Baharak Rastegari

Classifying RNA pseudoknotted structures

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 find 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.

Size versus truthfulness in the house allocation problem

We study the House Allocation problem (also known as the Assignment problem), i.e., the problem of allocating a set of objects among a set of agents, where each agent has ordinal preferences (possibly involving ties) over a subset of the objects. We focus on truthful mechanisms without monetary transfers for finding large Pareto optimal matchings. It is straightforward to show that no deterministic truthful mechanism can approximate a maximum cardinality Pareto optimal matching with ratio better than 2. We thus consider randomized mechanisms. We give a natural and explicit extension of the classical Random Serial Dictatorship Mechanism (RSDM) specifically for the House Allocation problem where preference lists can include ties. We thus obtain a universally truthful randomized mechanism for finding a Pareto optimal matching and show that it achieves an approximation ratio of eovere-1. The same bound holds even when agents have priorities (weights) and our goal is to find a maximum weight (as opposed to maximum cardinality) Pareto optimal matching. On the other hand we give a lower bound of 18 over 13 on the approximation ratio of any universally truthful Pareto optimal mechanism in settings with strict preferences. In the case that the mechanism must additionally be non-bossy, an improved lower bound of eovere-1 holds. This lower bound is tight given that RSDM for strict preference lists is non-bossy. We moreover interpret our problem in terms of the classical secretary problem and prove that our mechanism provides the best randomized strategy of the administrator who interviews the applicants.

Two-sided matching with partial information

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).

Linear time algorithm for parsing RNA secondary structure

Accurate prediction of pseudoknotted RNA secondary structure is an important computational challenge. Typical prediction algorithms aim to find a structure with minimum free energy according to some thermodynamic (“sum of loop energies”) model that is implicit in the recurrences of the algorithm. However, a clear definition of what exactly are the loops and stems in pseudoknotted structures, and their associated energies, has been lacking. We present a comprehensive classification of loops in pseudoknotted RNA secondary structures. Building on an algorithm of Bader et al. [2] we obtain a linear time algorithm for parsing a secondary structures into its component loops. We also give a linear time algorithm to calculate the free energy of a pseudoknotted secondary structure. This is useful for heuristic prediction algorithms which are widely used since (pseudoknotted) RNA secondary structure prediction is NP-hard. Finally, we give a linear time algorithm to test whether a secondary structure is in the class handled by Akutsus algorithm [1]. Using our tests, we analyze the generality of Akutsus algorithm for real biological structures.

Stable Matching with Uncertain Linear Preferences

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.

Pareto Optimal Matchings in Many-to-Many Markets with Ties

We consider Pareto optimal matchings (POMs) in a many-to-many market of applicants and courses where applicants have preferences, which may include ties, over individual courses and lexicographic preferences over sets of courses. Since this is the most general setting examined so far in the literature, our work unifies and generalizes several known results. Specifically, we characterize POMs and introduce the Generalized Serial Dictatorship Mechanism with Ties (GSDT) that effectively handles ties via properties of network flows. We show that GSDT can generate all POMs using different priority orderings over the applicants, but it satisfies truthfulness only for certain such orderings. This shortcoming is not specific to our mechanism; we show that any mechanism generating all POMs in our setting is prone to strategic manipulation. This is in contrast to the one-to-one case (with or without ties), for which truthful mechanisms generating all POMs do exist.