6316461
Partitioned optimization algorithms for multiple sequence alignment
Multiple sequence alignment is an important and difficult problem in molecular biology and bioinformatics. In this paper, we propose a partitioning approach that significantly improves the solution time and quality by utilizing the locality structure of the problem. The algorithm solves the multiple sequence alignment in three stages. First, an automated and suboptimal partitioning strategy is used to divide the set of sequences into several subsections. Then a multiple sequence alignment algorithm based on ant colony optimization is used to align the sequences of each subsection. Finally, the alignment of original sequences can be obtained by assembling the result of each subsection. The ant colony algorithm is highly optimized in order to avoid local optimal traps and converge to global optimal efficiently. Experimental results show that the algorithm can significantly reduce the running time and improve the solution quality on large-scale multiple sequence alignment benchmarks.
832740
Constrained genetic algorithms and their applications in nonlinear constrained optimization
The paper presents a problem-independent framework that unifies various mechanisms for solving discrete constrained nonlinear programming (NLP) problems whose functions are not necessarily differentiable and continuous. The framework is based on the first-order necessary and sufficient conditions in the theory of discrete constrained optimization using Lagrange multipliers. It implements the search for discrete-neighborhood saddle points (SP/sub dn/) by performing ascents in the original-variable subspace and descents in the Lagrange-multiplier subspace. Our study on the various mechanisms shows that CSAGA, a combined constrained simulated annealing and genetic algorithm, performs well. Finally, we apply iterative deepening to determine the optimal number of generations in CSAGA.
10621466
Regression Cubes with Lossless Compression and Aggregation
As OLAP engines are widely used to support multidimensional data analysis, it is desirable to support in data cubes advanced statistical measures, such as regression and filtering, in addition to the traditional simple measures such as count and average. Such new measures allow users to model, smooth, and predict the trends and patterns of data. Existing algorithms for simple distributive and algebraic measures are inadequate for efficient computation of statistical measures in a multidimensional space. In this paper, we propose a fundamentally new class of measures, compressible measures, in order to support efficient computation of the statistical models. For compressible measures, we compress each cell into an auxiliary matrix with a size independent of the number of tuples. We can then compute the statistical measures for any data cell from the compressed data of the lower-level cells without accessing the raw data. Time- and space-efficient lossless aggregation formulae are derived for regression and filtering measures. Our analytical and experimental studies show that the resulting system, regression cube, substantially reduces the memory usage and the overall response time for statistical analysis of multidimensional data
9555510
Long-Distance Mutual Exclusion for Propositional Planning
The use of mutual exclusion (mutex) has led to significant advances in propositional planning. However, previous mutex can only detect pairs of actions or facts that cannot be arranged at the same time step. In this paper, we introduce a new class of constraints that significantly generalizes mutex and can be efficiently computed. The proposed long-distance mutual exclusion (londex) can capture constraints over actions and facts not only at the same time step but also across multiple steps. Londex provides a powerful and general approach for improving planning efficiency. As an application, we have integrated londex into SATPLAN04, a leading optimal planner. Experimental results show that londex can effectively prune the search space and reduce the planning time. The resulting planner, MaxPlan, has won the First Place Award in the Optimal Track of the 5th International Planning Competition.
16524073
Partitioning of temporal planning problems in mixed space using the theory of extended saddle points
We study the partitioning of temporal planning problems formulated as mixed-integer nonlinear programming problems, develop methods to reduce the search space of partitioned subproblems, and propose algorithms for resolving unsatisfied global constraints. The algorithms are based on the necessary and sufficient extended saddle-point condition for constrained local minimization developed in this paper. When compared with the MIPS planner in solving some PDDL2.1 planning problems, our distributed implementation of MIPS shows significant improvements in time and quality.
