Determining interactions between entities and the overall organization and clustering of nodes in networks is a major challenge when analyzing biological and social network data. Here we extend the Indian Buffet Process (IBP), a nonparametric Bayesian model, to integrate noisy interaction scores with properties of individual entities for inferring interaction networks and clustering nodes within these networks. We present an application of this method to study how microRNAs regulate mRNAs in cells. Analysis of synthetic and real data indicates that the method improves upon prior methods, correctly recovers interactions and clusters, and provides accurate biological predictions.

State-of-the-art statistical methods in neuroscience have enabled us to fit mathematical models to experimental data and subsequently to infer the dynamics of hidden parameters underlying the observable phenomena. Here, we develop a Bayesian method for inferring the time-varying mean and variance of the synaptic input, along with the dynamics of each ion channel from a single voltage trace of a neuron. An estimation problem may be formulated on the basis of the state-space model with prior distributions that penalize large fluctuations in these parameters. After optimizing the hyperparameters by maximizing the marginal likelihood, the state-space model provides the time-varying parameters of the input signals and the ion channel states. The proposed method is tested not only on the simulated data from the Hodgkin-Huxley type models but also on experimental data obtained from a cortical slice in vitro.

Cancer has complex patterns of progression that include converging as well as diverging progressional pathways. Vogelstein's path model of colon cancer was a pioneering contribution to cancer research. Since then, several attempts have been made at obtaining mathematical models of cancer progression, devising learning algorithms, and applying these to cross-sectional data. Beerenwinkel {\em et al.} provided, what they coined, EM-like algorithms for Oncogenetic Trees (OTs) and mixtures of such. Given the small size of current and future data sets, it is important to minimize the number of parameters of a model. For this reason, we too focus on tree-based models and introduce Hidden-variable Oncogenetic Trees (HOTs). In contrast to OTs, HOTs allow for errors in the data and thereby provide more realistic modeling. We also design global structural EM algorithms for learning HOTs and mixtures of HOTs (HOT-mixtures). The algorithms are global in the sense that, during the M-step, they find a structure that yields a global maximum of the expected complete log-likelihood rather than merely one that improves it. The algorithm for single HOTs performs very well on reasonable-sized data sets, while that for HOT-mixtures requires data sets of sizes obtainable only with tomorrow's more cost-efficient technologies.

There is much evidence that humans and other animals utilize a combination of model-based and model-free RL methods. Although it has been proposed that these systems may dominate according to their relative statistical efficiency in different circumstances, there is little specific evidence -- especially in humans -- as to the details of this trade-off. Accordingly, we examine the relative performance of different RL approaches under situations in which the statistics of reward are differentially noisy and volatile. Using theory and simulation, we show that model-free TD learning is relatively most disadvantaged in cases of high volatility and low noise. We present data from a decision-making experiment manipulating these parameters, showing that humans shift learning strategies in accord with these predictions. The statistical circumstances favoring model-based RL are also those that promote a high learning rate, which helps explain why, in psychology, the distinction between these strategies is traditionally conceived in terms of rule-based vs. incremental learning.

Computing a good strategy in a large extensive form game often demands an extraordinary amount of computer memory, necessitating the use of abstraction to reduce the game size. Typically, strategies from abstract games perform better in the real game as the granularity of abstraction is increased. This paper investigates two techniques for stitching a base strategy in a coarse abstraction of the full game tree, to expert strategies in fine abstractions of smaller subtrees. We provide a general framework for creating static experts, an approach that generalizes some previous strategy stitching efforts. In addition, we show that static experts can create strong agents for both 2-player and 3-player Leduc and Limit Texas Hold'em poker, and that a specific class of static experts can be preferred among a number of alternatives. Furthermore, we describe a poker agent that used static experts and won the 3-player events of the 2010 Annual Computer Poker Competition.

