The Singular Value Decomposition (SVD) of matrices and the related Principal Components Analysis (PCA) express a matrix in terms of singular vectors, which are linear combinations of all the input data and lack an intuitive physical interpretation. Motivated by the application of PCA and SVD in the analysis of populations genetics data, we will discuss the notion of leverage scores: a simple statistic that reveals columns/rows of a matrix that lie in the subspace spanned by the top principal components (left/right singular vectors). We will then use the leverage scores to present matrix decompositions that express the structure in a matrix in terms of actual columns (and/or rows) of the matrix. Such decompositions are easier to interpret in applications, since the selected columns and rows are subsets of the data. We will also discuss extensions of the leverage scores to reveal influential entries of a matrix.

We present a trust region algorithm for solving nonconvex optimization problems that, in the worst-case, is able to drive the norm of the gradient of the objective below a prescribed threshold $\epsilon > 0$ after at most ${\cal O}(\epsilon^{-3/2})$ function evaluations, gradient evaluations, or iterations.  Our work has been inspired by the recently proposed Adaptive Regularisation framework using Cubics (i.e., the ARC algorithm), which attains the same worst-case complexity bound.  Our algorithm is modeled after a traditional trust region algorithm, but employs modified step acceptance criteria and a novel trust region updating mechanism that allows it to achieve this desirable property.  Importantly, our method also maintains standard global and fast local convergence guarantees.

Although Toeplitz matrices are often dense, matrix-vector products with Toeplitz matrices can be quickly performed via circulant embedding and the fast Fourier transform. This makes their solution by preconditioned Krylov subspace methods attractive. 

For a wide class of symmetric Toeplitz matrices, symmetric positive definite circulant preconditioners that cluster eigenvalues have been proposed. MINRES or the conjugate gradient method can be applied to these problems and descriptive convergence theory based on eigenvalues guarantees fast convergence. 

In contrast, although circulant preconditioners have been proposed for nonsymmetric Toeplitz systems, guarantees of fast convergence are generally only available for CG for the normal equations (CGNE). This is somewhat unsatisfactory because CGNE has certain drawbacks, including slow convergence and a larger condition number. In this talk we discuss a simple alternative symmetrization of nonsymmetric Toeplitz matrices, that allows us to use MINRES to solve the resulting linear system. We show how existing circulant preconditioners for nonsymmetric Toeplitz matrices can be straightforwardly adapted to this situation and give convergence estimates similar to those in the symmetric case.

Numerical simulation tools for fluid and solid mechanics are often based on the discretisation of coupled systems of partial differential equations, which can easily be identified in terms of physical
conservation laws.  In contrast, much physical insight is often gained from the equivalent formulation of the relevant energy or free-energy functional, possibly subject to constraints.  Motivated by the
nonlinear static and dynamic behaviour of nematic liquid crystals and of magnetosensitive elastomers, we propose a finite-element framework for minimising these free-energy functionals, using Lagrange multipliers to enforce additional constraints.  This talk will highlight challenges, limitations, and successes, both in the formulation of these models and their use in numerical simulation.
This is joint work with PhD students Thomas Benson, David Emerson, and Dong Han, and with James Adler, Timothy Atherton, and Luis Dorfmann.

As the fundamental unit of life, the biological cell is a natural focus for computational simulations of growing cell population and tissues. However, models developed at the cellular scale can also be integrated into more complex multiscale models in order to examine complex biological and physical process that scan scales from the molecule to the organ.

This seminar will present a selection of the cellular scale agent-based modelling that has taken place at the University of Sheffield (where one software agent represents one biological cell) and how such models can be used to examine collective behaviour in cellular systems. Finally some of the issues in extending to multiscale models and the theoretical and computational methodologies being developed in Sheffield and by the wider community in this area will be presented.

Data in many areas of science and sociology is now routinely represented in the form of networks. A fundamental task often required is to compare two datasets (networks) to assess the level of similarity between them. In the context of biological sciences, networks often represent either direct or indirect molecular interactions and an active research area is to assess the level of conservation of interaction patterns across species.

Currently biological network comparison software largely relies on the concept of alignment where close matches between the nodes of two or more networks are sought. These node matches are based on sequence similarity and/or interaction patterns. However, because of the incomplete and error-prone datasets currently available, such methods have had limited success. Moreover, the results of network alignment are in general not amenable for distance-based evolutionary analysis of sets of networks. In this talk I will describe Netdis, a topology-based distance measure between networks, which offers the possibility of network phylogeny reconstruction.

Sudden cardiac arrhythmic death remains a major health challenge in Western Society. Recent advances in computational methods and technologies have made clinically-based cardiac modelling a reality. An important current focus is the use of modelling to understand the nature of arrhythmias in the setting of different forms of structural heart disease. However, many challenges remain regarding the best use of these models to inform clinical decision making and guide therapies. In this talk, I will introduce a diverse sample of applications of modelling in this context, ranging from basic science studies which aim to leverage a fundamental mechanistic understanding of different aspects of pathological cardiac function, to direct clinical-application projects which aim to use modelling to immediately inform a clinical therapy. I will also discuss the challenges involved in clinically-driven modelling, and how to both engage, and manage, the expectations of clinicians at the same time, particularly with respect to the potential uses of 'patient-specific' modelling.

I this talk I will try to give an overview of recent progress in
spatial stochastic modeling within the reaction-diffusion
framework. While much of the initial motivation for this work came
from problems in cell biology, I will also highlight some examples
from epidemics and neuroscience.

As a motivating introduction, some newly discovered properties of
optimal controls in stochastic enzymatic reaction networks will be
presented. I will next detail how diffusive and subdiffusive reactive
processes in realistic geometries at the cellular scale may be modeled
mesoscopically. Along the way, some different means by which these
models may be analyzed with respect to consistency and convergence
will also be discussed. These analytical techniques hint at how
effective (i.e. parallel) numerical implementations can be
designed. Large-scale simulations will serve as illustrations.