StochKit-FF: Efficient Systems Biology on Multicore Architectures

The stochastic modelling of biological systems is an informative, and in some cases, very adequate technique, which may however result in being more expensive than other modelling approaches, such as differential equations. We present StochKit-FF, a parallel version of StochKit, a reference toolkit for stochastic simulations. StochKit-FF is based on the FastFlow programming toolkit for multicores and exploits the novel concept of selective memory. We experiment StochKit-FF on a model of HIV infection dynamics, with the aim of extracting information from efficiently run experiments, here in terms of average and variance and, on a longer term, of more structured data.Comment: 14 pages + cover pag

Cooperative coevolution of partially heterogeneous multiagent systems

Cooperative coevolution algorithms (CCEAs) facilitate the evolution of heterogeneous, cooperating multiagent systems. Such algorithms are, however, subject to inherent scalability issues, since the number of required evaluations increases with the number of agents. A possible solution is to use partially heterogeneous (hybrid) teams: behaviourally heterogeneous teams composed of homogeneous sub-teams. By having different agents share controllers, the number of coevolving populations in the system is reduced. We propose HybCCEA, an extension of cooperative coevolution to partially heterogeneous multiagent systems. In Hyb-CCEA, both the agent controllers and the team composition are under evolutionary control. During the evolutionary process, we rely on measures of behaviour similarity for the formation of homogeneous sub-teams (merging), and propose a stochastic mechanism to increase heterogeneity (splitting). We evaluate Hyb-CCEA in multiple variants of a simulated herding task, and compare it with a fully heterogeneous CCEA. Our results show that Hyb-CCEA can achieve solutions of similar quality using significantly fewer evaluations, and in most setups, Hyb-CCEA even achieves significantly higher fitness scores than the CCEA. Overall, we show that merging and splitting populations are viable mechanisms for the cooperative coevolution of hybrid teams.info:eu-repo/semantics/publishedVersio

Synthetic Gene Circuits: Design with Directed Evolution

Synthetic circuits offer great promise for generating insights into nature's underlying design principles or forward engineering novel biotechnology applications. However, construction of these circuits is not straightforward. Synthetic circuits generally consist of components optimized to function in their natural context, not in the context of the synthetic circuit. Combining mathematical modeling with directed evolution offers one promising means for addressing this problem. Modeling identifies mutational targets and limits the evolutionary search space for directed evolution, which alters circuit performance without the need for detailed biophysical information. This review examines strategies for integrating modeling and directed evolution and discusses the utility and limitations of available methods

