Protein structure prediction is an unsolved problem in computational biology. One great difficulty is due to the unknown factors in the actual energy function. Moreover, the energy models available are often not very informative particularly when spatially similar structures are compared during search. We introduce several novel heuristics to augment the energy model and present a new local search algorithm that exploits these heuristics in a mixed fashion. Although the heuristics individually are weaker in performance than the energy function, their combination interestingly produces stronger results. For standard benchmark proteins on the face centered cubic lattice and a realistic 20x20 energy model, we obtain structures with significantly lower energy than those obtained by the state-of-the-art algorithms. We also report results for these proteins using the same energy model on the cubic lattice.

Markov processes are increasingly used to generate finite-length sequences that imitate a given style. However, Markov processes are notoriously difficult to control. Recently, Markov constraints have been introduced to give users some control on generated sequences. Markov constraints reformulate finite-length Markov sequence generation in the framework of constraint satisfaction (CSP). However, in practice, this approach is limited to local constraints and its performance is low for global constraints, such as cardinality or arithmetic constraints. This limitation prevents generated sequences to follow structural properties which are independent of the style, but inherent to the domain, such as meter. In this article, we introduce meter, a constraint that ensures a sequence is 1) Markovian with regards to a given corpus and 2) follows metrical rules expressed as cumulative cost functions. Additionally, meter can simultaneously enforce cardinality constraints. We propose a domain consistency algorithm whose complexity is pseudo-polynomial. This result is obtained thanks to a theorem on the growth of sumsets by Khovanskii. We illustrate our constraint on meter-constrained music generation problems that were so far not solvable by any other technique.

When used for structured regression, powerful Conditional Random Fields (CRFs) are typically restricted to modeling effects of interactions among examples in local neighborhoods. Using more expressive representation would result in dense graphs, making these methods impractical for large-scale applications. To address this issue, we propose an effective CRF model with linear scale-up properties regarding approximate learning and inference for structured regression on large, fully connected graphs. The proposed method is validated on real-world large-scale problems of image de-noising and remote sensing. In conducted experiments, we demonstrated that dense connectivity provides an improvement in prediction accuracy. Inference time of less than ten seconds on graphs with millions of nodes and trillions of edges makes the proposed model an attractive tool for large-scale, structured regression problems.

Several mechanisms have been proposed for incentivizing truthful reports of a private signals owned by rational agents, among them the peer prediction method and the Bayesian truth serum. The robust Bayesian truth serum (RBTS) for small populations and binary signals is particularly interesting since it does not require a common prior to be known to the mechanism. We further analyze the problem of the common prior not known to the mechanism and give several results regarding the restrictions that need to be placed in order to have an incentive-compatible mechanism. Moreover, we construct a Bayes-Nash incentive-compatible scheme called multi-valued RBTS that generalizes RBTS to operate on both small populations and non-binary signals.

Minimal explanations of infeasibility find a wide range of uses. In the Boolean domain, these are referred to as Minimal Unsatisfiable Subsets (MUSes). In some settings, one needs to enumerate MUSes of a Boolean formula. Most often the goal is to enumerate all MUSes. In cases where this is computationally infeasible, an alternative is to enumerate some MUSes. This paper develops a novel approach for partial enumeration of MUSes, that complements existing alternatives. If the enumeration of all MUSes is viable, then existing alternatives represent the best option. However, for formulas where the enumeration of all MUSes is unrealistic, our approach provides a solution for enumerating some MUSes within a given time bound. The experimental results focus on formulas for which existing solutions are unable to enumerate MUSes, and shows that the new approach can in most cases enumerate a non-negligible number of MUSes within a given time bound.

We consider a multi-agent scenario where a collection of agents needs to select a common decision from a large set of decisions over which they express their preferences. This decision set has a combinatorial structure, that is, each decision is an element of the Cartesian product of the domains of some variables. Agents express their preferences over the decisions via soft constraints. We consider both sequential preference aggregation methods (they aggregate the preferences over one variable at a time) and one-step methods and we study the computational complexity of influencing them through bribery. We prove that bribery is NPcomplete for the sequential aggregation methods (based on Plurality, Approval, and Borda) for most of the cost schemes we defined, while it is polynomial for one-step Plurality.

Current exploration algorithms can be classified in two broad categories: Heuristic, and PAC optimal. While numerous researchers have used heuristic approaches such as epsilon-greedy exploration successfully, such approaches lack formal, finite sample guarantees and may need a significant amount of fine-tuning to produce good results. PAC optimal exploration algorithms, on the other hand, offer strong theoretical guarantees but are inapplicable in domains of realistic size. The goal of this paper is to bridge the gap between theory and practice, by introducing C-PACE, an algorithm which offers strong theoretical guarantees and can be applied to interesting, continuous space problems.

Recent deployments of Stackelberg security games (SSG) have led to two competing approaches to handle boundedly rational human adversaries: (1) integrating models of human (adversary) decision-making into the game-theoretic algorithms, and (2) applying robust optimization techniques that avoid adversary modeling. A recent algorithm (MATCH) based on the second approach was shown to outperform the leading modeling-based algorithm even in the presence of significant amount of data. Is there then any value in using human behavior models in solving SSGs? Through extensive experiments with 547 human subjects playing 11102 games in total, we emphatically answer the question in the affirmative, while providing the following key contributions: (i) we show that our algorithm, SU-BRQR, based on a novel integration of human behavior model with the subjective utility function, significantly outperforms both MATCH and its improvements; (ii) we are the first to present experimental results with security intelligence experts, and find that even though the experts are more rational than the Amazon Turk workers, SU-BRQR still outperforms an approach assuming perfect rationality (and to a more limited extent MATCH); (iii) we show the advantage of SU-BRQR in a new, large game setting and demonstrate that sufficient data enables it to improve its performance over MATCH.

A challenging problem in machine learning, information retrieval and computer vision research is how to recover a low-rank representation of the given data in the presence of outliers and missing entries. The L1-norm low-rank matrix factorization (LRMF) has been a popular approach to solving this problem. However, L1-norm LRMF is difficult to achieve due to its non-convexity and non-smoothness, and existing methods are often inefficient and fail to converge to a desired solution. In this paper we propose a novel cyclic weighted median (CWM) method, which is intrinsically a coordinate decent algorithm, for L1-norm LRMF. The CWM method minimizes the objective by solving a sequence of scalar minimization sub-problems, each of which is convex and can be easily solved by the weighted median filter. The extensive experimental results validate that the CWM method outperforms state-of-the-arts in terms of both accuracy and computational efficiency.

Collusion is the practice of two or more parties deliberately cooperating to the detriment of others. While such behavior may be desirable in certain circumstances, in many it is considered dishonest and unfair. If agents otherwise hold strictly to the established rules, though, collusion can be challenging to police. In this paper, we introduce an automatic method for collusion detection in sequential games. We achieve this through a novel object, called a collusion table, that captures the effects of collusive behavior, i.e., advantage to the colluding parties, without assuming any particular pattern of behavior. We show the effectiveness of this method in the domain of poker, a popular game where collusion is prohibited.