Publications from members of the group

2022

1. Spherical accretion of collisional gas in modified gravity I: self-similar solutions and a new cosmological hydrodynamical code
   Zhang, Zhang, Weinzierl, Tobias, Schulz, Holger, and Li, Baojiu
   Monthly Notices of the Royal Astronomical Society
   arXiv:2203.01174
2. AnoDDPM: Anomaly Detection With Denoising Diffusion Probabilistic Models Using Simplex Noise
   Wyatt, Julian, Leach, Adam, Schmon, Sebastian M, and Willcocks, Chris G
   in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)
   doi
3. Principles of Parallel Scientific Computing–-A First Guide to Numerical Concepts and Programming Methods
   Weinzierl, Tobias
   Undergraduate Topics in Computer Science book series (UTICS)
4. A multiresolution Discrete Element Method for triangulated objects with implicit timestepping
   Noble, Peter and Weinzierl, Tobias
   SIAM Journal on Scientific Computing (SISC)
5. Megapixel Image Generation with Step-Unrolled Denoising Autoencoders
   McKinney, Alex F and Willcocks, Chris G
   arXiv preprint arXiv:2206.12351
6. Computing the Square Root of a Low-Rank Perturbation of the Scaled Identity Matrix
   Massimiliano Fasi, Nicholas J. Higham, and Xiaobo Liu
   MIMS EPrint
7. Matrix Multiplication in Multiword Arithmetic: Error Analysis and Application to GPU Tensor Cores
   Massimiliano Fasi, Nicholas J. Higham, Florent Lopez, Theo Mary, and Mantas Mikaitis
   MIMS EPrint
8. Dynamic task fusion for a block-structured finite volume solver over a dynamically adaptive mesh with local time stepping
   Li, Baojiu, Schulz, Holger, Weinzierl, Tobias, and Zhang, Han
   in ISC High Performance 2022, Lecture Notes in Computer Science book series
9. Computational Graphs for Matrix Functions
   Jarlebring, Elias, Fasi, Massimiliano, and Ringh, Emil
   ACM Trans. Math. Software
10. Cross-Modal Image Synthesis Within Dual-Energy X-Ray Security Imagery
    Isaac-Medina, Brian KS, Bhowmik, Neelanjan, Willcocks, Chris G, and Breckon, Toby P
    in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)
    doi
11. The Dynamical Functional Particle Method for Multi-Term Linear Matrix Equations
    Dmytryshyn, Andrii, Fasi, Massimiliano, and Gulliksson, Mårten
    Appl. Math. Comput.
12. Stochastic Rounding: Implementation, Error Analysis and Applications
    Croci, Matteo, Fasi, Massimiliano, Higham, Nicholas J., Mary, Theo, and Mikaitis, Mantas
    Roy. Soc. Open Sci.
13. MedNeRF: Medical Neural Radiance Fields for Reconstructing 3D-aware CT-Projections from a Single X-ray
    Corona-Figueroa, Abril, Frawley, Jonathan, Taylor, Sam Bond-, Bethapudi, Sarath, Shum, Hubert P. H., and Willcocks, Chris G.
    in 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)
    doi
14. Sparse grid approximation spaces for space-time boundary integral formulations of the heat equation
    Chernov, Alexey and Reinarz, Anne in OWR
    doi
15. Unleashing Transformers: Parallel Token Prediction with Discrete Absorbing Diffusion for Fast High-Resolution Image Generation from Vector-Quantized Codes
    Bond-Taylor, Sam, Hessey, Peter, Sasaki, Hiroshi, Breckon, Toby P, and Willcocks, Chris G
    European Conference on Computer Vision (ECCV)
    doi
16. Multi-view Vision Transformers for Object Detection
    B.K.S. Isaac-Medina, C.G. Willcocks, and T.P. Breckon
    in International Conference on Pattern Recognition (ICPR)Denoising Diffusion Probabilistic Models on SO(3) for Rotational Alignment
    Adam Leach, Sebastian M Schmon, Matteo T. Degiacomi, and Chris G. Willcocks
    in ICLR 2022 Workshop on Geometrical and Topological Representation Learning
    

