Networks are ubiquitous in science and have become a focal point for discussion in everyday life. Formal statistical models for the analysis of network data have emerged as a major topic of interest in diverse areas of study, and most of these involve a form of graphical representation. Probability models on graphs date back to 1959. Along with empirical studies in social psychology and sociology from the 1960s, these early works generated an active network community and a substantial literature in the 1970s. This effort moved into the statistical literature in the late 1970s and 1980s, and the past decade has seen a burgeoning network literature in statistical physics and computer science. The growth of the World Wide Web and the emergence of online networking communities such as Facebook, MySpace, and LinkedIn, and a host of more specialized professional network communities has intensified interest in the study of networks and network data. Our goal in this review is to provide the reader with an entry point to this burgeoning literature. We begin with an overview of the historical development of statistical network modeling and then we introduce a number of examples that have been studied in the network literature. Our subsequent discussion focuses on a number of prominent static and dynamic network models and their interconnections. We emphasize formal model descriptions, and pay special attention to the interpretation of parameters and their estimation. We end with a description of some open problems and challenges for machine learning and statistics.

In this paper, we propose causality as a unified framework to explain query answers and non-answers, thus generalizing and extending several previously proposed approaches of provenance and missing query result explanations. We develop our framework starting from the well-studied definition of actual causes by Halpern and Pearl. After identifying some undesirable characteristics of the original definition, we propose functional causes as a refined definition of causality with several desirable properties. These properties allow us to apply our notion of causality in a database context and apply it uniformly to define the causes of query results and their individual contributions in several ways: (i) we can model both provenance as well as non-answers, (ii) we can define explanations as either data in the input relations or relational operations in a query plan, and (iii) we can give graded degrees of responsibility to individual causes, thus allowing us to rank causes. In particular, our approach allows us to explain contributions to relational aggregate functions and to rank causes according to their respective responsibilities. We give complexity results and describe polynomial algorithms for evaluating causality in tractable cases. Throughout the paper, we illustrate the applicability of our framework with several examples. Overall, we develop in this paper the theoretical foundations of causality theory in a database context.

This paper presents several new tractability results for planning based on macros. We describe an algorithm that optimally solves planning problems in a class that we call inverted tree reducible, and is provably tractable for several subclasses of this class. By using macros to store partial plans that recur frequently in the solution, the algorithm is polynomial in time and space even for exponentially long plans. We generalize the inverted tree reducible class in several ways and describe modifications of the algorithm to deal with these new classes. Theoretical results are validated in experiments.

The problem is sequence prediction in the following setting. A sequence $x_1,...,x_n,...$ of discrete-valued observations is generated according to some unknown probabilistic law (measure) $\mu$. After observing each outcome, it is required to give the conditional probabilities of the next observation. The measure $\mu$ belongs to an arbitrary but known class $C$ of stochastic process measures. We are interested in predictors $\rho$ whose conditional probabilities converge (in some sense) to the "true" $\mu$-conditional probabilities if any $\mu\in C$ is chosen to generate the sequence. The contribution of this work is in characterizing the families $C$ for which such predictors exist, and in providing a specific and simple form in which to look for a solution. We show that if any predictor works, then there exists a Bayesian predictor, whose prior is discrete, and which works too. We also find several sufficient and necessary conditions for the existence of a predictor, in terms of topological characterizations of the family $C$, as well as in terms of local behaviour of the measures in $C$, which in some cases lead to procedures for constructing such predictors. It should be emphasized that the framework is completely general: the stochastic processes considered are not required to be i.i.d., stationary, or to belong to any parametric or countable family.

This paper formulates a necessary and sufficient condition for a generic graph matching problem to be equivalent to the maximum vertex and edge weight clique problem in a derived association graph. The consequences of this results are threefold: first, the condition is general enough to cover a broad range of practical graph matching problems; second, a proof to establish equivalence between graph matching and clique search reduces to showing that a given graph matching problem satisfies the proposed condition; and third, the result sets the scene for generic continuous solutions for a broad range of graph matching problems. To illustrate the mathematical framework, we apply it to a number of graph matching problems, including the problem of determining the graph edit distance.

