Publications
Scientific Computing’s latest publications can be viewed below.
Annual Reviews
STFC’s Scientific Computing Annual Review:
STFC Scientific Computing Science Highlights:
Research Papers
Many of our Themes publish, and collaborate in publishing, research papers. The full catalogue of these can be accessed via ePubs, the open archive for STFC research publications.
AI for Science
iADMM: Global Convergence of Alternating Direction Method of Multipliers for Invex Objective Losses, Samuel Pinilla, Siu-Lun Yeung, and Jeyan Thiyagalingam, International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2024, 14 April 2024
EMinsight: A Tool to Capture CryoEM Microscope Configuration and Experimental Outcomes for Analysis and Deposition, Daniel Hatton, Jaehoon Cha, Stephen Riggs, Peter J Harrison, Jeyan Thiyagalingam, Daniel K Clare, Kyle L Morris, Acta Crystallographica Section D: Structural Biology, 16 February 2024
Global Optimality for Non-Linear Constrained Image Restoration via Invexity, Samuel Pinilla, Siu-Lun Yeung, and Jeyan Thiyagalingam, International Conference on Machine Learning (ICML), 2024, 16 January 2024
Padding-free Convolution based on Preservation of Differential Characteristics of Kernels, Kuangdai Leng, and Jeyan Thiyagalingam, 2023 International Conference on Machine Learning and Applications (ICMLA), 15 December 2023
Templated Hybrid Reusable Computational Analytics Workflow Management with Cloudmesh, Gregor von Laszewski, J.P. Fleischer, Geoffrey C. Fox, Juri Papay, Sam Jackson, Jeyan Thiyagalingam, 2023 IEEE 19th International Conference on e-Science (e-Science), 9 October 2023
Unsupervised Few-shot Image Segmentation with Dense Feature Learning and Sparse Clustering, Kuangdai Leng, Robert C. Atwood, Winfried Kockelmann, Deniza Chekrygina, and Jeyan Thiyagalingam, International Conference on Computer Vision, Imaging and Computer Graphics Theory and Application (VISAPP), 2024, 11 May 2023
Learning Disentangled Representations in Autoencoders by Introducing Orthogonality in the Latent Space, Jaehoon Cha, and Jeyan Thiyagalingam, Proceedings of Machine Learning Research, 24 April 2023
Using Generative Adversarial Networks to Match Experimental and Simulated Inelastic Neutron Scattering Data, Andy Sode Anker, Keith Butler, Manh Duc Le, Toby G. Perring, and Jeyan Thiyagalingam, Digital Discovery, 15 March 2023
Unified Graph Neural Network Force-Field for the Periodic Table: Solid State Applications, Kamal Choudhary, Brian DeCost, Lily Major, Keith Butler, Jeyan Thiyagalingam, and Francesca Tavazza, Digital Discovery, 23 January 2023
AI Benchmarking for Science: Efforts from the MLCommons Science Working Group, Jeyan Thiyagalingam, Gregor von Laszewski, Junqi Yin, Murali Emani, Juri Papay, Gregg Barrett, Piotr Luszczek, Aristeidis Tsaris, Christine Kirkpatrick, Feiyi Wang, Tom Gibbs, Venkatram Vishwanath, Mallikarjun Shankar, Geoffrey Fox, and Tony Hey, International Conference on High Performance Computing, 4 January 2023
Computational Biology and Imaging
The CCP4 suite: Integrative Software for Macromolecular Crystallography Jon Agirre, Charles B. Ballard, Tarik R. Drevon, Maria Fando, Ronan M. Keegan, Eugene B. Krissinel, Oleg Kovalevskiy, Andrey A. Lebedev, Kyle Stevenson, Ville Uski, David Waterman, Martyn D. Winn et al., Acta Cryst D79, 449-461, 2023