2021

1. Real Time Fencing Move Classification and Detection at Touch Time during a Fencing Match
   Sunal, Cem Ekin, Willcocks, Chris G, and Obara, Boguslaw
   in 2020 25th International Conference on Pattern Recognition (ICPR)
   doi
2. High Performance Uncertainty Quantification with Parallelized Multilevel Markov Chain Monte Carlo
   Seelinger, Linus, Reinarz, Anne, Rannabauer, Leonhard, Bader, Michael, Bastian, Peter, and Scheichl, Robert
   in Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis
   doi
3. Task Inefficiency Patterns for a Wave Equation Solver
   Schulz, Holger, Gadeschi, Gonzalo Brito, Rudyy, Oleksandr, and Weinzierl, Tobias
   in OpenMP: Enabling Massive Node-Level Parallelism
4. UNIT-DDPM: Unpaired Image Translation with Denoising Diffusion Probabilistic Models
   Sasaki, Hiroshi, Willcocks, Chris G, and Breckon, Toby P
   arXiv preprint arXiv:2104.05358
5. 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
   doi
6. Doubt and Redundancy Kill Soft Errors – Towards Detection and Correction of Silent Data Corruption in Task-based Numerical Software
   Samfass, Philipp, Weinzierl, Tobias, Reinarz, Anne, and Bader, Michael
   in 2021 IEEE/ACM 11th Workshop on Fault Tolerance for HPC at eXtreme Scale (FTXS)
   doi
7. Gradient Origin Networks
   Sam Bond-Taylor and Chris G. Willcocks
   in International Conference on Learning Representations (ICLR)
8. Deep Learning Protein Conformational Space with Convolutions and Latent Interpolations
   Ramaswamy, Venkata K., Musson, Samuel C., Willcocks, Chris G., and Degiacomi, Matteo T.
   Phys. Rev. X
   doi
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.
   in 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI)
   doi
10. Robust Data Assimilation with Noise: Applications to Cardiac Dynamics
    Marcotte, Christopher D, Fenton, Flavio H, Hoffman, Matthew J, and Cherry, Elizabeth M
    Chaos: An Interdisciplinary Journal of Nonlinear Science
    doi
11. Unmanned Aerial Vehicle Visual Detection and Tracking using Deep Neural Networks: A Performance Benchmark
    Isaac-Medina, Brian K. S., Poyser, Matt, Organisciak, Daniel, Willcocks, Chris G., Breckon, Toby P., and Shum, Hubert P. H.
    in 2021 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)
    doi
12. Robust 3D U-Net Segmentation of Macular Holes
    Frawley, Jonathan, Willcocks, Chris G, Habib, Maged, Geenen, Caspar, Steel, David H, and Obara, Boguslaw
    in Proc. Artificial Intelligence and Cognitive Science (AICS 2021)
13. Sampling the Eigenvalues of Random Orthogonal and Unitary Matrices
    Fasi, Massimiliano and Robol, Leonardo
    Linear Algebra Appl.
14. Algorithms for Stochastically Rounded Elementary Arithmetic Operations in IEEE 754 Floating-Point Arithmetic
    Fasi, Massimiliano and Mikaitis, Mantas
    IEEE Trans. Emerg. Topics Comput.
15. The Dual Inverse Scaling and Squaring Algorithm for the Matrix Logarithm
    Fasi, Massimiliano and Iannazzo, Bruno
    IMA J. Numer. Anal.
16. Numerical Behavior of NVIDIA Tensor Cores
    Fasi, Massimiliano, Higham, Nicholas J., Mikaitis, Mantas, and Pranesh, Srikara
    PeerJ Comput. Sci.
17. Generating Extreme-Scale Matrices with Specified Singular Values or Condition Numbers
    Fasi, Massimiliano and Higham, Nicholas J.
    SIAM J. Sci. Comput.
18. Matrices with Tunable Infinity-Norm Condition Number and No Need for Pivoting in LU Factorization
    Fasi, Massimiliano and Higham, Nicholas J.
    SIAM J. Matrix Anal. Appl.
19. Corrigendum to “Determinants of Normalized Bohemian Upper Hessenberg Matrices”
    Fasi, Massimiliano, Feng, Jishe, and Negri Porzio, Gian Maria
    Electron. J. Linear Algebra
20. Stabilized asynchronous fast adaptive composite multigrid using additive damping
    Charles D. Murray and Tobias Weinzierl
    Numer. Linear Algebra Appl.
    doi
21. Delayed approximate matrix assembly in multigrid with dynamic precisions
    Charles D. Murray and Tobias Weinzierl
    Concurr. Comput. Pract. Exp.
    doi
22. Deep Generative Modelling: A Comparative Review of VAEs, GANs, Normalizing Flows, Energy-Based and Autoregressive Models
    Bond-Taylor, Sam, Leach, Adam, Long, Yang, and Willcocks, Chris G.
    IEEE Transactions on Pattern Analysis and Machine Intelligence
    doi
23. Unparalleled Parallelism? CPU & GPU Architecture Trends and Their Implications for HPC Software
    Morgenstern, Laura, Kabadshow, Ivo, and Werner, Matthias
    in Tagungsband des FB-SYS Frühjahrstreffens

