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Publications from members of the group

2021
  1. PCPATCH: software for the topological construction of multigrid relaxation methods
    Patrick E. Farrell, Matthew G. Knepley, Lawrence Mitchell, and Florian Wechsung
    ACM Transactions on Mathematical Software
    To appear
    arxiv:1912.08516 bib
  2. A Reynolds-robust preconditioner for the Reynolds-robust Scott–Vogelius discretization of the stationary incompressible Navier–Stokes equations
    Patrick E. Farrell, Lawrence Mitchell, L. Ridgway Scott, and Florian Wechsung
    SMAI Journal of Computational Mathematics
    To appear
    arxiv:2004.09398 bib
2020
  1. A study of vectorization for matrix-free finite element methods
    Tianjiao Sun, Lawrence Mitchell, Kaushik Kulkarni, Andreas Klöckner, David A. Ham, and Paul H. J. Kelly
    International Journal of High Performance Computing Applications
    doi arxiv:1903.08243 bib
  2. Slate: extending Firedrake’s domain-specific abstraction to hybridized solvers for geoscience and beyond
    Thomas H. Gibson, Lawrence Mitchell, David A. Ham, and Colin J. Cotter
    Geoscientific Model Development
    doi arxiv:1802.00303 bib
  3. Real Time Fencing Move Classification and Detection at Touch Time during a Fencing Match
    Sunal, Cem Ekin, Willcocks, Chris G., and Obara, Boguslaw
    in Proc. Int. Conf. Pattern Recognition
    To appear
    bib
  4. Data Augmentation via Mixed Class Interpolation using Cycle-Consistent Generative Adversarial Networks Applied to Cross-Domain Imagery
    Sasaki, H., Willcocks, C.G., and Breckon, T.P.
    in Proc. Int. Conf. Pattern Recognition
    bib
  5. Lightweight task offloading exploiting MPI wait times for parallel adaptive mesh refinement
    Samfass, Philipp, Weinzierl, Tobias, Charrier, Dominic E., and Bader, Michael
    Concurrency and Computation: Practice and Experience
    doi bib
  6. TeaMPI–-Replication-Based Resilience Without the (Performance) Pain
    Samfass, Philipp, Weinzierl, Tobias, Hazelwood, Benjamin, and Bader, Michael
    in High Performance Computing
    bib
  7. Computer Vision for Protein-protein Docking
    Rudden, Lucas SP, Degiacomi, Matteo T, and Willcocks, Chris G
    Biophysical Journal
    doi bib
  8. Robust multigrid methods for nearly incompressible elasticity using macro elements
    Patrick E. Farrell, Lawrence Mitchell, L. Ridgway Scott, and Florian Wechsung
    Submitted to SIAM Journal on Numerical Analysis
    arxiv:2002.02051 bib
  9. Unsupervised Region-based Anomaly Detection in Brain MRI with Adversarial Image Inpainting
    Nguyen, Bao, Feldman, Adam, Bethapudi, Sarath, Jennings, Andrew, and Willcocks, Chris G
    arXiv preprint arXiv:2010.01942
    bib
  10. Delayed approximate matrix assembly in multigrid with dynamic precisions
    Murray, Charles D. and Weinzierl, Tobias
    Concurrency and Computation: Practice and Experience
    doi bib
  11. Stabilized asynchronous fast adaptive composite multigrid using additive damping
    Murray, Charles D. and Weinzierl, Tobias
    Numerical Linear Algebra with Applications
    doi bib
  12. Segmentation of Macular Edema Datasets with Small Residual 3D U-Net Architectures
    Jonathan Frawley, Chris G. Willcocks, Maged Habib, Caspar Geenen, David H. Steel, and Boguslaw Obara
    arXiv preprint arXiv:2005.04697
    bib
  13. Vectorization and Minimization of Memory Footprint for Linear High-Order Discontinuous Galerkin Schemes
    Jean-Matthieu Gallard, Leonhard Rannabauer, Anne Reinarz, and Michael Bader
    in PDSEC
    bib
  14. Multi-view Object Detection Using Epipolar Constraints within Cluttered X-ray Security Imagery
    Isaac-Medina, B.K.S., Willcocks, C.G., and Breckon, T.P.
