arXiv subjects

James Grant

Publications and source records attributed to James Grant.

13 recordsLinked to original sources

arXiv2023

RadImageGAN -- A Multi-modal Dataset-Scale Generative AI for Medical Imaging

Deep learning in medical imaging often requires large-scale, high-quality data or initiation with suitably pre-trained weights. However, medical datasets are limited by data availability, domain-specific knowledge, and privacy concerns, and the creation of large and diverse radiologic databases like RadImageNet is highly resource-intensive. To address these limitations, we introduce RadImageGAN, the first multi-modal radiologic data generator, which was developed by training StyleGAN-XL on the real RadImageNet dataset of 102,774 patients. RadImageGAN can generate high-resolution synthetic medical imaging datasets across 12 anatomical regions and 130 pathological classes in 3 modalities. Furthermore, we demonstrate that RadImageGAN generators can be utilized with BigDatasetGAN to generate multi-class pixel-wise annotated paired synthetic images and masks for diverse downstream segmentation tasks with minimal manual annotation. We showed that using synthetic auto-labeled data from RadImageGAN can significantly improve performance on four diverse downstream segmentation datasets by augmenting real training data and/or developing pre-trained weights for fine-tuning. This shows that RadImageGAN combined with BigDatasetGAN can improve model performance and address data scarcity while reducing the resources needed for annotations for segmentation tasks.

eess.IV↗

arXiv2021

A new algorithm for electrostatic interactions in Monte Carlo simulations of charged particles

To minimise systematic errors in Monte Carlo simulations of charged particles, long range electrostatic interactions have to be calculated accurately and efficiently. Standard approaches, such as Ewald summation or the naive application of the classical Fast Multipole Method, result in a cost per Metropolis-Hastings step which grows in proportion to some positive power of the number of particles $N$ in the system. This prohibitively large cost prevents accurate simulations of systems with a sizeable number of particles. Currently, large systems are often simulated by truncating the Coulomb potential which introduces uncontrollable systematic errors. In this paper we present a new multilevel method which reduces the computational complexity to $\mathcal{O}(\log(N))$ per Metropolis-Hastings step, while maintaining errors which are comparable to direct Ewald summation. We show that compared to related previous work, our approach reduces the overall cost by better balancing time spent in the proposal- and acceptance- stages of each Metropolis-Hastings step. By simulating large systems with up to $N=10^5$ particles we demonstrate that our implementation is competitive with state-of-the-art MC packages and allows the simulation of very large systems of charged particles with accurate electrostatics.

physics.comp-ph↗

arXiv2020

Teaching Programming for Mathematical Scientists

Over the past thirty years or so the authors have been teaching various programming for mathematics courses at our respective Universities, as well as incorporating computer algebra and numerical computation into traditional mathematics courses. These activities are, in some important ways, natural precursors to the use of Artificial Intelligence in Mathematics Education. This paper reflects on some of our course designs and experiences and is therefore a mix of theory and practice. Underlying both is a clear recognition of the value of computer programming for mathematics education. We use this theory and practice to suggest good techniques for and to raise questions about the use of AI in Mathematics Education.

math.HO↗

arXiv2020

Parallel Performance of ARM ThunderX2 for Atomistic Simulation Algorithms

Atomistic simulation drives scientific advances in modern material science and accounts for a significant proportion of wall time on High Performance Computing facilities. It is important that algorithms are efficient and implementations are performant in a continuously diversifying hardware landscape. Furthermore, they have to be portable to make best use of the available computing resource. In this paper we assess the parallel performance of some key algorithms implemented in a performance portable framework developed by us. We consider Molecular Dynamics with short range interactions, the Fast Multipole Method and Kinetic Monte Carlo. To assess the performance of emerging architectures, we compare the Marvell ThunderX2 (ARM) architecture to traditional x86_64 hardware made available through the Azure cloud computing service.

cs.DC↗

arXiv2020

Assessing molecular simulation for the analysis of lipid monolayer reflectometry

Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This work presents the first direct comparison between the reflectometry profiles obtained from different all-atom and coarse-grained molecular dynamics simulations. These are compared with a traditional model layer structure analysis method to determine the minimum simulation resolution required to accurately reproduce experimental data. We find that systematic limits reduce the efficacy of the MARTINI potential model, while the Berger united-atom and Slipids all-atom potential models agree similarly well with the experimental data. The model layer structure gives the best agreement, however, the higher resolution simulation-dependent methods produce an agreement that is comparable. Finally, we use the atomistic simulation to advise on possible improvements that may be offered to the model layer structures, creating a more realistic monolayer model.

cond-mat.soft↗

arXiv2020

An introduction to classical molecular dynamics simulation for experimental scattering users

Classical molecular dynamics simulations are a common component of multi-modal analyses from scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a "black box" analysis technique. In this article, we describe an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open source software repository, which can be freely copied, modified, and redistributed by educators. The topic covered in this OER includes classical atomistic modelling, parameterising interatomic potentials, molecular dynamics simulations, typical sources of error, and some of the approaches to using simulations in the analysis of scattering data.

