Ranking relations using analogies in biological and information networks

Analogical reasoning depends fundamentally on the ability to learn and generalize about relations between objects. We develop an approach to relational learning which, given a set of pairs of objects $\mathbf{S}=\{A^{(1)}:B^{(1)},A^{(2)}:B^{(2)},\ldots,A^{(N)}:B ^{(N)}\}$, measures how well other pairs A:B fit in with the set $\mathbf{S}$. Our work addresses the following question: is the relation between objects A and B analogous to those relations found in $\mathbf{S}$? Such questions are particularly relevant in information retrieval, where an investigator might want to search for analogous pairs of objects that match the query set of interest. There are many ways in which objects can be related, making the task of measuring analogies very challenging. Our approach combines a similarity measure on function spaces with Bayesian analysis to produce a ranking. It requires data containing features of the objects of interest and a link matrix specifying which relationships exist; no further attributes of such relationships are necessary. We illustrate the potential of our method on text analysis and information networks. An application on discovering functional interactions between pairs of proteins is discussed in detail, where we show that our approach can work in practice even if a small set of protein pairs is provided.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS321 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Edge Label Inference in Generalized Stochastic Block Models: from Spectral Theory to Impossibility Results

The classical setting of community detection consists of networks exhibiting a clustered structure. To more accurately model real systems we consider a class of networks (i) whose edges may carry labels and (ii) which may lack a clustered structure. Specifically we assume that nodes possess latent attributes drawn from a general compact space and edges between two nodes are randomly generated and labeled according to some unknown distribution as a function of their latent attributes. Our goal is then to infer the edge label distributions from a partially observed network. We propose a computationally efficient spectral algorithm and show it allows for asymptotically correct inference when the average node degree could be as low as logarithmic in the total number of nodes. Conversely, if the average node degree is below a specific constant threshold, we show that no algorithm can achieve better inference than guessing without using the observations. As a byproduct of our analysis, we show that our model provides a general procedure to construct random graph models with a spectrum asymptotic to a pre-specified eigenvalue distribution such as a power-law distribution.Comment: 17 page

A survey of statistical network models

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.Comment: 96 pages, 14 figures, 333 reference

Co-evolution of Selection and Influence in Social Networks

Many networks are complex dynamical systems, where both attributes of nodes and topology of the network (link structure) can change with time. We propose a model of co-evolving networks where both node at- tributes and network structure evolve under mutual influence. Specifically, we consider a mixed membership stochastic blockmodel, where the probability of observing a link between two nodes depends on their current membership vectors, while those membership vectors themselves evolve in the presence of a link between the nodes. Thus, the network is shaped by the interaction of stochastic processes describing the nodes, while the processes themselves are influenced by the changing network structure. We derive an efficient variational inference procedure for our model, and validate the model on both synthetic and real-world data.Comment: In Proc. of the Twenty-Fifth Conference on Artificial Intelligence (AAAI-11

Integral projection models for species with complex demography

Matrix projection models occupy a central role in population and conservation biology. Matrix models divide a population into discrete classes, even if the structuring trait exhibits continuous variation ( e. g., body size). The integral projection model ( IPM) avoids discrete classes and potential artifacts from arbitrary class divisions, facilitates parsimonious modeling based on smooth relationships between individual state and demographic performance, and can be implemented with standard matrix software. Here, we extend the IPM to species with complex demographic attributes, including dormant and active life stages, cross- classification by several attributes ( e. g., size, age, and condition), and changes between discrete and continuous structure over the life cycle. We present a general model encompassing these cases, numerical methods, and theoretical results, including stable population growth and sensitivity/ elasticity analysis for density- independent models, local stability analysis in density- dependent models, and optimal/ evolutionarily stable strategy life- history analysis. Our presentation centers on an IPM for the thistle Onopordum illyricum based on a 6- year field study. Flowering and death probabilities are size and age dependent, and individuals also vary in a latent attribute affecting survival, but a predictively accurate IPM is completely parameterized by fitting a few regression equations. The online edition of the American Naturalist includes a zip archive of R scripts illustrating our suggested methods

Topics in social network analysis and network science

This chapter introduces statistical methods used in the analysis of social networks and in the rapidly evolving parallel-field of network science. Although several instances of social network analysis in health services research have appeared recently, the majority involve only the most basic methods and thus scratch the surface of what might be accomplished. Cutting-edge methods using relevant examples and illustrations in health services research are provided