In this paper we investigate the computational complexity of learning the graph structure underlying a discrete undirected graphical model from i.i.d. samples. We first observe that the notoriously difficult problem of learning parities with noise can be captured as a special case of learning graphical models. This leads to an unconditional computational lower bound of $\Omega (p^{d/2})$ for learning general graphical models on $p$ nodes of maximum degree $d$, for the class of so-called statistical algorithms recently introduced by Feldman et al (2013). The lower bound suggests that the $O(p^d)$ runtime required to exhaustively search over neighborhoods cannot be significantly improved without restricting the class of models. Aside from structural assumptions on the graph such as it being a tree, hypertree, tree-like, etc., many recent papers on structure learning assume that the model has the correlation decay property. Indeed, focusing on ferromagnetic Ising models, Bento and Montanari (2009) showed that all known low-complexity algorithms fail to learn simple graphs when the interaction strength exceeds a number related to the correlation decay threshold. Our second set of results gives a class of repelling (antiferromagnetic) models that have the opposite behavior: very strong interaction allows efficient learning in time $O(p^2)$. We provide an algorithm whose performance interpolates between $O(p^2)$ and $O(p^{d+2})$ depending on the strength of the repulsion.

Within the Kolmogorov theory of probability, Bayes' rule allows one to perform statistical inference by relating conditional probabilities to unconditional probabilities. As we show here, however, there is a continuous set of alternative inference rules that yield the same results, and that may have computational or practical advantages for certain problems. We formulate generalized axioms for probability theory, according to which the reverse conditional probability distribution P(B|A) is not specified by the forward conditional probability distribution P(A|B) and the marginals P(A) and P(B). Thus, in order to perform statistical inference, one must specify an additional "inference axiom," which relates P(B|A) to P(A|B), P(A), and P(B). We show that when Bayes' rule is chosen as the inference axiom, the axioms are equivalent to the classical Kolmogorov axioms. We then derive consistency conditions on the inference axiom, and thereby characterize the set of all possible rules for inference. The set of "first-order" inference axioms, defined as the set of axioms in which P(B|A) depends on the first power of P(A|B), is found to be a 1-simplex, with Bayes' rule at one of the extreme points. The other extreme point, the "inversion rule," is studied in depth.

We develop estimation for potentially high-dimensional additive structural equation models. A key component of our approach is to decouple order search among the variables from feature or edge selection in a directed acyclic graph encoding the causal structure. We show that the former can be done with nonregularized (restricted) maximum likelihood estimation while the latter can be efficiently addressed using sparse regression techniques. Thus, we substantially simplify the problem of structure search and estimation for an important class of causal models. We establish consistency of the (restricted) maximum likelihood estimator for low- and high-dimensional scenarios, and we also allow for misspecification of the error distribution. Furthermore, we develop an efficient computational algorithm which can deal with many variables, and the new method's accuracy and performance is illustrated on simulated and real data.

We consider the problem of reconstructing the graph underlying an Ising model from i.i.d. samples. Over the last fifteen years this problem has been of significant interest in the statistics, machine learning, and statistical physics communities, and much of the effort has been directed towards finding algorithms with low computational cost for various restricted classes of models. Nevertheless, for learning Ising models on general graphs with $p$ nodes of degree at most $d$, it is not known whether or not it is possible to improve upon the $p^{d}$ computation needed to exhaustively search over all possible neighborhoods for each node. In this paper we show that a simple greedy procedure allows to learn the structure of an Ising model on an arbitrary bounded-degree graph in time on the order of $p^2$. We make no assumptions on the parameters except what is necessary for identifiability of the model, and in particular the results hold at low-temperatures as well as for highly non-uniform models. The proof rests on a new structural property of Ising models: we show that for any node there exists at least one neighbor with which it has a high mutual information. This structural property may be of independent interest.

