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The NP-hard graph bisection problem is to partition the nodes of an undirected graph into two equal-sized groups so as to minimize the number of edges that cross the partition. The more general graph l-partition problem is to partition the nodes of an undirected graph into l equal-sized groups so as to minimize the total number of edges that cross between(More)
  • Anne Condon
  • Advances In Computational Complexity Theory
  • 1990
We survey a number of algorithms for the simple stochastic game problem, which is to determine the winning probability of a type of stochastic process, where the transitions are partially controlled by two players. We show that four natural approaches to solving the problem are incorrect, and present two new algorithms for the problem. The rst reduces the(More)
We present HotKnots, a new heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming stable stems, our algorithm explores many alternative secondary structures, using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate(More)
The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for(More)
The function of many RNAs depends crucially on their structure. Therefore, the design of RNA molecules with specific structural properties has many potential applications, e.g. in the context of investigating the function of biological RNAs, of creating new ribozymes, or of designing artificial RNA nanostructures. Here, we present a new algorithm for(More)
Automated planning, the problem of how an agent achieves a goal given a repertoire of actions, is one of the foundational and most widely studied problems in the AI literature. The original formulation of the problem makes strong assumptions regarding the agent's knowledge and control over the world, namely that its information is complete and correct, and(More)
We consider the problem of designing DNA codes, namely sets of equi-length words over the alphabet [A, C, G, T] that satisfy certain combinatorial constraints. This problem is motivated by the task of reliably storing and retrieving information in synthetic DNA strands for use in DNA computing or as molecular bar codes in chemical libraries. The primary(More)
We prove two results on interactive proof systems with 2-way probabilistic finite state verifiers. The first is a lower bound on the power of such proof systems, if they are not required to halt with high probability on rejected inputs: we show that they can accept any recursively enumerable language. The second is an upper bound on the power of interactive(More)