2020

1. 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 arxiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/cpe.5916
2. Computer Vision for Protein-protein Docking
   Rudden, Lucas SP, Degiacomi, Matteo T, and Willcocks, Chris G
   Biophysical Journal
   doi TeaMPI—Replication-Based Resilience Without the (Performance) Pain
   Philipp Samfass, Tobias Weinzierl, Benjamin Hazelwood, and Michael Bader
   in High Performance Computing
   doi
3. Lazy Stencil Integration in Multigrid Algorithms
   Murray, Charles D. and Weinzierl, Tobias
   in Parallel Processing and Applied Mathematics
4. Predicting Critical Ignition in Slow-Fast Excitable Models
   Marcotte, Christopher D. and Biktashev, Vadim N.
   Physical Review E
   doi
5. 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
6. 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
   doi
7. Segmentation of Macular Edema Datasets with Small Residual 3D U-Net Architectures
   Frawley, Jonathan, Willcocks, Chris G, Habib, Maged, Geenen, Caspar, Steel, David H, and Obara, Boguslaw
   in 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE)
   doi
8. Determinants of Normalized Bohemian Upper Hessenberg Matrices
   Fasi, Massimiliano and Negri Porzio, Gian Maria
   Electron. J. Linear Algebra
9. Substitution Algorithms for Rational Matrix Equations
   Fasi, Massimiliano and Iannazzo, Bruno
   Electron. Trans. Numer. Anal.
10. Enclave Tasking for DG Methods on Dynamically Adaptive Meshes
    Charrier, Dominic Etienne, Hazelwood, Benjamin, and Weinzierl, Tobias
    SIAM Journal on Scientific Computing
    doi arxiv:https://doi.org/10.1137/19M1276194
11. 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
12. 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
13. Shape tracing: An extension of sphere tracing for 3D non-convex collision in protein docking
    A. Leach, L. S. P. Rudden, S. Bond-Taylor, J. C. Brigham, M. T. Degiacomi, and C. G. Willcocks
    in 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE)
    doi
14. NUMA-Awareness as a Plug-In for an Eventify-Based Fast Multipole Method
    Morgenstern, Laura, Haensel, David, Beckmann, Andreas, and Kabadshow, Ivo
    in Proceedings of the International Conference on Computational Science (ICCS)