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge C.L.Lawson, Tom Burnley, Agnel P. Joseph, Colin M. Palmer, Martyn D. Winn et al., Nature Methods 21, 1340–1348, 2024
A Directional Regularization Method for the Limited-Angle Helsinki Tomography Challenge using the Core Imaging Library (CIL) Jakob Sauer Jørgensen, Evangelos Papoutsellis, Laura Murgatroyd, Gemma Fardell, Edoardo Pasca, Applied Mathematics for Modern Challenges 1, 143-169, 2023
Curate and Share Complex Biomolecular Simulation Workflows Jas Kalayan, Kin Chao, Sarah Rouse, James Gebbie-Rayet, 2024
Computational Mathematics
Sparse Linear Least Squares Problems, J Scott, M Tuma, Acta Numerica, 5 October 2024
Multipreconditioning with Directional Sweeping Methods for High-Frequency Helmholtz Problems, N Bootland, T Rees, Proceedings of ENUMATH 2024, 21 August 2024
Avoiding Breakdown in Incomplete Factorizations in Low Precision Arithmetic, J Scott, M Tuma, ACM Transactions on Mathematical Software, 1 May 2024
Approximating sparse Hessian matrices using large-scale linear least squares, JM Fowkes, NIM Gould, JA Scott, Numerical Algorithms, 2 November 2023
GALAHAD 4.0: An Open Source Library of Fortran Packages with C and Matlab Interfaces for Continuous Optimization, Jaroslav M. Fowkes and Nicholas I. M. Gould, The Journal of Open Source Software, 25 July 2023
Efficient Algebraic Two-Level Schwarz Preconditioner for Sparse Matrices, H Al Daas, P Jolivet, T Rees, SIAM Journal on Scientific Computing, 30 June 2023
Parallel Memory-Independent Communication Bounds for SYRK, Hussam Al Daas, Grey Ballard, Laura Grigori, Suraj Kumar, Kathryn Rouse, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 17 June 2023
Communication Lower Bounds and Optimal Algorithms for Multiple Tensor-Times-Matrix Computation, H Al Daas, G Ballard, L Grigori, S Kumar, K Rouse, SIAM Journal on Matrix Analysis and Applications, 31 March 2023
Data Engineering
The FAIR Data Registry (V1.2.0-rc3), Blackwell, R., Brett, A., Cook, J., Cummings, N., Field, R., Gonzalez-Beltran, A., Hollocombe, J., Lahiff, A., Richard, R., Wilson, A., & Zarębski, K., Zenodo, 2024
FAIR-IMPACT M4.3 – Specification of semantic artefact description, Gonzalez Beltran, A. N., & Wilson, A., Zenodo, 2024
Connecting Infrastructures: The Physical Sciences Data Infrastructure (PSDI) in the UK, Bicarregui, J., Coles, S., Matthews, B., Frey, J., Montanari, B., Bunakov, V., Knight, N., 1st Conference on Research Data Infrastructure (CoRDI) – Connecting Communities (CoRDI), 2023
DAFNI: a computational platform to support infrastructure systems research, Matthews, B., Hall, J., Batty, M., Blainey, S., Cassidy, N., Choudhary, R., Coca, D., Hallett, S., Harrou, J.J., James, P., Lomax, N., Oliver, P., Sivakumar, A., Tryfonas, T., Varga, L., Proceedings of the Institution of Civil Engineers – Smart Infrastructure and Construction 176, no. 3 (2023): 108-116, 2023
ExPaNDS: Laying the Foundations for Achieving Open Science for Everyone, Westbury, S., Fuhrmann, P., Marauska, J., Matthews, B., Ashton, A., McBirnie, A., Minotti, C., Barty, A., Ounsy, M., Valcarcel-Orti, A., Konrad, U.,Roarty, K., Millar, P., Syn Rad News: 1-4, 2023
FAIR Data Pipeline: Provenance-Driven Data Management for Traceable Scientific Workflows, Mitchell et al., Phil. Trans. R. Soc. A.380:20210300, 2022