Echo state model of non-Markovian reinforcement learning, An

Department Head: Dale H. Grit.2008 Spring.Includes bibliographical references (pages 137-142).There exists a growing need for intelligent, autonomous control strategies that operate in real-world domains. Theoretically the state-action space must exhibit the Markov property in order for reinforcement learning to be applicable. Empirical evidence, however, suggests that reinforcement learning also applies to domains where the state-action space is approximately Markovian, a requirement for the overwhelming majority of real-world domains. These domains, termed non-Markovian reinforcement learning domains, raise a unique set of practical challenges. The reconstruction dimension required to approximate a Markovian state-space is unknown a priori and can potentially be large. Further, spatial complexity of local function approximation of the reinforcement learning domain grows exponentially with the reconstruction dimension. Parameterized dynamic systems alleviate both embedding length and state-space dimensionality concerns by reconstructing an approximate Markovian state-space via a compact, recurrent representation. Yet this representation extracts a cost; modeling reinforcement learning domains via adaptive, parameterized dynamic systems is characterized by instability, slow-convergence, and high computational or spatial training complexity. The objectives of this research are to demonstrate a stable, convergent, accurate, and scalable model of non-Markovian reinforcement learning domains. These objectives are fulfilled via fixed point analysis of the dynamics underlying the reinforcement learning domain and the Echo State Network, a class of parameterized dynamic system. Understanding models of non-Markovian reinforcement learning domains requires understanding the interactions between learning domains and their models. Fixed point analysis of the Mountain Car Problem reinforcement learning domain, for both local and nonlocal function approximations, suggests a close relationship between the locality of the approximation and the number and severity of bifurcations of the fixed point structure. This research suggests the likely cause of this relationship: reinforcement learning domains exist within a dynamic feature space in which trajectories are analogous to states. The fixed point structure maps dynamic space onto state-space. This explanation suggests two testable hypotheses. Reinforcement learning is sensitive to state-space locality because states cluster as trajectories in time rather than space. Second, models using trajectory-based features should exhibit good modeling performance and few changes in fixed point structure. Analysis of performance of lookup table, feedforward neural network, and Echo State Network (ESN) on the Mountain Car Problem reinforcement learning domain confirm these hypotheses. The ESN is a large, sparse, randomly-generated, unadapted recurrent neural network, which adapts a linear projection of the target domain onto the hidden layer. ESN modeling results on reinforcement learning domains show it achieves performance comparable to lookup table and neural network architectures on the Mountain Car Problem with minimal changes to fixed point structure. Also, the ESN achieves lookup table caliber performance when modeling Acrobot, a four-dimensional control problem, but is less successful modeling the lower dimensional Modified Mountain Car Problem. These performance discrepancies are attributed to the ESN’s excellent ability to represent complex short term dynamics, and its inability to consolidate long temporal dependencies into a static memory. Without memory consolidation, reinforcement learning domains exhibiting attractors with multiple dynamic scales are unlikely to be well-modeled via ESN. To mediate this problem, a simple ESN memory consolidation method is presented and tested for stationary dynamic systems. These results indicate the potential to improve modeling performance in reinforcement learning domains via memory consolidation

Fully-Coupled Simulation of Cosmic Reionization. I: Numerical Methods and Tests

We describe an extension of the Enzo code to enable fully-coupled radiation hydrodynamical simulation of inhomogeneous reionization in large $\sim (100 Mpc)^3$ cosmological volumes with thousands to millions of point sources. We solve all dynamical, radiative transfer, thermal, and ionization processes self-consistently on the same mesh, as opposed to a postprocessing approach which coarse-grains the radiative transfer. We do, however, employ a simple subgrid model for star formation which we calibrate to observations. Radiation transport is done in the grey flux-limited diffusion (FLD) approximation, which is solved by implicit time integration split off from the gas energy and ionization equations, which are solved separately. This results in a faster and more robust scheme for cosmological applications compared to the earlier method. The FLD equation is solved using the hypre optimally scalable geometric multigrid solver from LLNL. By treating the ionizing radiation as a grid field as opposed to rays, our method is scalable with respect to the number of ionizing sources, limited only by the parallel scaling properties of the radiation solver. We test the speed and accuracy of our approach on a number of standard verification and validation tests. We show by direct comparison with Enzo's adaptive ray tracing method Moray that the well-known inability of FLD to cast a shadow behind opaque clouds has a minor effect on the evolution of ionized volume and mass fractions in a reionization simulation validation test. We illustrate an application of our method to the problem of inhomogeneous reionization in a 80 Mpc comoving box resolved with $3200^3$ Eulerian grid cells and dark matter particles.Comment: 32 pages, 23 figures. ApJ Supp accepted. New title and substantial revisions re. v

Bio-inspired computation: where we stand and what's next

In recent years, the research community has witnessed an explosion of literature dealing with the adaptation of behavioral patterns and social phenomena observed in nature towards efficiently solving complex computational tasks. This trend has been especially dramatic in what relates to optimization problems, mainly due to the unprecedented complexity of problem instances, arising from a diverse spectrum of domains such as transportation, logistics, energy, climate, social networks, health and industry 4.0, among many others. Notwithstanding this upsurge of activity, research in this vibrant topic should be steered towards certain areas that, despite their eventual value and impact on the field of bio-inspired computation, still remain insufficiently explored to date. The main purpose of this paper is to outline the state of the art and to identify open challenges concerning the most relevant areas within bio-inspired optimization. An analysis and discussion are also carried out over the general trajectory followed in recent years by the community working in this field, thereby highlighting the need for reaching a consensus and joining forces towards achieving valuable insights into the understanding of this family of optimization techniques