AL
Ard A. Louis
cond-mat.softcond-mat.stat-mechq-bio.BMcs.LGphysics.bio-phevolutionary biologyModels, Geneticstat.MLMolecular Dynamics SimulationDNA nanotechnology
On Valency
published · living versionsW_knywpq4g·v1 · currentpublished
How symmetry and complexity shape three-dimensional programmable self-assembly
with Prarthana Agrawal, Joakim Bohlin
1 version
W_hy4un5bc·v1published
Preprints & journals
134 papers in the corpus · 1992–2026The Sign Code: The Hidden Binary Nature of Deep Networks2610.23616v1 · Niclas Goring, Shuofeng Zhang, Roi Holtzman et al.2026 · 0 citationsarXiv
Escaping Parameter Space: Tight Generalization Bounds via Representation Quality2610.23729v1 · Niclas Goring, Shuofeng Zhang, Branton DeMoss et al.2026 · 0 citationsarXiv
Counting Connected and Disconnected Ways to Assemble a Jigsaw Puzzle2607.11923v1 · Prarthana Agrawal, Abdurrahman Hadi Erturk, Ard A. Louis2026 · 0 citationsarXiv
Successive vertex orderings of graphs2604.07408v2 · Prarthana Agrawal, Abdurrahman Hadi Erturk, Ard A. Louis2026 · 0 citationsarXiv
Predicting the topography of fitness landscapes from the structure of genotype-phenotype maps.41628884 · Srivastava, Malvika, Louis, Ard A, Martin, Nora S2026 · 5 citationsGenetics. 2026;232(4)
Sufficient Conditions for Stability of Minimum-Norm Interpolating Deep ReLU Networks2602.13910v1 · Ouns El Harzli, Yoonsoo Nam, Ilja Kuzborskij et al.2026 · 0 citationsarXiv
Position: Many generalization measures for deep learning are fragile2510.18934v3 · Shuofeng Zhang, Ard Louis2025 · 0 citationsarXiv
A simple mean field model of feature learning2510.15174v1 · Niclas Goring, Chris Mingard, Yoonsoo Nam et al.2025 · 0 citationsarXiv
Bounding phenotype transition probabilities via conditional complexity.41056992 · Dingle, Kamal, Hagolani, Pascal, Zimm, Roland et al.2025 · 4 citationsJournal of the Royal Society, Interface. 2025;22(231):20240916
Closed-form norm scaling with data for overparameterized linear regression and diagonal linear networks under bias2509.21181v4 · Shuofeng Zhang, Ard Louis2025 · 0 citationsarXiv
Natural protein structures have evolved exceptional robustness to mutations10.1101/2025.08.27.672565v2 · Von der Dunk, S. H. A., Dingle, K., Louis, A. et al.2025 · 2 citationsbioRxiv
Developmental bias explains the evolutionary trend towards simple leaf shapes10.1101/2025.08.17.670617v3 · Malone, J. S., Martin, N. S., von der Dunk, S. H. A. et al.2025 · 2 citationsbioRxiv
RNA secondary structures are conserved but random10.1101/2025.08.18.670923v1 · Von der Dunk, S. H. A., Martin, N. S., Dingle, K. et al.2025 · 3 citationsbioRxiv
Controlling DNA-RNA strand displacement kinetics with base distribution.40478881 · Ratajczyk, Eryk J, Bath, Jonathan, Šulc, Petr et al.2025 · 9 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(23):e2416988122
Characterising the Inductive Biases of Neural Networks on Boolean Data2505.24060v1 · Chris Mingard, Lukas Seier, Niclas Goring et al.2025 · 0 citationsarXiv
Deep neural networks have an inbuilt Occam's razor.39809746 · Mingard, Chris, Rees, Henry, Valle-Pérez, Guillermo et al.2025 · 14 citationsNature communications. 2025;16(1):220
Decoupling Dynamical Richness from Representation Learning: Towards Practical Measurement2410.04264v3 · Yoonsoo Nam, Nayara Fonseca, Seok Hyeong Lee et al.2024 · 0 citationsarXiv