There is a growing trend towards the convergence of cyber-physical systems (CPS) and social computing, which will lead to the emergence of smart communities composed of various objects (including both human individuals and physical things) that interact and cooperate with each other. These smart communities promise to enable a number of innovative applications and services that will improve the quality of life. This position paper addresses some opportunities and challenges of building smart communities characterized by cyber-physical and social intelligence.

The problem of adversarial multi-robot patrol has gained interest in recent years, mainly due to its immediate relevance to various security applications. In this problem, robots are required to repeatedly visit a target area in a way that maximizes their chances of detecting an adversary trying to penetrate through the patrol path. When facing a strong adversary that knows the patrol strategy of the robots, if the robots use a deterministic patrol algorithm, then in many cases it is easy for the adversary to penetrate undetected (in fact, in some of those cases the adversary can guarantee penetration). Therefore this paper presents a non-deterministic patrol framework for the robots. Assuming that the strong adversary will take advantage of its knowledge and try to penetrate through the patrol's weakest spot, hence an optimal algorithm is one that maximizes the chances of detection in that point. We therefore present a polynomial-time algorithm for determining an optimal patrol under the Markovian strategy assumption for the robots, such that the probability of detecting the adversary in the patrol's weakest spot is maximized. We build upon this framework and describe an optimal patrol strategy for several robotic models based on their movement abilities (directed or undirected) and sensing abilities (perfect or imperfect), and in different environment models - either patrol around a perimeter (closed polygon) or an open fence (open polyline).

We describe Dr.Fill, a program that solves American-style crossword puzzles. From a technical perspective, Dr.Fill works by converting crosswords to weighted CSPs, and then using a variety of novel techniques to find a solution. These techniques include generally applicable heuristics for variable and value selection, a variant of limited discrepancy search, and postprocessing and partitioning ideas. Branch and bound is not used, as it was incompatible with postprocessing and was determined experimentally to be of little practical value. Dr.Filll's performance on crosswords from the American Crossword Puzzle Tournament suggests that it ranks among the top fifty or so crossword solvers in the world.

Often, high dimensional data lie close to a low-dimensional submanifold and it is of interest to understand the geometry of these submanifolds. The homology groups of a manifold are important topological invariants that provide an algebraic summary of the manifold. These groups contain rich topological information, for instance, about the connected components, holes, tunnels and sometimes the dimension of the manifold. In this paper, we consider the statistical problem of estimating the homology of a manifold from noisy samples under several different noise models. We derive upper and lower bounds on the minimax risk for this problem. Our upper bounds are based on estimators which are constructed from a union of balls of appropriate radius around carefully selected points. In each case we establish complementary lower bounds using Le Cam's lemma.

Let us envision a new class of IT systems, the "Support Systems for Knowledge Works" or SSKW. An SSKW can be defined as a system built for providing comprehensive support to human knowledge-workers while performing instances of complex knowledge-works of a particular type within a particular domain of professional activities. To get an idea what an SSKW-enabled work environment can be like, let us look into a hypothetical scenario that depicts the interaction between a physician and a patient-care SSKW during the activity of diagnosing a patient. The patient-care task is practiced by healthcare professionals, typically within organizational setups like hospitals. An instance of the task, known as a case, is carried out by a group of professionals (physicians, surgeons, nurses, laboratory technicians etc.) led by a physician (often known as the lead physician for the case) with the primary goal of restoring an ailing patient to state of health. However, the performance also serves various secondary goals achieved through capture and reuse of information about the case. The overall task is usually divided into subtasks or activities such as examination, identification of possible diseases, clinical tests, diagnosis, treatment, followup etc. The actions taken during these activities and their results have complex interrelationships. The patient-care SSKW realizes an integrated ITbased system platform which supports all the constituent activities in ways consistent with their interrelationships. Our hypothetical scenario depicts a particular activity by the lead physician (shall be referred as LP hereafter), i.e., diagnosing a patient P with the help of a patient-care SSKW. Making a diagnosis results in identifying a particular disease based on available evidence (e.g., symptoms, signs and medical history of the patient, results of various clinical tests conducted) for which the patient will be treated. Such a scenario is described below.