RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.]

Learning the Structure and Parameters of Large-Population Graphical Games from Behavioral Data

We consider learning, from strictly behavioral data, the structure and parameters of linear influence games (LIGs), a class of parametric graphical games introduced by Irfan and Ortiz (2014). LIGs facilitate causal strategic inference (CSI): Making inferences from causal interventions on stable behavior in strategic settings. Applications include the identification of the most influential individuals in large (social) networks. Such tasks can also support policy-making analysis. Motivated by the computational work on LIGs, we cast the learning problem as maximum-likelihood estimation (MLE) of a generative model defined by pure-strategy Nash equilibria (PSNE). Our simple formulation uncovers the fundamental interplay between goodness-of-fit and model complexity: good models capture equilibrium behavior within the data while controlling the true number of equilibria, including those unobserved. We provide a generalization bound establishing the sample complexity for MLE in our framework. We propose several algorithms including convex loss minimization (CLM) and sigmoidal approximations. We prove that the number of exact PSNE in LIGs is small, with high probability; thus, CLM is sound. We illustrate our approach on synthetic data and real-world U.S. congressional voting records. We briefly discuss our learning framework's generality and potential applicability to general graphical games.Comment: Journal of Machine Learning Research. (accepted, pending publication.) Last conference version: submitted March 30, 2012 to UAI 2012. First conference version: entitled, Learning Influence Games, initially submitted on June 1, 2010 to NIPS 201

Markov Network Structure Learning via Ensemble-of-Forests Models

Real world systems typically feature a variety of different dependency types and topologies that complicate model selection for probabilistic graphical models. We introduce the ensemble-of-forests model, a generalization of the ensemble-of-trees model. Our model enables structure learning of Markov random fields (MRF) with multiple connected components and arbitrary potentials. We present two approximate inference techniques for this model and demonstrate their performance on synthetic data. Our results suggest that the ensemble-of-forests approach can accurately recover sparse, possibly disconnected MRF topologies, even in presence of non-Gaussian dependencies and/or low sample size. We applied the ensemble-of-forests model to learn the structure of perturbed signaling networks of immune cells and found that these frequently exhibit non-Gaussian dependencies with disconnected MRF topologies. In summary, we expect that the ensemble-of-forests model will enable MRF structure learning in other high dimensional real world settings that are governed by non-trivial dependencies.Comment: 13 pages, 6 figure