Towards Designing Artificial Universes for Artificial Agents under Interaction Closure

We are interested in designing artificial universes for artificial agents. We view artificial agents as networks of highlevel processes on top of of a low-level detailed-description system. We require that the high-level processes have some intrinsic explanatory power and we introduce an extension of informational closure namely interaction closure to capture this. Then we derive a method to design artificial universes in the form of finite Markov chains which exhibit high-level processes that satisfy the property of interaction closure. We also investigate control or information transfer which we see as an building block for networks representing artificial agent

Dynamic Bayesian networks in molecular plant science: inferring gene regulatory networks from multiple gene expression time series

To understand the processes of growth and biomass production in plants, we ultimately need to elucidate the structure of the underlying regulatory networks at the molecular level. The advent of high-throughput postgenomic technologies has spurred substantial interest in reverse engineering these networks from data, and several techniques from machine learning and multivariate statistics have recently been proposed. The present article discusses the problem of inferring gene regulatory networks from gene expression time series, and we focus our exposition on the methodology of Bayesian networks. We describe dynamic Bayesian networks and explain their advantages over other statistical methods. We introduce a novel information sharing scheme, which allows us to infer gene regulatory networks from multiple sources of gene expression data more accurately. We illustrate and test this method on a set of synthetic data, using three different measures to quantify the network reconstruction accuracy. The main application of our method is related to the problem of circadian regulation in plants, where we aim to reconstruct the regulatory networks of nine circadian genes in Arabidopsis thaliana from four gene expression time series obtained under different experimental conditions

A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology

An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional homogeneous DBNs fail to model the non-stationarity and time-varying nature of the gene regulatory processes. Various authors have therefore recently proposed combining DBNs with multiple changepoint processes to obtain time varying dynamic Bayesian networks (TV-DBNs). However, TV-DBNs are not without problems. Gene expression time series are typically short, which leaves the model over-flexible, leading to over-fitting or inflated inference uncertainty. In the present paper, we introduce a Bayesian regularization scheme that addresses this difficulty. Our approach is based on the rationale that changes in gene regulatory processes appear gradually during an organism's life cycle or in response to a changing environment, and we have integrated this notion in the prior distribution of the TV-DBN parameters. We have extensively tested our regularized TV-DBN model on synthetic data, in which we have simulated short non-homogeneous time series produced from a system subject to gradual change. We have then applied our method to real-world gene expression time series, measured during the life cycle of Drosophila melanogaster, under artificially generated constant light condition in Arabidopsis thaliana, and from a synthetically designed strain of Saccharomyces cerevisiae exposed to a changing environment

Stochastic Gradient Hamiltonian Monte Carlo

Hamiltonian Monte Carlo (HMC) sampling methods provide a mechanism for defining distant proposals with high acceptance probabilities in a Metropolis-Hastings framework, enabling more efficient exploration of the state space than standard random-walk proposals. The popularity of such methods has grown significantly in recent years. However, a limitation of HMC methods is the required gradient computation for simulation of the Hamiltonian dynamical system-such computation is infeasible in problems involving a large sample size or streaming data. Instead, we must rely on a noisy gradient estimate computed from a subset of the data. In this paper, we explore the properties of such a stochastic gradient HMC approach. Surprisingly, the natural implementation of the stochastic approximation can be arbitrarily bad. To address this problem we introduce a variant that uses second-order Langevin dynamics with a friction term that counteracts the effects of the noisy gradient, maintaining the desired target distribution as the invariant distribution. Results on simulated data validate our theory. We also provide an application of our methods to a classification task using neural networks and to online Bayesian matrix factorization.Comment: ICML 2014 versio