One-Dimensional Population Density Approaches to Recurrently Coupled Networks of Neurons with Noise

Mean-field systems have been previously derived for networks of coupled, two-dimensional, integrate-and-fire neurons such as the Izhikevich, adapting exponential (AdEx) and quartic integrate and fire (QIF), among others. Unfortunately, the mean-field systems have a degree of frequency error and the networks analyzed often do not include noise when there is adaptation. Here, we derive a one-dimensional partial differential equation (PDE) approximation for the marginal voltage density under a first order moment closure for coupled networks of integrate-and-fire neurons with white noise inputs. The PDE has substantially less frequency error than the mean-field system, and provides a great deal more information, at the cost of analytical tractability. The convergence properties of the mean-field system in the low noise limit are elucidated. A novel method for the analysis of the stability of the asynchronous tonic firing solution is also presented and implemented. Unlike previous attempts at stability analysis with these network types, information about the marginal densities of the adaptation variables is used. This method can in principle be applied to other systems with nonlinear partial differential equations.Comment: 26 Pages, 6 Figure

Data-driven modelling of biological multi-scale processes

Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript we review mathematical modelling approaches used to describe the individual spatial scales and how they are integrated into holistic models. We discuss the relation between spatial and temporal scales and the implication of that on multi-scale modelling. Based upon this overview over state-of-the-art modelling approaches, we formulate key challenges in mathematical and computational modelling of biological multi-scale and multi-physics processes. In particular, we considered the availability of analysis tools for multi-scale models and model-based multi-scale data integration. We provide a compact review of methods for model-based data integration and model-based hypothesis testing. Furthermore, novel approaches and recent trends are discussed, including computation time reduction using reduced order and surrogate models, which contribute to the solution of inference problems. We conclude the manuscript by providing a few ideas for the development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and Multiscale Dynamics (American Scientific Publishers

Optimal Control of Transient Flow in Natural Gas Networks

We outline a new control system model for the distributed dynamics of compressible gas flow through large-scale pipeline networks with time-varying injections, withdrawals, and control actions of compressors and regulators. The gas dynamics PDE equations over the pipelines, together with boundary conditions at junctions, are reduced using lumped elements to a sparse nonlinear ODE system expressed in vector-matrix form using graph theoretic notation. This system, which we call the reduced network flow (RNF) model, is a consistent discretization of the PDE equations for gas flow. The RNF forms the dynamic constraints for optimal control problems for pipeline systems with known time-varying withdrawals and injections and gas pressure limits throughout the network. The objectives include economic transient compression (ETC) and minimum load shedding (MLS), which involve minimizing compression costs or, if that is infeasible, minimizing the unfulfilled deliveries, respectively. These continuous functional optimization problems are approximated using the Legendre-Gauss-Lobatto (LGL) pseudospectral collocation scheme to yield a family of nonlinear programs, whose solutions approach the optima with finer discretization. Simulation and optimization of time-varying scenarios on an example natural gas transmission network demonstrate the gains in security and efficiency over methods that assume steady-state behavior

A machine learning framework for data driven acceleration of computations of differential equations

We propose a machine learning framework to accelerate numerical computations of time-dependent ODEs and PDEs. Our method is based on recasting (generalizations of) existing numerical methods as artificial neural networks, with a set of trainable parameters. These parameters are determined in an offline training process by (approximately) minimizing suitable (possibly non-convex) loss functions by (stochastic) gradient descent methods. The proposed algorithm is designed to be always consistent with the underlying differential equation. Numerical experiments involving both linear and non-linear ODE and PDE model problems demonstrate a significant gain in computational efficiency over standard numerical methods

Lipid Metabolism and Comparative Genomics

Unilever asked the Study Group to focus on two problems. The first concerned dysregulated lipid metabolism which is a feature of many diseases including metabolic syndrome, obesity and coronary heart disease. The Study Group was asked to develop a model of the kinetics of lipoprotein metabolism between healthy and obese states incorporating the activities of key enzymes. The second concerned the use of comparative genomics in understanding and comparing metabolic networks in bacterium. Comparative genomics is a method to make inferences on the genome of a new organism using information of a previously charaterised organism. The first mathematical question is how one would quantify such a metabolic map in a statistical sense, in particular, where there are different levels of confidence for presense of different parts of the map. The next and most important question is how one can design a measurement strategy to maximise the confidence in the accuracy of the metabolic map