Exploiting the equivalence between quantum neural networks and perceptrons2407.04371v1 · Chris Mingard, Jessica Pointing, Charles London et al.2024 · 0 citationsarXiv
Non-Poissonian Bursts in the Arrival of Phenotypic Variation Can Strongly Affect the Dynamics of Adaptation.38693911 · Martin, Nora S, Schaper, Steffen, Camargo, Chico Q et al.2024 · 5 citationsMolecular biology and evolution. 2024;41(6)
Exploring Simplicity Bias in 1D Dynamical Systems.38785675 · Dingle, Kamal, Alaskandarani, Mohammad, Hamzi, Boumediene et al.2026 · 4 citationsEntropy (Basel, Switzerland). 2024;26(5)
An exactly solvable model for emergence and scaling laws in the multitask sparse parity problem2404.17563v3 · Yoonsoo Nam, Nayara Fonseca, Seok Hyeong Lee et al.2024 · 0 citationsarXiv
Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs.38536880 · Martin, Nora S, Camargo, Chico Q, Louis, Ard A2024 · 8 citationsPLoS computational biology. 2024;20(3):e1011893
Coarse-grained modeling of DNA-RNA hybrids.38497475 · Ratajczyk, Eryk J, Šulc, Petr, Turberfield, Andrew J et al.2024 · 22 citationsThe Journal of chemical physics. 2024;160(11)
Exploring simplicity bias in 1D dynamical systems2403.06989v2 · Kamaludin Dingle, Mohammad Alaskandarani, Boumediene Hamzi et al.2024 · 4 citationsarXiv
Maximum mutational robustness in genotype-phenotype maps follows a self-similar blancmange-like curve.37491910 · Mohanty, Vaibhav, Greenbury, Sam F, Sarkany, Tasmin et al.2023 · 17 citationsJournal of the Royal Society, Interface. 2023;20(204):20230169
Bias in the arrival of variation can dominate over natural selection in Richard Dawkins' biomorphs10.1101/2023.05.24.542053v1 · Martin, N. S., Camargo, C. Q., Louis, A. A.2023 · 1 citationbioRxiv
Designing the Self-Assembly of Arbitrary Shapes Using Minimal Complexity Building Blocks.36763807 · Bohlin, Joakim, Turberfield, Andrew J, Louis, Ard A et al.2023 · 35 citationsACS nano. 2023;17(6):5387-5398
Robustness and stability of spin-glass ground states to perturbed interactions.36797942 · Mohanty, Vaibhav, Louis, Ard A2023 · 6 citationsPhysical review. E. 2023;107(1-1):014126
The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami.37166713 · Doye, Jonathan P K, Fowler, Hannah, Prešern, Domen et al.2023 · 31 citationsMethods in molecular biology (Clifton, N.J.). 2023;2639:93-112
Predicting phenotype transition probabilities via conditional algorithmic probability approximations.36514888 · Dingle, Kamaludin, Novev, Javor K, Ahnert, Sebastian E et al.2022 · 13 citationsJournal of the Royal Society, Interface. 2022;19(197):20220694
The structure of genotype-phenotype maps makes fitness landscapes navigable.36175543 · Greenbury, Sam F, Louis, Ard A, Ahnert, Sebastian E2022 · 76 citationsNature ecology & evolution. 2022;6(11):1742-1752
Reply to Ocklenburg and Mundorf: The interplay of developmental bias and natural selection.35787035 · Johnston, Iain G, Dingle, Kamaludin, Greenbury, Sam F et al.2022 · 6 citationsProceedings of the National Academy of Sciences of the United States of America. 2022;119(28):e2205299119
The long and winding road to understanding organismal construction: Reply to comments on "From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics".35636230 · Manrubia, Susanna, Cuesta, José A, Aguirre, Jacobo et al.2022 · 0 citationsPhysics of life reviews. 2022;42:19-24