In this paper we consider the problem of learning undirected graphical models from data generated according to the Glauber dynamics. The Glauber dynamics is a Markov chain that sequentially updates individual nodes (variables) in a graphical model and it is frequently used to sample from the stationary distribution (to which it converges given sufficient time). Additionally, the Glauber dynamics is a natural dynamical model in a variety of settings. This work deviates from the standard formulation of graphical model learning in the literature, where one assumes access to i.i.d. samples from the distribution. Much of the research on graphical model learning has been directed towards finding algorithms with low computational cost. As the main result of this work, we establish that the problem of reconstructing binary pairwise graphical models is computationally tractable when we observe the Glauber dynamics. Specifically, we show that a binary pairwise graphical model on $p$ nodes with maximum degree $d$ can be learned in time $f(d)p^2\log p$, for a function $f(d)$, using nearly the information-theoretic minimum number of samples.

We discuss two views on extending existing methods for complex network modeling which we dub the communities first and the networks first view, respectively. Inspired by the networks first view that we attribute to White, Boorman, and Breiger (1976)[1], we formulate the multiple-networks stochastic blockmodel (MNSBM), which seeks to separate the observed network into subnetworks of different types and where the problem of inferring structure in each subnetwork becomes easier. We show how this model is specified in a generative Bayesian framework where parameters can be inferred efficiently using Gibbs sampling. The result is an effective multiple-membership model without the drawbacks of introducing complex definitions of "groups" and how they interact. We demonstrate results on the recovery of planted structure in synthetic networks and show very encouraging results on link prediction performances using multiple-networks models on a number of real-world network data sets.

Rodent hippocampal population codes represent important spatial information about the environment during navigation. Several computational methods have been developed to uncover the neural representation of spatial topology embedded in rodent hippocampal ensemble spike activity. Here we extend our previous work and propose a nonparametric Bayesian approach to infer rat hippocampal population codes during spatial navigation. To tackle the model selection problem, we leverage a nonparametric Bayesian model. Specifically, to analyze rat hippocampal ensemble spiking activity, we apply a hierarchical Dirichlet process-hidden Markov model (HDP-HMM) using two Bayesian inference methods, one based on Markov chain Monte Carlo (MCMC) and the other based on variational Bayes (VB). We demonstrate the effectiveness of our Bayesian approaches on recordings from a freely-behaving rat navigating in an open field environment. We find that MCMC-based inference with Hamiltonian Monte Carlo (HMC) hyperparameter sampling is flexible and efficient, and outperforms VB and MCMC approaches with hyperparameters set by empirical Bayes.

We propose a new algorithm called PLUTO for building logistic regression trees to binary response data. PLUTO can capture the nonlinear and interaction patterns in messy data by recursively partitioning the sample space. It fits a simple or a multiple linear logistic regression model in each partition. PLUTO employs the cyclical coordinate descent method for estimation of multiple linear logistic regression models with elastic net penalties, which allows it to deal with high-dimensional data efficiently. The tree structure comprises a graphical description of the data. Together with the logistic regression models, it provides an accurate classifier as well as a piecewise smooth estimate of the probability of "success". PLUTO controls selection bias by: (1) separating split variable selection from split point selection; (2) applying an adjusted chi-squared test to find the split variable instead of exhaustive search. A bootstrap calibration technique is employed to further correct selection bias. Comparison on real datasets shows that on average, the multiple linear PLUTO models predict more accurately than other algorithms.

We present a new package in R implementing Bayesian additive regression trees (BART). The package introduces many new features for data analysis using BART such as variable selection, interaction detection, model diagnostic plots, incorporation of missing data and the ability to save trees for future prediction. It is significantly faster than the current R implementation, parallelized, and capable of handling both large sample sizes and high-dimensional data.

In this report paper we first present a report of the Advanced Machine Learning Course Project on the provided data set and then present a novel heuristic algorithm for exact Bayesian network (BN) structure discovery that uses decomposable scoring functions. Our algorithm follows a different approach to solve the problem of BN structure discovery than the previously used methods such as Dynamic Programming (DP) and Branch and Bound to reduce the search space and find the global optima space for the problem. The algorithm we propose has some degree of flexibility that can make it more or less greedy. The more the algorithm is set to be greedy, the more the speed of the algorithm will be, and the less optimal the final structure. Our algorithm runs in a much less time than the previously known methods and guarantees to have an optimality of close to 99%. Therefore, it sacrifices less than one percent of score of an optimal structure in order to gain a much lower running time and make the algorithm feasible for large data sets (we may note that we never used any toolbox except for result validation)