5374807
Automated Planning and Scheduling using Calculus of Variations in Discrete Space
In this paper, we propose new dominance relations that can speed up significantly the solution process of planning problems formulated as nonlinear constrained dynamic optimization in discrete time and space. We first show that path dominance in dynamic programming cannot be applied when there are general constraints that span across multiple stages, and that node dominance, in the form of Euler-Lagrange conditions developed in optimal control theory in continuous space, cannot be extended to that in discrete space. This paper is the first to propose efficient node-dominance relations, in the form of local saddle-point conditions in each stage of a discrete-space planning problem, for pruning states that will not lead to locally optimal paths. By utilizing these dominance relations, we present efficient search algorithms whose complexity, despite exponential, has a much smaller base as compared to that without using the relations. Finally, we demonstrate the performance of our approach by integrating it in the ASPEN planner and show significant improvements in CPU time and solution quality on some spacecraft scheduling and planning benchmarks.
34645664
Applying Family Competition to Evolution Strategies for Constrained Optimization
This paper applies family competition to evolution strategies to solve constrained optimization problems. The family competition of Family Competition Evolution Strategy (FCES) can be viewed as a local competition involving the children generated from the same parent, while the selection is a global competition among all of the members in the population. According to our experimental results, the self-adaptation of strategy parameters with deterministic elitist selection may trap ESs into local optima when they are applied to heavy constrained optimization problems. By controlling strategy parameters with non-self adaptive rule, FCES can reduce the computation time of self-adaptive Gaussian mutation, diminish the complexity of selection from (m+1) to (m+m), and avoid to be premature. Therefore, FCES is capable of obtaining better performance and saving the computation time. In this paper, FCES is compared with other evolutionary algorithms on various benchmark problems and the results indicate that FCES is a powerful optimization technique.
14028105
Scalability of heterogeneous computing
Scalability is a key factor of the design of distributed systems and parallel algorithms and machines. However, conventional scalabilities are designed for homogeneous parallel processing. There is no suitable and commonly accepted definition of scalability metric for heterogeneous systems. Isospeed scalability is a well-defined metric for homogeneous computing. This study extends the isospeed scalability metric to general heterogeneous computing systems. The proposed isospeed-efficiency metric is suitable for both homogeneous and heterogeneous computing. Through theoretical analysis, we derive methodologies of scalability measurement and prediction for heterogeneous systems. Experimental results verify the analytical results and confirm that the proposed isospeed-efficiency scalability works well in both homogeneous and heterogeneous environments.
9845542
Back Propagation with Randomized Cost Function for Training Neural Networks
A novel method to improve both the generalization and convergence performance of the back propagation algorithm (BP) by using multiple cost functions with a randomizing scheme is proposed in this paper. Under certain conditions, the randomized technique will converge to the global minimum with probability one. Experimental results on benchmark Encoder-Decoder problems and the NC2 classification problem show that the method is effective in enhancing BP's convergence and generalization performance
7335648
A Systolic Algorithm for the k-Nearest Neighbors Problem
The authors present a systolic algorithm and its variations for the k-nearest neighbors problem (kNNP). Multiple-shot queries with different ranges (k values) can be served in a pipelined fashion. A partitioning scheme is developed to handle large size problems. Performance of the algorithm is analyzed. Formulas for the optimal array size in terms of computation time and area-time-time product (ATT) are derived. The algorithm can solve a multiple-shot kNNP in N+2 square root N*K systolic steps using square root N*K processing elements, where N is the problem size (i.e. the number of points), and K is the sum of all k-values. >
22185885
Artificial Life for Image Segmentation
Artificial life has been successfully used for understanding biological systems and in many applications in robotics, computer graphics, etc. In this paper, we pioneer the use of artificial life for image segmentation, a challenging area in image processing. Our method associates each pixel in an image with a life and it evolves according to a system of rules. The segmented partitions emerge when the state of the lives reaches an equilibrium. The artificial life approach is promising in image processing because it is inherently parallel and coincides with the self-governing biological process. In addition, it has the advantage of the integration of both detail preservation and noise removal. The experiments demonstrate the feasibility of the artificial life approach on both intensity images and color images. We also compared the approach with other four commonly used methods for three different kinds of noise corrupted images.