The interplay of supercoiling and thymine dimers in DNA.35188542 · Lim, Wilber, Randisi, Ferdinando, Doye, Jonathan P K et al.2022 · 13 citationsNucleic acids research. 2022;50(5):2480-2492
Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution.35275794 · Johnston, Iain G, Dingle, Kamaludin, Greenbury, Sam F et al.2022 · 128 citationsProceedings of the National Academy of Sciences of the United States of America. 2022;119(11):e2113883119
Phenotype Bias Determines How Natural RNA Structures Occupy the Morphospace of All Possible Shapes.34542628 · Dingle, Kamaludin, Ghaddar, Fatme, Šulc, Petr et al.2022 · 48 citationsMolecular biology and evolution. 2022;39(1)
Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling2111.10166v1 · Jonathan P. K. Doye, Ard A. Louis, John S. Schreck et al.2021 · 2 citationsFrontiers of Nanoscience, Vol. 21, Ch. 9, pp 195-210 (2022)
From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics.34088608 · Manrubia, Susanna, Cuesta, José A, Aguirre, Jacobo et al.2021 · 88 citationsPhysics of life reviews. 2021;38:55-106
Why flatness does and does not correlate with generalization for deep neural networks2103.06219v2 · Shuofeng Zhang, Isaac Reid, Guillermo Valle P'erez et al.2021 · 4 citationsarXiv
Double-descent curves in neural networks: a new perspective using Gaussian processes2102.07238v5 · Ouns El Harzli, Bernardo Cuenca Grau, Guillermo Valle-P'erez et al.2021 · 5 citationsarXiv
Generalization bounds for deep learning2012.04115v2 · Guillermo Valle-P'erez, Ard A. Louis2020 · 11 citationsarXiv
Phenotype bias determines how RNA structures occupy the morphospace of all possible shapes10.1101/2020.12.03.410605v2 · Dingle, K., Ghaddar, F., Sulc, P. et al.2020 · 10 citationsbioRxiv
Measuring internal forces in single-stranded DNA: Application to a DNA force clamp2007.13865v1 · Megan C. Engel, Flavio Romano, Ard A. Louis et al.2020 · 10 citationsJ. Chem. Theor. Comput. 16, 7764-7775 (2020)
Reconfigurable T-junction DNA Origami.32524699 · Young, Katherine G, Najafi, Behnam, Sant, William M et al.2020 · 4 citationsAngewandte Chemie (International ed. in English). 2020;59(37):15942-15946
Is SGD a Bayesian sampler? Well, almost2006.15191v2 · Chris Mingard, Guillermo Valle-P'erez, Joar Skalse et al.2020 · 15 citationsJournal of Machine Learning Research, 22 79 (2021), 1-64
Characterising DNA T-motifs by Simulation and Experiment2005.11545v1 · Behnam Najafi, Katherine G. Young, Jonathan Bath et al.2020 · 0 citationsarXiv
Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement.32444600 · Haley, Natalie E C, Ouldridge, Thomas E, Mullor Ruiz, Ismael et al.2020 · 103 citationsNature communications. 2020;11(1):2562
Generic predictions of output probability based on complexities of inputs and outputs.32157160 · Dingle, Kamaludin, Pérez, Guillermo Valle, Louis, Ard A2020 · 4 citationsScientific reports. 2020;10(1):4415
Neural networks are a priori biased towards Boolean functions with low entropy1909.11522v3 · Chris Mingard, Joar Skalse, Guillermo Valle-P'erez et al.2019 · 18 citationsarXiv
Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model.31282669 · Harrison, Ryan M, Romano, Flavio, Ouldridge, Thomas E et al.2019 · 33 citationsJournal of chemical theory and computation. 2019;15(8):4660-4672
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