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Spatio-temporal log-Gaussian Cox process models play a central role in the analysis of spatially distributed systems in several disciplines. Yet, scalable inference remains computationally challenging both due to the high-resolution modeling generally required and the analytically intractable likelihood function. Here, we exploit the sparsity structure typical of (spatially) discretized log-Gaussian Cox process models by using approximate message-passing algorithms. The proposed algorithms scale well with the state dimension and the length of the temporal horizon with moderate loss in distributional accuracy. They hence provide a flexible and faster alternative to both nonlinear filtering-smoothing type algorithms and to approaches that implement the Laplace method or expectation propagation on (block) sparse latent Gaussian models. We infer the parameters of the latent Gaussian model using a structured variational Bayes approach. We demonstrate the proposed framework on simulation studies with both Gaussian and point-process observations and use it to reconstruct the conflict intensity and dynamics in Afghanistan from the WikiLeaks Afghan War Diary. Supplementary materials for this article are available online. [ABSTRACT FROM AUTHOR]

Epistatic interactions play a fundamental role in molecular evolution, but little is known about the spatial distribution of these interactions within genes.To systematically survey a model landscape of intragenic epistasis, we quantified the fitness of ∼60,000 Saccharomyces cerevisiae strains expressing randomly mutated variants of the 333-nucleotide-long U3 small nucleolar RNA (snoRNA).The fitness effects of individual mutations were correlated with evolutionary conservation and structural stability. Many mutations had small individual effects but had large effects in the context of additional mutations, which indicated negative epistasis. Clusters of negative interactions were explained by local thermodynamic threshold effects, whereas positive interactions were enriched among large-effect sites and between base-paired nucleotides.We conclude that high-throughputmapping of intragenic epistasis can identify key structural and functional features of macromolecules. [ABSTRACT FROM AUTHOR]

Background Cell-specific gene expression is controlled by epigenetic modifications and transcription factor binding. While genome-wide maps for these protein-DNA interactions have become widely available, quantitative comparison of the resulting ChIP-Seq data sets remains challenging. Current approaches to detect differentially bound or modified regions are mainly borrowed from RNA-Seq data analysis, thus focusing on total counts of fragments mapped to a region, ignoring any information encoded in the shape of the peaks. Results Here, we present MMDiff, a robust, broadly applicable method for detecting differences between sequence count data sets. Based on quantifying shape changes in signal profiles, it overcomes challenges imposed by the highly structured nature of the data and the paucity of replicates. We first use a simulated data set to compare the performance of MMDiff with results obtained by four alternative methods. We demonstrate that MMDiff excels when peak profiles change between samples. We next use MMDiff to re-analyse a recent data set of the histone modification H3K4me3 elucidating the establishment of this prominent epigenomic marker. Our empirical analysis shows that the method yields reproducible results across experiments, and is able to detect functional important changes in histone modifications. To further explore the broader applicability of MMDiff, we apply it to two ENCODE data sets: one investigating the histone modification H3K27ac and one measuring the genome-wide binding of the transcription factor CTCF. In both cases, MMDiff proves to be complementary to count-based methods. In addition, we can show that MMDiff is capable of directly detecting changes of homotypic binding events at neighbouring binding sites. MMDiff is readily available as a Bioconductor package. Conclusion Our results demonstrate that higher order features of ChIP-Seq peaks carry relevant and often complementary information to total counts, and hence are important in assessing differential histone modifications and transcription factor binding. We have developed a new computational method, MMDiff, that is capable of exploring these features and therefore closes an existing gap in the analysis of ChIPSeq data sets. [ABSTRACT FROM AUTHOR]

We consider the problem of improving the Gaussian approximate posterior marginals computed by expectation propagation and the Laplace method in latent Gaussian models and propose methods that are similar in spirit to the Laplace approximation of Tierney and Kadane (1986). We show that in the case of sparse Gaussian models, the computational complexity of expectation propagation can be made comparable to that of the Laplace method by using a parallel updating scheme. In some cases, expectation propagation gives excellent estimates where the Laplace approximation fails. Inspired by bounds on the correct marginals, we arrive at factorized approximations, which can be applied on top of both expectation propagation and the Laplace method. The factorized approximations can give nearly indistinguishable results from the non-factorized approximations and their computational complexity scales linearly with the number of variables. We experienced that the expectation propagation based marginal approximations we introduce are typically more accurate than the methods of similar complexity proposed by Rue et al. (2009). [ABSTRACT FROM AUTHOR]

Abstract: Bayesian logistic regression with a multivariate Laplace prior is introduced as a multivariate approach to the analysis of neuroimaging data. It is shown that, by rewriting the multivariate Laplace distribution as a scale mixture, we can incorporate spatio-temporal constraints which lead to smooth importance maps that facilitate subsequent interpretation. The posterior of interest is computed using an approximate inference method called expectation propagation and becomes feasible due to fast inversion of a sparse precision matrix. We illustrate the performance of the method on an fMRI dataset acquired while subjects were shown handwritten digits. The obtained models perform competitively in terms of predictive performance and give rise to interpretable importance maps. Estimation of the posterior of interest is shown to be feasible even for very large models with thousands of variables. [Copyright &y& Elsevier]

We consider the problem of computing first-passage time distributions for reaction processes modeled by master equations. We show that this generally intractable class of problems is equivalent to a sequential Bayesian inference problem for an auxiliary observation process. The solution can be approximated efficiently by solving a closed set of coupled ordinary differential equations (for the low-order moments of the process) whose size scales with the number of species. We apply it to an epidemic model and a trimerization process and show good agreement with stochastic simulations. [ABSTRACT FROM AUTHOR]

Placing robotsoutside controlled conditions requires versatile movement representations that allow robots to learn new tasks and adapt them to environmental changes. The introduction of obstacles or the placement of additional robots in the workspace and the modification of the joint range due to faults or range-of-motion constraints are typical cases, where the adaptation capabilities play a key role for safely performing the robot’s task. Probabilistic movement primitives (ProMPs) have been proposed for representing adaptable movement skills, which are modeled as Gaussian distributions over trajectories. These are analytically tractable and can be learned from a small number of demonstrations. However, both the original ProMP formulation and the subsequent approaches only provide solutions to specific movement adaptation problems, e.g., obstacle avoidance, and a generic, unifying, probabilistic approach to adaptation is missing. In this article, we develop a generic probabilistic framework for adapting ProMPs. We unify previous adaptation techniques, for example, various types of obstacle avoidance, via-points, and mutual avoidance, in one single framework and combine them to solve complex robotic problems. Additionally, we derive novel adaptation techniques such as temporally unbound via-points and mutual avoidance. We formulate adaptation as a constrained optimization problem, where we minimize the Kullback–Leibler divergence between the adapted distribution and the distribution of the original primitive,while we constrain the probability mass associated with undesired trajectories to be low. We demonstrate our approach on several adaptation problems on simulated planar robot arms and seven-degree-of-freedom Franka Emika robots in a dual-robot-arm setting. [ABSTRACT FROM AUTHOR]