2019

1. 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
2. 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
3. A High-Performance Implementation of a Robust Preconditioner for Heterogeneous Problems
   Linus Seelinger, Anne Reinarz, and Robert Scheichl
   in PPAM 2019
4. 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
5. Computing Primary Solutions of Equations Involving Primary Matrix Functions
   Fasi, Massimiliano and Iannazzo, Bruno
   Linear Algebra Appl.
6. An Arbitrary Precision Scaling and Squaring Algorithm for the Matrix Exponential
   Fasi, Massimiliano and Higham, Nicholas J.
   SIAM J. Matrix Anal. Appl.
7. Optimality of the Paterson–Stockmeyer Method for Evaluating Matrix Polynomials and Rational Matrix Functions
   Fasi, Massimiliano
   Linear Algebra Appl.
8. 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
9. Sparse grid approximation spaces for space–time boundary integral formulations of the heat equation
   Alexey Chernov and Anne Reinarz
   Computers & Mathematics with Applications
   doi
10. GROMEX: A Scalable and Versatile Fast Multipole Method for Biomolecular Simulation
    Kohnke, Bartosz, Ullmann, Thomas R., Beckmann, Andreas, Kabadshow, Ivo, Haensel, David, Morgenstern, Laura, Dobrev, Plamen, Groenhof, Gerrit, Kutzner, Carsten, Hess, Berk, Dachsel, Holger, and Grubmüller, Helmut
    in Software for Exascale Computing – SPPEXA 2016-2019

2018

1. 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
2. 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
3. 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
4. Computing the Weighted Geometric Mean of Two Large-Scale Matrices and Its Inverse Times a Vector
   Fasi, Massimiliano and Iannazzo, Bruno
   SIAM J. Matrix Anal. Appl.
5. Multiprecision Algorithms for Computing the Matrix Logarithm
   Fasi, Massimiliano and Higham, Nicholas J.
   SIAM J. Matrix Anal. Appl.
6. 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
7. 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
8. 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
9. Eventify: Event-Based Task Parallelism for Strong Scaling
   Haensel, David, Morgenstern, Laura, Beckmann, Andreas, Kabadshow, Ivo, and Dachsel, Holger
   in Proceedings of the Platform for Advanced Scientific Computing Conference (PASC)

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
2. Dynamical Mechanism of Atrial Fibrillation: A Topological Approach
   Marcotte, Christopher D. and Grigoriev, Roman O.
   Chaos
   doi arxiv:1703.10680
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
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

2016

1. Adjoint Eigenfunctions of Temporally Recurrent Single-Spiral Solutions in a Simple Model of Atrial Fibrillation
   Marcotte, Christopher D. and Grigoriev, Roman O.
   Chaos
   doi arxiv:1605.00115
2. 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
3. A Backward/Forward Recovery Approach for the Preconditioned Conjugate Gradient Method
   Fasi, Massimiliano, Langou, Julien, Robert, Yves, and Uçar, Bora
   J. Comput. Sci.
4. Coping with Silent Errors in HPC Applications
   Aupy, Guillaume, Benoit, Anne, Cavelan, Aurélien, Fasi, Massimiliano, Robert, Yves, Sun, Hongyang, and Uçar, Bora
   Emergent Computation. Emergence, Complexity and Computation
   https://doi.org/10.1007/978-3-319-46376-6
   

2015

1. Unstable Spiral Waves and Local Euclidean Symmetry in a Model of Cardiac Tissue
   Marcotte, Christopher D. and Grigoriev, Roman O.
   Chaos: An Interdisciplinary Journal of Nonlinear Science
   doi arxiv:1412.4731
2. Combining Backward and Forward Recovery to Cope with Silent Errors in Iterative Solvers
   Fasi, Massimiliano, Robert, Yves, and Uçar, Bora
   Proceedings of the 29th Parallel and Distributed Processessing Symposium Workshop
3. An Algorithm for the Matrix Lambert $W$ Function
   Fasi, Massimiliano, Higham, Nicholas J., and Iannazzo, Bruno
   SIAM J. Matrix Anal. Appl.
4. Exact Coherent Structures and Chaotic Dynamics in a Model of Cardiac Tissue
   Byrne, Greg, Marcotte, Christopher D., and Grigoriev, Roman O.
   Chaos: An Interdisciplinary Journal of Nonlinear Science
   doi arxiv:1404.2316