This paper extends k-means algorithms from the Euclidean domain to the domain of graphs. To recompute the centroids, we apply subgradient methods for solving the optimization-based formulation of the sample mean of graphs. To accelerate the k-means algorithm for graphs without trading computational time against solution quality, we avoid unnecessary graph distance calculations by exploiting the triangle inequality of the underlying distance metric following Elkan's k-means algorithm proposed in \cite{Elkan03}. In experiments we show that the accelerated k-means algorithm are faster than the standard k-means algorithm for graphs provided there is a cluster structure in the data.

We introduce the Reduced-Rank Hidden Markov Model (RR-HMM), a generalization of HMMs that can model smooth state evolution as in Linear Dynamical Systems (LDSs) as well as non-log-concave predictive distributions as in continuous-observation HMMs. RR-HMMs assume an m-dimensional latent state and n discrete observations, with a transition matrix of rank k <= m. This implies the dynamics evolve in a k-dimensional subspace, while the shape of the set of predictive distributions is determined by m. Latent state belief is represented with a k-dimensional state vector and inference is carried out entirely in R^k, making RR-HMMs as computationally efficient as k-state HMMs yet more expressive. To learn RR-HMMs, we relax the assumptions of a recently proposed spectral learning algorithm for HMMs (Hsu, Kakade and Zhang 2009) and apply it to learn k-dimensional observable representations of rank-k RR-HMMs. The algorithm is consistent and free of local optima, and we extend its performance guarantees to cover the RR-HMM case. We show how this algorithm can be used in conjunction with a kernel density estimator to efficiently model high-dimensional multivariate continuous data. We also relax the assumption that single observations are sufficient to disambiguate state, and extend the algorithm accordingly. Experiments on synthetic data and a toy video, as well as on a difficult robot vision modeling problem, yield accurate models that compare favorably with standard alternatives in simulation quality and prediction capability.

We study clustering algorithms based on neighborhood graphs on a random sample of data points. The question we ask is how such a graph should be constructed in order to obtain optimal clustering results. Which type of neighborhood graph should one choose, mutual k-nearest neighbor or symmetric k-nearest neighbor? What is the optimal parameter k? In our setting, clusters are defined as connected components of the t-level set of the underlying probability distribution. Clusters are said to be identified in the neighborhood graph if connected components in the graph correspond to the true underlying clusters. Using techniques from random geometric graph theory, we prove bounds on the probability that clusters are identified successfully, both in a noise-free and in a noisy setting. Those bounds lead to several conclusions. First, k has to be chosen surprisingly high (rather of the order n than of the order log n) to maximize the probability of cluster identification. Secondly, the major difference between the mutual and the symmetric k-nearest neighbor graph occurs when one attempts to detect the most significant cluster only.

Boolean Satisfiability (SAT) solvers are now routinely used in the verification of large industrial problems. However, their application in safety-critical domains such as the railways, avionics, and automotive industries requires some form of assurance for the results, as the solvers can (and sometimes do) have bugs. Unfortunately, the complexity of modern, highly optimized SAT solvers renders impractical the development of direct formal proofs of their correctness. This paper presents an alternative approach where an untrusted, industrial-strength, SAT solver is plugged into a trusted, formally certified, SAT proof checker to provide industrial-strength certified SAT solving. The key novelties and characteristics of our approach are (i) that the checker is automatically extracted from the formal development, (ii), that the combined system can be used as a standalone executable program independent of any supporting theorem prover, and (iii) that the checker certifies any SAT solver respecting the agreed format for satisfiability and unsatisfiability claims. The core of the system is a certified checker for unsatisfiability claims that is formally designed and verified in Coq. We present its formal design and outline the correctness proofs. The actual standalone checker is automatically extracted from the the Coq development. An evaluation of the certified checker on a representative set of industrial benchmarks from the SAT Race Competition shows that, albeit it is slower than uncertified SAT checkers, it is significantly faster than certified checkers implemented on top of an interactive theorem prover.

We extend multi-way, multivariate ANOVA-type analysis to cases where one covariate is the view, with features of each view coming from different, high-dimensional domains. The different views are assumed to be connected by having paired samples; this is a common setup in recent bioinformatics experiments, of which we analyze metabolite profiles in different conditions (disease vs. control and treatment vs. untreated) in different tissues (views). We introduce a multi-way latent variable model for this new task, by extending the generative model of Bayesian canonical correlation analysis (CCA) both to take multi-way covariate information into account as population priors, and by reducing the dimensionality by an integrated factor analysis that assumes the metabolites to come in correlated groups.