cond-mat.stat-mech↗

arXiv2020

Fast electrostatic solvers for kinetic Monte Carlo simulations

Kinetic Monte Carlo (KMC) is an important computational tool in physics and chemistry. In contrast to standard Monte Carlo, KMC permits the description of time dependent dynamical processes and is not restricted to systems in equilibrium. Recently KMC has been applied successfully in modelling of novel energy materials such as Lithium-ion batteries and solar cells. We consider general solid state systems which contain free, interacting particles which can hop between localised sites in the material. The KMC transition rates for those hops depend on the change in total potential energy of the system. For charged particles this requires the frequent calculation of electrostatic interactions, which is usually the bottleneck of the simulation. To avoid this issue and obtain results in reasonable times, many studies replace the long-range potential by a short range approximation. This, however, leads to systematic errors and unphysical results. On the other hand standard electrostatic solvers such as Ewald summation or fast Poisson solvers are highly inefficient or introduce uncontrollable systematic errors at high resolution. In this paper we describe how the Fast Multipole Method by Greengard and Rokhlin can be adapted to overcome this issue by dramatically reducing computational costs. We exploit the fact that each update in the transition rate calculation corresponds to a single particle move and changes the configuration only by a small amount. This allows us to construct an algorithm which scales linearly in the number of charges for each KMC step, something which had not been deemed to be possible before. We demonstrate the performance and parallel scalability of the method by implementing it in a performance portable software library. We describe the high-level Python interface of the code which makes it easy to adapt to specific cases.

physics.comp-ph↗

arXiv2018

DL_MONTE: A multipurpose code for Monte Carlo simulation

DL_MONTE is an open source, general-purpose software package for performing Monte Carlo simulations. It includes a wide variety of force fields and MC techniques, and thus is applicable to a broad range of problems in molecular simulation. Here we provide an overview of DL_MONTE, focusing on key features recently added to the package. These include the ability to treat systems confined to a planar pore (i.e. `slit' or `slab' boundary conditions); the lattice-switch Monte Carlo (LSMC) method for evaluating precise free energy differences between competing polymorphs; various commonly-used methods for evaluating free energy profiles along transition pathways (including umbrella sampling, Wang-Landau and transition matrix); and a supplementary Python toolkit for simulation management and application of the histogram reweighting analysis method. We provide two `real world' examples to elucidate the use of these methods in DL_MONTE. In particular, we apply umbrella sampling to calculate the free energy profile associated with the translocation of a lipid through a bilayer. Moreover we employ LSMC to examine the thermodynamic stability of two plastic crystal phases of water at high pressure. Beyond this, we provide instructions on how to access DL_MONTE, and point to additional information valuable to existing and prospective users.

physics.comp-ph↗

arXiv2017

A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms

Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics/chemistry/biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a "Separation of Concerns" approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework.

cs.DC↗

arXiv2017

Long range forces in a performance portable Molecular Dynamics framework

Molecular Dynamics (MD) codes predict the fundamental properties of matter by following the trajectories of a collection of interacting model particles. To exploit diverse modern manycore hardware, efficient codes must use all available parallelism. At the same time they need to be portable and easily extendible by the domain specialist (physicist/chemist) without detailed knowledge of this hardware. To address this challenge, we recently described a new Domain Specific Language (DSL) for the development of performance portable MD codes based on a "Separation of Concerns": a Python framework automatically generates efficient parallel code for a range of target architectures. Electrostatic interactions between charged particles are important in many physical systems and often dominate the runtime. Here we discuss the inclusion of long-range interaction algorithms in our code generation framework. These algorithms require global communications and careful consideration has to be given to any impact on parallel scalability. We implemented an Ewald summation algorithm for electrostatic forces, present scaling comparisons for different system sizes and compare to the performance of existing codes. We also report on further performance optimisations delivered with OpenMP shared memory parallelism.

cs.DC↗

arXiv2015

Valiente Kroon's obstructions to smoothness at infinity

We conjecture an interpretation in terms of multipole moments of the obstructions to smoothness at infinity found for time-symmetric, conformally-flat initial data by Valiente Kroon (Comm. Math. Phys. 244 (2004), 133-156).

gr-qc↗

arXiv2012

Quantifying reversibility in a phase-separating lattice gas: an analogy with self-assembly

We present dynamic measurements of a lattice gas during phase separation, which we use as an analogy for self-assembly of equilibrium ordered structures. We use two approaches to quantify the degree of 'reversibility' of this process: firstly, we count events in which bonds are made and broken; secondly, we use correlation-response measurements and fluctuation-dissipation ratios to probe reversibility during different time intervals. We show how correlation and response functions can be related directly to microscopic (ir)reversibility and we discuss time-dependence and observable- dependence of these measurements, including the role of fast and slow degrees of freedom during assembly.

cond-mat.soft↗

arXiv2011

Analyzing mechanisms and microscopic reversibility of self-assembly

We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements of dynamical activity and assembly progress to compare their propensities for kinetic trapping. We use the analytic solution of a simple minimal model to illustrate the key features associated with such trapping, paying particular attention to the number of ways that particles can misbind. We discuss the relevance of our results for the design and control of self-assembly in general.

cond-mat.soft↗