How can we model networks with a mathematically tractable model that allows for rigorous analysis of network properties? Networks exhibit a long list of surprising properties: heavy tails for the degree distribution; small diameters; and densification and shrinking diameters over time. Most present network models either fail to match several of the above properties, are complicated to analyze mathematically, or both. In this paper we propose a generative model for networks that is both mathematically tractable and can generate networks that have the above mentioned properties. Our main idea is to use the Kronecker product to generate graphs that we refer to as "Kronecker graphs". First, we prove that Kronecker graphs naturally obey common network properties. We also provide empirical evidence showing that Kronecker graphs can effectively model the structure of real networks. We then present KronFit, a fast and scalable algorithm for fitting the Kronecker graph generation model to large real networks. A naive approach to fitting would take super- exponential time. In contrast, KronFit takes linear time, by exploiting the structure of Kronecker matrix multiplication and by using statistical simulation techniques. Experiments on large real and synthetic networks show that KronFit finds accurate parameters that indeed very well mimic the properties of target networks. Once fitted, the model parameters can be used to gain insights about the network structure, and the resulting synthetic graphs can be used for null- models, anonymization, extrapolations, and graph summarization.

The perennial problem of "how many clusters?" remains an issue of substantial interest in data mining and machine learning communities, and becomes particularly salient in large data sets such as populational genomic data where the number of clusters needs to be relatively large and open-ended. This problem gets further complicated in a co-clustering scenario in which one needs to solve multiple clustering problems simultaneously because of the presence of common centroids (e.g., ancestors) shared by clusters (e.g., possible descents from a certain ancestor) from different multiple-cluster samples (e.g., different human subpopulations). In this paper we present a hierarchical nonparametric Bayesian model to address this problem in the context of multi-population haplotype inference. Uncovering the haplotypes of single nucleotide polymorphisms is essential for many biological and medical applications. While it is uncommon for the genotype data to be pooled from multiple ethnically distinct populations, few existing programs have explicitly leveraged the individual ethnic information for haplotype inference. In this paper we present a new haplotype inference program, Haploi, which makes use of such information and is readily applicable to genotype sequences with thousands of SNPs from heterogeneous populations, with competent and sometimes superior speed and accuracy comparing to the state-of-the-art programs. Underlying Haploi is a new haplotype distribution model based on a nonparametric Bayesian formalism known as the hierarchical Dirichlet process, which represents a tractable surrogate to the coalescent process. The proposed model is exchangeable, unbounded, and capable of coupling demographic information of different populations.

We propose a family of statistical models for social network evolution over time, which represents an extension of Exponential Random Graph Models (ERGMs). Many of the methods for ERGMs are readily adapted for these models, including maximum likelihood estimation algorithms. We discuss models of this type and their properties, and give examples, as well as a demonstration of their use for hypothesis testing and classification. We believe our temporal ERG models represent a useful new framework for modeling time-evolving social networks, and rewiring networks from other domains such as gene regulation circuitry, and communication networks.

Many real-world decision making tasks require us to choose among several expensive observations. In a sensor network, for example, it is important to select the subset of sensors that is expected to provide the strongest reduction in uncertainty. In medical decision making tasks, one needs to select which tests to administer before deciding on the most effective treatment. It has been general practice to use heuristic-guided procedures for selecting observations. In this paper, we present the first efficient optimal algorithms for selecting observations for a class of probabilistic graphical models. For example, our algorithms allow to optimally label hidden variables in Hidden Markov Models (HMMs). We provide results for both selecting the optimal subset of observations, and for obtaining an optimal conditional observation plan. Furthermore we prove a surprising result: In most graphical models tasks, if one designs an efficient algorithm for chain graphs, such as HMMs, this procedure can be generalized to polytree graphical models. We prove that the optimizing value of information is $NP^{PP}$-hard even for polytrees. It also follows from our results that just computing decision theoretic value of information objective functions, which are commonly used in practice, is a #P-complete problem even on Naive Bayes models (a simple special case of polytrees). In addition, we consider several extensions, such as using our algorithms for scheduling observation selection for multiple sensors. We demonstrate the effectiveness of our approach on several real-world datasets, including a prototype sensor network deployment for energy conservation in buildings.

Burst contention is a well-known challenging problem in Optical Burst Switching (OBS) networks. Contention resolution approaches are always reactive and attempt to minimize the BLR based on local information available at the core node. On the other hand, a proactive approach that avoids burst losses before they occur is desirable. To reduce the probability of burst contention, a more robust routing algorithm than the shortest path is needed. This paper proposes a new routing mechanism for JET-based OBS networks, called Graphical Probabilistic Routing Model (GPRM) that selects less utilized links, on a hop-by-hop basis by using a bayesian network. We assume no wavelength conversion and no buffering to be available at the core nodes of the OBS network. We simulate the proposed approach under dynamic load to demonstrate that it reduces the Burst Loss Ratio (BLR) compared to static approaches by using Network Simulator 2 (ns-2) on NSFnet network topology and with realistic traffic matrix. Simulation results clearly show that the proposed approach outperforms static approaches in terms of BLR.

