External information propagates in the cell mainly through signaling cascades and transcriptional activation, allowing it to react to a wide spectrum of environmental changes. High throughput experiments identify numerous molecular components of such cascades that may, however, interact through unknown partners. Some of them may be detected using data coming from the integration of a protein-protein interaction network and mRNA expression profiles. This inference problem can be mapped onto the problem of finding appropriate optimal connected subgraphs of a network defined by these datasets. The optimization procedure turns out to be computationally intractable in general. Here we present a new distributed algorithm for this task, inspired from statistical physics, and apply this scheme to alpha factor and drug perturbations data in yeast. We identify the role of the COS8 protein, a member of a gene family of previously unknown function, and validate the results by genetic experiments. The algorithm we present is specially suited for very large datasets, can run in parallel, and can be adapted to other problems in systems biology. On renowned benchmarks it outperforms other algorithms in the field.

We consider the problem of analyzing the heterogeneity of clustering distributions for multiple groups of observed data, each of which is indexed by a covariate value, and inferring global clusters arising from observations aggregated over the covariate domain. We propose a novel Bayesian nonparametric method reposing on the formalism of spatial modeling and a nested hierarchy of Dirichlet processes. We provide an analysis of the model properties, relating and contrasting the notions of local and global clusters. We also provide an efficient inference algorithm, and demonstrate the utility of our method in several data examples, including the problem of object tracking and a global clustering analysis of functional data where the functional identity information is not available.

Engineered systems are designed to deftly operate under predetermined conditions yet are notoriously fragile when unexpected perturbations arise. In contrast, biological systems operate in a highly flexible manner; learn quickly adequate responses to novel conditions, and evolve new routines/traits to remain competitive under persistent environmental change. A recent theory on the origins of biological flexibility has proposed that degeneracy - the existence of multi-functional components with partially overlapping functions - is a primary determinant of the robustness and adaptability found in evolved systems. While degeneracy's contribution to biological flexibility is well documented, there has been little investigation of degeneracy design principles for achieving flexibility in systems engineering. Actually, the conditions that can lead to degeneracy are routinely eliminated in engineering design. With the planning of transportation vehicle fleets taken as a case study, this paper reports evidence that degeneracy improves robustness and adaptability of a simulated fleet without incurring costs to efficiency. We find degeneracy dramatically increases robustness of a fleet to unpredicted changes in the environment while it also facilitates robustness to anticipated variations. When we allow a fleet's architecture to be adapted in response to environmental change, we find degeneracy can be selectively acquired, leading to faster rates of design adaptation and ultimately to better designs. Given the range of conditions where favorable short-term and long-term performance outcomes are observed, we propose that degeneracy design principles fundamentally alter the propensity for adaptation and may be useful within several engineering and planning contexts.

The context of a software developer is something hard to define and capture, as it represents a complex network of elements across different dimensions that are not limited to the work developed on an IDE. We propose the definition of a software developer context model that takes into account all the dimensions that characterize the work environment of the developer. We are especially focused on what the software developer context encompasses at the project level and how it can be captured. The experimental work done so far show that useful context information can be extracted from project management tools. The extraction, analysis and availability of this context information can be used to enrich the work environment of the developer with additional knowledge to support her/his work.

Weighted voting is a classic model of cooperation among agents in decision-making domains. In such games, each player has a weight, and a coalition of players wins the game if its total weight meets or exceeds a given quota. A player's power in such games is usually not directly proportional to his weight, and is measured by a power index, the most prominent among which are the Shapley-Shubik index and the Banzhaf index.In this paper, we investigate by how much a player can change his power, as measured by the Shapley-Shubik index or the Banzhaf index, by means of a false-name manipulation, i.e., splitting his weight among two or more identities. For both indices, we provide upper and lower bounds on the effect of weight-splitting. We then show that checking whether a beneficial split exists is NP-hard, and discuss efficient algorithms for restricted cases of this problem, as well as randomized algorithms for the general case. We also provide an experimental evaluation of these algorithms. Finally, we examine related forms of manipulative behavior, such as annexation, where a player subsumes other players, or merging, where several players unite into one. We characterize the computational complexity of such manipulations and provide limits on their effects. For the Banzhaf index, we describe a new paradox, which we term the Annexation Non-monotonicity Paradox.

We introduce a novel logical notion--partial entailment--to propositional logic. In contrast with classical entailment, that a formula P partially entails another formula Q with respect to a background formula set \Gamma intuitively means that under the circumstance of \Gamma, if P is true then some "part" of Q will also be true. We distinguish three different kinds of partial entailments and formalize them by using an extended notion of prime implicant. We study their semantic properties, which show that, surprisingly, partial entailments fail for many simple inference rules. Then, we study the related computational properties, which indicate that partial entailments are relatively difficult to be computed. Finally, we consider a potential application of partial entailments in reasoning about rational agents.

We motivate and analyse a new Tree Search algorithm, GPTS, based on recent theoretical advances in the use of Gaussian Processes for Bandit problems. We consider tree paths as arms and we assume the target/reward function is drawn from a GP distribution. The posterior mean and variance, after observing data, are used to define confidence intervals for the function values, and we sequentially play arms with highest upper confidence bounds. We give an efficient implementation of GPTS and we adapt previous regret bounds by determining the decay rate of the eigenvalues of the kernel matrix on the whole set of tree paths. We consider two kernels in the feature space of binary vectors indexed by the nodes of the tree: linear and Gaussian. The regret grows in square root of the number of iterations T, up to a logarithmic factor, with a constant that improves with bigger Gaussian kernel widths. We focus on practical values of T, smaller than the number of arms. Finally, we apply GPTS to Open Loop Planning in discounted Markov Decision Processes by modelling the reward as a discounted sum of independent Gaussian Processes. We report similar regret bounds to those of the OLOP algorithm.

Computational pool is a relatively recent entrant into the group of games played by computer agents. It features a unique combination of properties that distinguish it from oth- ers such games, including continuous action and state spaces, uncertainty in execution, a unique turn-taking structure, and of course an adversarial nature. This article discusses some of the work done to date, focusing on the software side of the pool-playing problem. We discuss in some depth CueCard, the program that won the 2008 computational pool tournament. Research questions and ideas spawned by work on this problem are also discussed. We close by announcing the 2011 computational pool tournament, which will take place in conjunction with the Twenty-Fifth AAAI Conference.

The basic notion of false-name-proofness allows for useful mechanisms under certain circumstances, but in general there are impossibility results that show that false-name-proof mechanisms have severe limitations. One may react to these impossibility results by saying that, since false-name-proof mechanisms are unsatisfactory, we should not run any important mechanisms in highly anonymous settings—unless, perhaps, we can find some methodology that directly prevents false-name manipulation even in such settings, so that we are back in a more typical mechanism design context. However, it seems unlikely that the phenomenon of false-name manipulation will disappear anytime soon. Because the Internet is so attractive as a platform for running certain types of mechanisms, it seems unlikely that the organizations running these mechanisms will take them offline. Moreover, because a goal of these organizations is often to get as many users to participate as possible, they will be reluctant to use high-overhead solutions that discourage users from participating. As a result, perhaps the most promising approaches at this point are those that combine techniques from mechanism design with other techniques discussed in this article. It appears that this is a rich domain for new, creative approaches that can have significant practical impact.

This article includes forthcoming AAAI sponsored conferences, conferences presented by AAAI Affiliates, and conferences held in cooperation with AAAI.