    in Proc. Int. Conf. Pattern Recognition
    bib
  15. Enclave Tasking for DG Methods on Dynamically Adaptive Meshes
    Charrier, Dominic Etienne, Hazelwood, Benjamin, and Weinzierl, Tobias
    SIAM Journal on Scientific Computing
    doi bib
  16. Gradient Origin Networks
    Bond-Taylor, Sam and Willcocks, Chris G
    arXiv preprint arXiv:2007.02798
    bib
  17. ExaHyPE: An engine for parallel dynamically adaptive simulations of wave problems
    Anne Reinarz, Dominic E. Charrier, Michael Bader, Luke Bovard, Michael Dumbser, Kenneth Duru, Francesco Fambri, Alice-Agnes Gabriel, Jean-Matthieu Gallard, Sven Köppel, Lukas Krenz, Leonhard Rannabauer, Luciano Rezzolla, Philipp Samfass, Maurizio Tavelli, and Tobias Weinzierl
    Computer Physics Communications
    doi bib
  18. The relationship between curvilinear structure enhancement and ridge detection methods
    Alhasson, Haifa F., Willcocks, Chris G., Alharbi, Shuaa S., Kasim, Adetayo, and Obara, Boguslaw
    The Visual Computer
    doi bib
2019
  1. The Peano Software—Parallel, Automaton-Based, Dynamically Adaptive Grid Traversals
    Weinzierl, Tobias
    ACM Trans. Math. Softw.
    doi bib
  2. Compatible finite element methods for geophysical flows: automation and implementation using Firedrake
    Thomas H. Gibson, Andrew T. T. McRae, Colin J. Cotter, Lawrence Mitchell, and David A. Ham
    SpringerBriefs in Mathematics of Planet Earth
    doi bib
  3. Code generation for generally mapped finite elements
    Robert C. Kirby and Lawrence Mitchell
    ACM Transactions on Mathematical Software
    doi arxiv:1808.05513 bib
  4. Learning protein conformational space by enforcing physics with convolutions and latent interpolations
    Ramaswamy, Venkata K, Willcocks, Chris G, and Degiacomi, Matteo T
    arXiv preprint arXiv:1910.04543
    bib
  5. High-performance dune modules for solving large-scale, strongly anisotropic elliptic problems with applications to aerospace composites
    R. Butler, T. Dodwell, A. Reinarz, A. Sandhu, R. Scheichl, and L. Seelinger
    Computer Physics Communications
    doi bib
  6. An augmented Lagrangian preconditioner for the 3D stationary incompressible Navier–Stokes equations at high Reynolds number
    Patrick E. Farrell, Lawrence Mitchell, and Florian Wechsung
    SIAM Journal on Scientific Computing
    doi arxiv:1810.03315 bib
  7. On GLM curl cleaning for a first order reduction of the CCZ4 formulation of the Einstein field equations
    Michael Dumbser, Francesco Fambri, Elena Gaburro, and Anne Reinarz
    Journal of Computational Physics
    doi bib
  8. A simple diffuse interface approach on adaptive Cartesian grids for the linear elastic wave equations with complex topography
    Maurizio Tavelli, Michael Dumbser, Dominic Etienne Charrier, Leonhard Rannabauer, Tobias Weinzierl, and Michael Bader
    Journal of Computational Physics
    doi bib
  9. A High-Performance Implementation of a Robust Preconditioner for Heterogeneous Problems
    Linus Seelinger, Anne Reinarz, and Robert Scheichl
    in PPAM 2019
    bib
  10. A multi-core ready discrete element method with triangles using dynamically adaptive multiscale grids
    Krestenitis, Konstantinos and Weinzierl, Tobias
    Concurrency and Computation: Practice and Experience
    doi bib
  11. Deep-learning based, automated segmentation of macular holes in optical coherence tomography
    Jonathan Frawley, Chris Willcocks, Habib Maged, Geenen Caspar, David Steel, and Boguslaw Obara
    in The Wolfson Research Institute for Health and Wellbeing Fourth Annual Early Career Researcher Conference
    bib
  12. Role-Oriented Code Generation in an Engine for Solving Hyperbolic PDE Systems
    Jean-Matthieu Gallard, Lukas Krenz, Leonhard Rannabauer, Anne Reinarz, and Michael Bader
