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 stems. In an empirical evaluation of the algorithm with 43 sequences taken from the Pseudobase database and from the literature on pseudoknotted structures, we found that overall, in terms of the sensitivity and specificity of predictions, HotKnots outperforms the well-known Pseudoknots algorithm of Rivas and Eddy and the NUPACK algorithm of Dirks and Pierce, both based on dynamic programming approaches for limited classes of pseudoknotted structures. It also outperforms the heuristic Iterated Loop Matching algorithm of Ruan and colleagues, and in many cases gives better results than the genetic algorithm from the STAR package of van Batenburg and colleagues and the recent pknotsRG-mfe algorithm of Reeder and Giegerich. The HotKnots algorithm has been implemented in C/C++ and is available from http://www. cs.ubc.ca/labs/beta/Software/HotKnots.

Abstract. We consider the two-sided stable matching setting in which there may be uncertainty about the agents' preferences due to limited information or communication. We consider three models of uncertainty:(1) lottery model -in which for each agent, there is a probability distribution over linear preferences, (2) compact indifference model -for each agent, a weak preference order is specified and each linear order compatible with the weak order is equally likely and (3) joint probability model -there is a lottery over preference profiles. For each of the models, we study the computational complexity of computing the stability probability of a given matching as well as finding a matching with the highest probability of being stable. We also examine more restricted problems such as deciding whether a certainly stable matching exists. We find a rich complexity landscape for these problems, indicating that the form uncertainty takes is significant.

Computational prediction of the minimum free energy (mfe) secondary structure of an RNA molecule from its base sequence is valuable in understanding the structure and function of the molecule. Since the general problem of predicting pseudoknotted secondary structures is NP-hard, several algorithms have been proposed that ÿnd the mfe secondary structure from a restricted class of secondary structures. In this work, we order the algorithms by generality of the structure classes that they handle. We provide simple characterizations of the classes of structures handled by four algorithms, as well as linear time methods to test whether a given secondary structure is in three of these classes. We report on the percentage of biological structures from the PseudoBase and Gutell databases that are handled by these three algorithms.

The assignment problem is one of the most wellstudied settings in social choice, matching, and discrete allocation. We consider this problem with the additional feature that agents' preferences involve uncertainty. The setting with uncertainty leads to a number of interesting questions including the following ones. How to compute an assignment with the highest probability of being Pareto optimal? What is the complexity of computing the probability that a given assignment is Pareto optimal? Does there exist an assignment that is Pareto optimal with probability one? We consider these problems under two natural uncertainty models: (1) the lottery model in which each agent has an independent probability distribution over linear orders and (2) the joint probability model that involves a joint probability distribution over preference profiles. For both of these models, we present a number of algorithmic and complexity results highlighting the difference and similarities in the complexity of the two models.

The traditional model of two-sided matching assumes that all agents fully know their own preferences. As markets grow large, however, it becomes impractical for agents to precisely assess their rankings over all agents on the other side of the market. We propose a novel model of two-sided matching in which agents are endowed with known partially ordered preferences and unknown true preferences drawn from known distributions consistent with the partial order. The true preferences are learned through interviews, revealing the pairwise rankings among all interviewed agents, performed according to a centralized interview policy, i.e., an algorithm that adaptively schedules interviews. Our goal is for the policy to guarantee both stability and optimality for a given side of the market, with respect to the underlying true preferences of the agents. As interviews are costly, we seek a policy that minimizes the number of interviews. We introduce three minimization objectives: (very weak) dominance, which minimizes the number of interviews for any underlying true preference profile; Pareto optimality, which guarantees that no other policy dominates the given policy; and optimality in expectation with respect to the preference distribution. We formulate our problem as a Markov decision process, implying an algorithm for computing an optimal-in-expectation policy in time polynomial in the number of possible preference orderings (and thus exponential in the size of the input). We then derive structural properties of dominant policies which we call optimality certificates. We show that computing a minimum optimality certificate is NP-hard, suggesting that optimal-in-expectation and/or Pareto optimal policies could be NP-hard to compute. Finally, we restrict attention to a setting in which agents on one side of the market have the same partially ordered preferences (but potentially distinct underlying true preferences), and in which agents must interview before matching. In this restricted setting, we show how to leverage the idea of minimum optimality certificates to design a computationally efficient interview-minimizing policy. This policy works without knowledge of the distributions and is dominant (and so is also Pareto optimal and optimal-in-expectation).