a ligand with respect to a protein molecule. The method is based on the iterative use of a convex, general quadratic approximation that underestimates a set of local minima, where the error in the approximation is minimized in the L¹ norm. The quadratic approximation is used to generate a reduced domain, which is assumed to contain the global minimum of the funnel shaped function. Additional local minima are computed in this reduced domain, and an improved approximation is computed. This process is iterated until a convergence tolerance is satisfied. The algorithm has been applied to find the global minimum of the energy function generated by the Docking Mesh Evaluator program. Results for three different protein docking examples are presented. Each of these energy functions has thousands of local minima. Convergence of the algorithm to an approximate global minimum is shown for all three examples.     

Rational Functions with Prescribed Global and Local Minimizers

A family of multivariate rational functions is constructed. It has strong local minimizers with prescribed function values at prescribed positions. While there might be additional local minima, such minima cannot be global. A second family of multivariate rational functions is given, having prescribed global minimizers and prescribed interpolating data.     

On global optimization in two-dimensional scaling

We consider multidimensional scaling for embedding dimension two, which allows the detection of structures in dissimilarity data by simply drawing two-dimensional figures. The corresponding objective function, called STRESS, is generally nondifferentiable and has many local minima. In this paper we investigate several features of this function, and discuss the application of different global optimization procedures. A method based on combining a local search algorithm with an evolutionary strategy of generating new initial points is proposed, and its efficiency is investigated by numerical examples.This paper was written while the second author was visiting Professor at Aachen University of Technology, funded by the Deutsche Forschungsgemeinschaft.     

Generalized weak sharp minima in cone-constrained convex optimization on Hadamard manifolds

In this paper, a convex optimization problem with cone constraint (for short, CPC) is introduced and studied on Hadamard manifolds. Some criteria and characterizations for the solution set to be a set of generalized global weak sharp minima, generalized local weak sharp minima and generalized bounded weak sharp minima for (CPC) are derived on Hadamard manifolds.     

On the numerical relaxation of single-slip plasticity in finite strains

The modeling of the elastoplastic behaviour of single crystals with infinite latent hardening leads to a nonconvex energy density, whose minimization produces fine structures. The computation of the quasiconvex envelope of the energy density is faced in this case with huge numerical difficulties caused by the clusters of local minima. By exploiting the structure of the problem, we present a fast and efficient numerical relaxation algorithm as alternative to global optimization techniques usually adopted in literature which are computationally more expensive. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Global Minimization via Piecewise-Linear Underestimation

Given a function on Rⁿ with many multiple local minima we approximate it from below, via concave minimization, with a piecewise-linear convex function by using sample points from the given function. The piecewise-linear function is then minimized using a single linear program to obtain an approximation to the global minimum of the original function. Successive shrinking of the original search region to which this procedure is applied leads to fairly accurate estimates, within 0.57%, of the global minima of synthetic nonconvex piecewise-quadratic functions for which the global minima are known exactly.     

Packing cylinders and rectangular parallelepipeds with distances between them into a given region

This paper considers the problem of packing cylinders and parallelepipeds into a given region so that the height of the occupied part of the region is minimal and the distances between each pair of items, and the distance between each packed item and the frontier of the region must be greater than or equal to given distances. A mathematical model of the problem is built and some characteristics of the mathematical model are investigated. Methods for fast construction of starting points, searching for local minima, and a special non-exhaustive search of local minima to obtain good approximations to a global minimum are offered. A numerical example is given. Runtimes to obtain starting points, local minima and approximations to a global minimum are adduced.     

On the Efficiency of a Global Non-differentiable Optimization Algorithm Based on the Method of Optimal Set Partitioning

The examined algorithm for global optimization of the multiextremal non-differentiable function is based on the following idea: the problem of determination of the global minimum point of the function f(x) on the set (f(x) has a finite number of local minima in this domain) is reduced to the problem of finding all local minima and their attraction spheres with a consequent choice of the global minimum point among them. This reduction is made by application of the optimal set partitioning method. The proposed algorithm is evaluated on a set of well-known one-dimensional, two-dimensional and three-dimensional test functions. Recommendations for choosing the algorithm parameters are given.     

A quasi-multistart framework for global optimization of expensive functions using response surface models

We present the AQUARS (A QUAsi-multistart Response Surface) framework for finding the global minimum of a computationally expensive black-box function subject to bound constraints. In a traditional multistart approach, the local search method is blind to the trajectories of the previous local searches. Hence, the algorithm might find the same local minima even if the searches are initiated from points that are far apart. In contrast, AQUARS is a novel approach that locates the promising local minima of the objective function by performing local searches near the local minima of a response surface (RS) model of the objective function. It ignores neighborhoods of fully explored local minima of the RS model and it bounces between the best partially explored local minimum and the least explored local minimum of the RS model. We implement two AQUARS algorithms that use a radial basis function model and compare them with alternative global optimization methods on an 8-dimensional watershed model calibration problem and on 18 test problems. The alternatives include EGO, GLOBALm, MLMSRBF (Regis and Shoemaker in INFORMS J Comput 19(4):497–509, 2007), CGRBF-Restart (Regis and Shoemaker in J Global Optim 37(1):113–135 2007), and multi level single linkage (MLSL) coupled with two types of local solvers: SQP and Mesh Adaptive Direct Search (MADS) combined with kriging. The results show that the AQUARS methods generally use fewer function evaluations to identify the global minimum or to reach a target value compared to the alternatives. In particular, they are much better than EGO and MLSL coupled to MADS with kriging on the watershed calibration problem and on 15 of the test problems.     

Generating Sum-of-Ratios Test Problems in Global Optimization

A method is presented for the construction of test problems involving the minimization over convex sets of sums of ratios of affine functions. Given a nonempty, compact convex set, the method determines a function that is the sum of linear fractional functions and attains a global minimum over the set at a point that can be found by convex programming and univariate search. Generally, the function will have also local minima over the set that are not global minima.     

A GA-Simplex Hybrid Algorithm for Global Minimization of Molecular Potential Energy Functions

In this paper we propose a hybrid genetic algorithm for minimizing molecular potential energy functions. Experimental evidence shows that the global minimum of the potential energy of a molecule corresponds to its most stable conformation, which dictates its properties. The search for the global minimum of a potential energy function is very difficult since the number of local minima grows exponentially with molecule size. The proposed approach was successfully applied to two cases: (i) a simplified version of more general molecular potential energy functions in problems with up to 100 degrees of freedom, and (ii) a realistic potential energy function modeling two different molecules.