An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids

It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such as melting temperature and equilibrium concentrations can be more reliably predicted. Even structure prediction by sampling from the ensemble and clustering those structures by Sfold [7] has proven to be more reliable than minimum free energy structure prediction. The main obstacle for ensemble based approaches is the computational complexity of the partition function and base pairing probabilities. For instance, the space complexity of the partition function for RNA-RNA interaction is $O(n^4)$ and the time complexity is $O(n^6)$ which are prohibitively large [4,12]. Our goal in this paper is to give a fast algorithm, based on sparse folding, to calculate an upper bound on the partition function. Our work is based on the recent algorithm of Hazan and Jaakkola [10]. The space complexity of our algorithm is the same as that of sparse folding algorithms, and the time complexity of our algorithm is $O(MFE(n)\ell)$ for single RNA and $O(MFE(m, n)\ell)$ for RNA-RNA interaction in practice, in which $MFE$ is the running time of sparse folding and $\ell \leq n$ ($\ell \leq n + m$) is a sequence dependent parameter

Dagstuhl Reports : Volume 1, Issue 2, February 2011

Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn

Contingency-Constrained Unit Commitment with Post-Contingency Corrective Recourse

We consider the problem of minimizing costs in the generation unit commitment problem, a cornerstone in electric power system operations, while enforcing an N-k-e reliability criterion. This reliability criterion is a generalization of the well-known $N$-$k$ criterion, and dictates that at least $(1-e_ j)$ fraction of the total system demand must be met following the failures of $k$ or fewer system components. We refer to this problem as the Contingency-Constrained Unit Commitment problem, or CCUC. We present a mixed-integer programming formulation of the CCUC that accounts for both transmission and generation element failures. We propose novel cutting plane algorithms that avoid the need to explicitly consider an exponential number of contingencies. Computational studies are performed on several IEEE test systems and a simplified model of the Western US interconnection network, which demonstrate the effectiveness of our proposed methods relative to current state-of-the-art

A new exact algorithm for the multi-depot vehicle routing problem under capacity and route length constraints

This article presents an exact algorithm for the multi-depot vehicle routing problem (MDVRP) under capacity and route length constraints. The MDVRP is formulated using a vehicle-flow and a set-partitioning formulation, both of which are exploited at different stages of the algorithm. The lower bound computed with the vehicle-flow formulation is used to eliminate non-promising edges, thus reducing the complexity of the pricing subproblem used to solve the set-partitioning formulation. Several classes of valid inequalities are added to strengthen both formulations, including a new family of valid inequalities used to forbid cycles of an arbitrary length. To validate our approach, we also consider the capacitated vehicle routing problem (CVRP) as a particular case of the MDVRP, and conduct extensive computational experiments on several instances from the literature to show its effectiveness. The computational results show that the proposed algorithm is competitive against stateof-the-art methods for these two classes of vehicle routing problems, and is able to solve to optimality some previously open instances. Moreover, for the instances that cannot be solved by the proposed algorithm, the final lower bounds prove stronger than those obtained by earlier methods