    in SC19 SE-HER
    bib
  13. Studies on the energy and deep memory behaviour of a cache-oblivious, task-based hyperbolic PDE solver
    Dominic E Charrier, Benjamin Hazelwood, Ekaterina Tutlyaeva, Michael Bader, Michael Dumbser, Andrey Kudryavtsev, Alexander Moskovsky, and Tobias Weinzierl
    The International Journal of High Performance Computing Applications
    doi bib
  14. Automated shape differentiation in the Unified Form Language
    David A. Ham, Lawrence Mitchell, Alberto Paganini, and Florian Wechsung
    Structural and Multidisciplinary Optimization
    doi arxiv:1808.08083 bib
  15. Sequential graph-based extraction of curvilinear structures
    Alharbi, Shuaa S., Willcocks, Chris G., Jackson, Philip T. G., Alhasson, Haifa F., and Obara, Boguslaw
    Signal, Image and Video Processing
    doi bib
  16. Sparse grid approximation spaces for space–time boundary integral formulations of the heat equation
    Alexey Chernov and Anne Reinarz
    Computers & Mathematics with Applications
    doi bib
2018
  1. Thetis coastal ocean model: discontinuous Galerkin discretization for the three-dimensional hydrostatic equations
    Tuomas Kärnä, Stephan C. Kramer, Lawrence Mitchell, David A. Ham, Matthew D. Piggott, and António M. Baptista
    Geoscientific Model Development
    doi arxiv:1711.08552 bib
  2. A Case Study for a New Invasive Extension of Intel’s Threading Building Blocks
    Schreiber, Martin and Weinzierl, Tobias
    in Proceedings of the 3rd Workshop on Co-Scheduling of HPC Applications (COSH 2018)
    doi bib
  3. Using Deep Convolutional Neural Network Architectures for Object Classification and Detection Within X-Ray Baggage Security Imagery
    S. Akcay, M. E. Kundegorski, Chris G. Willcocks, and T. P. Breckon
    IEEE Transactions on Information Forensics and Security
    doi bib
  4. Solver composition across the PDE/linear algebra barrier
    Robert C. Kirby and Lawrence Mitchell
    SIAM Journal on Scientific Computing
    doi arxiv:1706.01346 bib
  5. dune-composites – A New Framework for High-Performance Finite Element Modelling of Laminates
    Reinarz, Anne, Dodwell, Tim, Fletcher, Tim, Seelinger, Linus, Butler, Richard, and Scheichl, Robert
    Composite Structures
    doi bib
  6. Influence of a-posteriori subcell limiting on fault frequency in higher-order DG schemes
    Reinarz, A., Gallard, J.-M., and Bader, M.
    Proceedings of FTXS 2018: 8th Workshop on Fault Tolerance for HPC at eXtreme Scale, Held in conjunction with SC18: The International Conference for High Performance Computing, Networking, Storage and Analysis
    bib
  7. TSFC: a structure-preserving form compiler
    Miklós Homolya, Lawrence Mitchell, Fabio Luporini, and David A. Ham
    SIAM Journal on Scientific Computing
    doi arxiv:1705.03667 bib
  8. Deep learning for the classification and clustering of museum collections
    Matthew Roberts, Chris Willcocks, Anna Leone, and Boguslaw Obara
    in Annual Meeting of the European Association of Archaeologists
    bib
  9. Deep Learning for the Classification and Clustering of Museum Collections
    Matthew Roberts, Chris G. Willcocks, and Boguslaw Obara
    Computing Applications & Quantitative Methods in Archaeology
    bib
  10. TMIXT: A process flow for Transcribing MIXed handwritten and machine-printed Text
    F. Medhat, M. Mohammadi, S. Jaf, C. G. Willcocks, T. P. Breckon, P. Matthews, A. S. McGough, G. Theodoropoulos, and B. Obara
    in 2018 IEEE International Conference on Big Data (Big Data)
    doi bib
  11. Macular hole and edema segmentation with 3D image-to-image networks
    Chris G. Willcocks, Jonathan Frawley, Gregoire Payen de La Garanderie, Habib Maged, Geenen Caspar, David Steel, and Boguslaw Obara
    in International Society for Eye Research Conference