We present a procedure for effective estimation of entropy and mutual information from small-sample data, and apply it to the problem of inferring high-dimensional gene association networks. Specifically, we develop a James-Stein-type shrinkage estimator, resulting in a procedure that is highly efficient statistically as well as computationally. Despite its simplicity, we show that it outperforms eight other entropy estimation procedures across a diverse range of sampling scenarios and data-generating models, even in cases of severe undersampling. We illustrate the approach by analyzing E. coli gene expression data and computing an entropy-based gene-association network from gene expression data. A computer program is available that implements the proposed shrinkage estimator.

We present two algorithms for learning the structure of a Markov network from data: GSMN* and GSIMN. Both algorithms use statistical independence tests to infer the structure by successively constraining the set of structures consistent with the results of these tests. Until very recently, algorithms for structure learning were based on maximum likelihood estimation, which has been proved to be NP-hard for Markov networks due to the difficulty of estimating the parameters of the network, needed for the computation of the data likelihood. The independence-based approach does not require the computation of the likelihood, and thus both GSMN* and GSIMN can compute the structure efficiently (as shown in our experiments). GSMN* is an adaptation of the Grow-Shrink algorithm of Margaritis and Thrun for learning the structure of Bayesian networks. GSIMN extends GSMN* by additionally exploiting Pearl's well-known properties of the conditional independence relation to infer novel independences from known ones, thus avoiding the performance of statistical tests to estimate them. To accomplish this efficiently GSIMN uses the Triangle theorem, also introduced in this work, which is a simplified version of the set of Markov axioms. Experimental comparisons on artificial and real-world data sets show GSIMN can yield significant savings with respect to GSMN*, while generating a Markov network with comparable or in some cases improved quality. We also compare GSIMN to a forward-chaining implementation, called GSIMN-FCH, that produces all possible conditional independences resulting from repeatedly applying Pearl's theorems on the known conditional independence tests. The results of this comparison show that GSIMN, by the sole use of the Triangle theorem, is nearly optimal in terms of the set of independences tests that it infers.

Many fields have a need to build representative or predictive models from a number of unique individuals who each can contribute their experience and beliefs to the whole. For instance, intelligence agencies may wish to build a model from a number of experts to analyze potential terrorist attacks. In addition, a sociological survey may want a model representing the beliefs of cultural or political groups. However, challenges remain that have limited the success of merging opinions to form consensus models. Our research in progress presents a new approach to combine, or aggregate the beliefs of many individuals using graphical models. Existing Bayesian belief aggregation methods utilize an opinion pool function to find a single consensus on a given probability distribution. These opinion pool functions have many theoretical problems including breaking several assumptions for Bayesian reasoning. More practically, existing opinion pool functions do not represent reality well, especially in cases of diverse opinions.

Spam filtering, as a key problem in electronic communication, has drawn significant attention due to increasingly huge amounts of junk email on the Internet. Content-based filtering is one reliable method in combating with spammers' changing tactics. Naive Bayes (NB) is one of the earliest content-based machine learning methods both in theory and practice in combating with spammers, which is easy to implement while can achieve considerable accuracy. In this paper, the traditional online Bayesian classifier are enhanced  by two ways. First, from theory's point of view, we devise a self-adaptive mechanism to gradually weaken the assumption of independence required by original NB in the online training process, and as a result of that our NSNB is no longer ``naive''. Second, we propose other engineering ways to make the classifier more robust and accuracy. The experiment results show that our NSNB does give state-of-the-art classification performance on online spam filtering on large benchmark data sets while it is extremely fast and takes up little memory in comparison with other statistical methods.

We describe a new method for visualizing topics, the distributions over terms that are automatically extracted from large text corpora using latent variable models. Our method finds significant $n$-grams related to a topic, which are then used to help understand and interpret the underlying distribution. Compared with the usual visualization, which simply lists the most probable topical terms, the multi-word expressions provide a better intuitive impression for what a topic is "about." Our approach is based on a language model of arbitrary length expressions, for which we develop a new methodology based on nested permutation tests to find significant phrases. We show that this method outperforms the more standard use of $\chi^2$ and likelihood ratio tests. We illustrate the topic presentations on corpora of scientific abstracts and news articles.