The Experts below are selected from a list of 63102 Experts worldwide ranked by ideXlab platform

David H. Mathews - One of the best experts on this subject based on the ideXlab platform.

  • prediction of rna secondary structure by free Energy Minimization
    Current Opinion in Structural Biology, 2006
    Co-Authors: David H. Mathews, Douglas H Turner
    Abstract:

    RNA secondary structure is often predicted from sequence by free Energy Minimization. Over the past two years, advances have been made in the estimation of folding free Energy change, the mapping of secondary structure and the implementation of computer programs for structure prediction. The trends in computer program development are: efficient use of experimental mapping of structures to constrain structure prediction; use of statistical mechanics to improve the fidelity of structure prediction; inclusion of pseudoknots in secondary structure prediction; and use of two or more homologous sequences to find a common structure.

  • Predicting RNA secondary structure by free Energy Minimization
    Theoretical Chemistry Accounts, 2005
    Co-Authors: David H. Mathews
    Abstract:

    RNA structure is hierarchical. Secondary structure contacts, i.e. the canonical base pair contacts, are generally stronger and form faster than the tertiary structure. Therefore, RNA secondary structures can be predicted independently of tertiary structure prediction. Furthermore, the stability of a given RNA secondary structure can be quantified using nearest neighbor free Energy parameters. These parameters are the basis of a number of free Energy Minimization algorithms that predict RNA secondary structure for either a single sequence or multiple sequences. This article reviews the progress of RNA secondary structure prediction by free Energy Minimization and describes many of the algorithms that have been developed.

Douglas H Turner - One of the best experts on this subject based on the ideXlab platform.

Feng Chu - One of the best experts on this subject based on the ideXlab platform.

  • Approximate and exact algorithms for an Energy Minimization traveling salesman problem
    Journal of Cleaner Production, 2020
    Co-Authors: Shijin Wang, Ming Liu, Feng Chu
    Abstract:

    Energy saving is a great challenge for clean transportation. In this paper, we study the Energy Minimization Traveling Salesman Problem (EMTSP), which is a generation of the classical Traveling Salesman Problem (TSP), and an important theoretical basis and a special case of the Energy Minimization Vehicle Routing Problem (EMVRP). The objective of the studied problem is to minimize the sum of the product of load (including curb weight of the vehicle) and traveled distances. An approximation algorithm based on the Christofides's Heuristic is proposed and its worst-case ratio bound is proven. A branch and bound (B&B) algorithm integrated with a fast 1-tree based lower bound is developed to obtain optimal solutions. The results of computational experiments show the efficiency and the effectiveness of the B&B algorithm, as well as the heuristic methods.

Daniel Prusa - One of the best experts on this subject based on the ideXlab platform.

  • CVPR - Graph-based simplex method for pairwise Energy Minimization with binary variables
    2015 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2015
    Co-Authors: Daniel Prusa
    Abstract:

    We show how the simplex algorithm can be tailored to the linear programming relaxation of pairwise Energy Minimization with binary variables. A special structure formed by basic and nonbasic variables in each stage of the algorithm is identified and utilized to perform the whole iterative process combinatorially over the input Energy Minimization graph rather than algebraically over the simplex tableau. This leads to a new efficient solver. We demonstrate that for some computer vision instances it performs even better than methods reducing binary Energy Minimization to finding maximum flow in a network.

Shijin Wang - One of the best experts on this subject based on the ideXlab platform.

  • Approximate and exact algorithms for an Energy Minimization traveling salesman problem
    Journal of Cleaner Production, 2020
    Co-Authors: Shijin Wang, Ming Liu, Feng Chu
    Abstract:

    Energy saving is a great challenge for clean transportation. In this paper, we study the Energy Minimization Traveling Salesman Problem (EMTSP), which is a generation of the classical Traveling Salesman Problem (TSP), and an important theoretical basis and a special case of the Energy Minimization Vehicle Routing Problem (EMVRP). The objective of the studied problem is to minimize the sum of the product of load (including curb weight of the vehicle) and traveled distances. An approximation algorithm based on the Christofides's Heuristic is proposed and its worst-case ratio bound is proven. A branch and bound (B&B) algorithm integrated with a fast 1-tree based lower bound is developed to obtain optimal solutions. The results of computational experiments show the efficiency and the effectiveness of the B&B algorithm, as well as the heuristic methods.