    bib
  12. Multi-scale Segmentation and Surface Fitting for Measuring 3D Macular Holes
    A. V. Nasrulloh, C. G. Willcocks, P. T. G. Jackson, C. Geenen, M. S. Habib, D. H. W. Steel, and B. Obara
    IEEE Transactions on Medical Imaging
    doi bib
  13. A Bayesian framework for assessing the strength distribution of composite structures with random defects
    A. Sandhu, A. Reinarz, and T.J. Dodwell
    Composite Structures
    doi bib
2017
  1. Multiscale Modelling of Lamination Defects in Curved Structures
    Reinarz, Anne, Fletcher, Tim, Dodwell, Tim, Butler, Richard, and Scheichl, Robert
    in 21st International Conference on Composite Materials
    bib
  2. Vertical slice modelling of nonlinear Eady waves using a compatible finite element method
    Hiroe Yamazaki, Jemma Shipton, Mike J. P. Cullen, Lawrence Mitchell, and Colin J. Cotter
    Journal of Computational Physics
    doi arxiv:1611.04929 bib
  3. Extracting 3D Parametric Curves from 2D Images of Helical Objects
    Chris G. Willcocks, Philip T.G. Jackson, Carl J. Nelson, and Boguslaw Obara
    IEEE Transactions on Pattern Analysis and Machine Intelligence
    doi bib
  4. Interactive GPU Active Contours for Segmenting Inhomogeneous Objects
    Chris G. Willcocks, Philip T.G. Jackson, Carl J. Nelson, Amar Nasrulloh, and Boguslaw Obara
    Journal of Real-time Image Processing
    video url: https://youtube.com/watch?v=6W4mO7BPeGg
    doi bib
2016
  1. Real-time segmentation of brain vasculature and identification of anomalies in magnetic resonance angiography
    Nitin Mukerji, Carl J. Nelson, Chris G. Willcocks, Philip T.G. Jackson, and Boguslaw Obara
    in European Congress of Neurosurgery
    bib
  2. Efficient mesh management in Firedrake using PETSc-DMPlex
    Michael Lange, Lawrence Mitchell, Matthew G. Knepley, and Gerard J. Gorman
    SIAM Journal on Scientific Computing
    doi arxiv:1506.07749 bib
  3. High level implementation of geometric multigrid solvers for finite element problems: applications in atmospheric modelling
    Lawrence Mitchell and Eike Hermann Müller
    Journal of Computational Physics
    doi arxiv:1605.00492 bib
  4. A structure-exploiting numbering algorithm for finite elements on extruded meshes, and its performance evaluation in Firedrake
    Gheorghe-Teodor Bercea, Andrew T. T. McRae, David A. Ham, Lawrence Mitchell, Florian Rathgeber, Luigi Nardi, Fabio Luporini, and Paul H. J. Kelly
    Geoscientific Model Development
    doi arxiv:1604.05937 bib
  5. Firedrake: automating the finite element method by composing abstractions
    Florian Rathgeber, David A. Ham, Lawrence Mitchell, Michael Lange, Fabio Luporini, Andrew T. T. McRae, Gheorghe-Teodor Bercea, Graham R. Markall, and Paul H. J. Kelly
    ACM Transactions on Mathematical Software
    doi arxiv:1501.01809 bib
  6. Efficient Modelling and Accurate Certification of Curved Aerospace Laminates
    Fletcher, Tim, Reinarz, Anne, Dodwell, Tim, Butler, Richard, Scheichl, Robert, and Newley, Richard
    in 17th European Conference on Composite Materials
    bib
  7. Application of high-speed level set segmentation to light sheet fluorescence microscopy
    Carl J. Nelson, Chris G. Willcocks, Philip T.G. Jackson, Philippe Laissue, and Boguslaw Obara
    in Light Sheet Fluorescence Microscopy International
    bib
  8. Automated generation and symbolic manipulation of tensor product finite elements
    Andrew T. T. McRae, Gheorghe-Teodor Bercea, Lawrence Mitchell, David A. Ham, and Colin J. Cotter
    SIAM Journal on Scientific Computing
    doi arxiv:1411.2940 bib
2015
  1. Developing a scalable hybrid MPI/OpenMP unstructured finite element model
    Xiaohu Guo, Michael Lange, Gerard Gorman, Lawrence Mitchell, and Michèle Weiland
    Computers & Fluids
    doi bib