Suboptimal alignments always reveal additional interesting biological features and have been successfully used to informally estimate the significance of an optimal alignment. Besides, traditional dynamic programming algorithms for sequence comparison require quadratic space, and hence are infeasible for long protein or DNA sequences. In this paper, a space-efficient sampling algorithm for computing suboptimal alignments is described. The algorithm uses a general gap model, where the cost associated with gaps is given by an affine score, and randomly selects an alignment according to the distribution of weights of all potential alignments. If x and y are two sequences with lengths n and m, respectively, then the space requirement of this algorithm is linear to the sum of n and m. Finally, an example illustrates the utility of the algorithm.
A reduction of truss topology design problem formulated by semidefinite optimization （SDO） is considered. The finite groups and their representations are introduced to reduce the stiffness and mass matrices of truss in size. Numerical results are given for both the original problem and the reduced problem to make a comparison.
In this paper, we use the discontinuous exact penalty functions to solve the constrained minimization problems with an integral approach. We examine a general form of the constrained deviation integral and its analytical properties. The optimality conditions of the penalized minimization problems are proven. To implement the al- gorithm, the cross-entropy method and the importance sampling are used based on the Monte-Carlo technique. Numerical tests show the effectiveness of the proposed algorithm.
The choice of self-concordant functions is the key to efficient algorithms for linear and quadratic convex optimizations, which provide a method with polynomial-time iterations to solve linear and quadratic convex optimization problems. The parameters of a self-concordant barrier function can be used to compute the complexity bound of the proposed algorithm. In this paper, it is proved that the finite barrier function is a local self-concordant barrier function. By deriving the local values of parameters of this barrier function, the desired complexity bound of an interior-point algorithm based on this local self-concordant function for linear optimization problem is obtained. The bound matches the best known bound for small-update methods.
A polynomial interior-point algorithm is presented for monotone linear complementarity problem （MLCP） based on a class of kernel functions with the general barrier term, which are called general kernel functions. Under the mild conditions for the barrier term, the complexity bound of algorithm in terms of such kernel function and its derivatives is obtained. The approach is actually an extension of the existing work which only used the specific kernel functions for the MLCP.
