Publications

"Wallpaper Group-Based Mechanical Metamaterials: Dataset Including Mechanical Responses"
Fleur Hendriks, Vlado Menkovski, Martin Doškář, Marc G. D. Geers, Kevin Verbeek, Ondřej Rokoš
Scientific Data (November 2025)
"Micellangelo: a Generative Model of Cell-Topography Interactions"
Nikita Konshin, Koen Minartz, Jan de Boer, Vlado Menkovski
(November 2025)
"Efficient Probabilistic Modeling of Crystallization at Mesoscopic Scale"
Pol Timmer, Koen Minartz, Vlado Menkovski
Lecture Notes in Computer Science (October 2025)
"Acquisition, quality control, and architecture of a large image dataset as a tool for in silico cell biological research"
Nikita Konshin, Marta Garcia Valverde, Danila Solodennikov, Koen Minartz, Vlado Menkovski, Rosalinde Masereeuw, Shantanu Singh, Silvia M. Mihăilă, Jan de Boer
Materials Today Bio (September 2025)
"Equivariant Flow Matching for Symmetry-Breaking Bifurcation Problems"
Fleur Hendriks, Ondřej Rokoš, Martin Doškář, Marc G. D. Geers, Vlado Menkovski
arXiv (September 2025)
"Wallpaper Group-Based Mechanical Metamaterials and their Mechanical Responses"
Fleur Hendriks, Vlado Menkovski, Martin Doškář, Marc Geers, Kevin Verbeek, Ondřej Rokoš
Zenodo (September 2025)
"Towards Fully Automated Molecular Simulations: Multi-Agent Framework for Simulation Setup and Force Field Extraction"
Marko Petković, Vlado Menkovski, Sofía Calero
arXiv (September 2025)
"Plasma state monitoring and disruption characterization using multimodal VAEs"
Yoeri Poels, Alessandro Pau, Christian Donner, Giulio Romanelli, Olivier Sauter, Cristina Venturini, Vlado Menkovski,
Nuclear Fusion (July 2025)
"Robust confinement state classification with uncertainty quantification through ensembled data-driven methods"
Yoeri Poels, Cristina Venturini, Alessandro Pau, Olivier Sauter, Vlado Menkovski
Nuclear Fusion (July 2025)
"Symmetry-informed graph neural networks for carbon dioxide isotherm and adsorption prediction in aluminum-substituted zeolites"
Marko Petković, José-Manuel Vicent Luna, Elīza Beate Dinne, Vlado Menkovski, Sofía Calero
Journal of Materials Chemistry A (May 2025)
"Flow Matching for Geometric Trajectory Simulation"
Kiet Bennema ten Brinke, Koen Minartz, Vlado Menkovski
arXiv (May 2025)
"Similarity equivariant graph neural networks for homogenization of metamaterials"
Fleur Hendriks, Vlado Menkovski, Martin Doškář, Marc G.D. Geers, Ondřej Rokoš
Computer Methods in Applied Mechanics and Engineering (March 2025)
"Discovering interaction mechanisms in crowds via deep generative surrogate experiments"
Koen Minartz, Fleur Hendriks, Simon Martinus Koop, Alessandro Corbetta, Vlado Menkovski
Scientific Reports (March 2025)
"Deep Neural Cellular Potts Models"
Koen Minartz, Tim d'Hondt, Leon Hillmann, Jörn Starruß, Lutz Brusch, Vlado Menkovski
arXiv (February 2025)
"VADA: A Data-Driven Simulator for Nanopore Sequencing"
Jonas Niederle, Simon Koop, Marc Pagès-Gallego, Vlado Menkovski
Lecture Notes in Computer Science (January 2025)
"Understanding complex crowd dynamics with generative neural simulators"
Koen Minartz, Fleur Hendriks, Simon Martinus Koop, Alessandro Corbetta, Vlado Menkovski
arXiv (December 2024)
"Mechanical Metamaterial: Square Array of Circular Holes Under Deformation"
Fleur Hendriks, Ondrej Rokos, Vlado Menkovski, Martin Doškář, Marc Geers
Zenodo (November 2024)
"Description Generation Using Variational Auto-Encoders for Precursor microRNA"
Marko Petković, Vlado Menkovski
Entropy (October 2024)
"Graph Neural Networks for Carbon Dioxide Adsorption Prediction in Aluminum-Substituted Zeolites"
Marko Petković, José Manuel Vicent-Luna, Vlado Menkovski, Sofía Calero
ACS Applied Materials & Interfaces (October 2024)
"Fast dynamic 1D simulation of divertor plasmas with neural PDE surrogates"
Yoeri Poels, Gijs Derks, Egbert Westerhof, Koen Minartz, Sven Wiesen, Vlado Menkovski
Nuclear fusion 63(12) (May 2024)
"Accelerating Simulation of Two-Phase Flows with Neural PDE Surrogates"
Yoeri Poels, Koen Minartz, Harshit Bansal, Vlado Menkovski
arXiv (May 2024)
"Equivariant Parameter Sharing for Porous Crystalline Materials"
Marko Petković, Pablo Romero Marimon, Vlado Menkovski, Sofía Calero
Lecture Notes in Computer Science (April 2024)
"Graph Neural Networks for Carbon Dioxide Adsorption Prediction in Aluminium-Exchanged Zeolites"
Marko Petković, José Manuel Vicent-Luna, Vlado Menkovski, Sofía Calero
arXiv (March 2024)
"Equivariant Neural Simulators for Stochastic Spatiotemporal Dynamics"
Koen Minartz, Yoeri Poels, Simon Koop, Vlado Menkovski
arXiv (May 2023)
"Towards Learned Simulators for Cell Migration"
Koen Minartz, Yoeri Poels, Vlado Menkovski
arXiv (October 2022)
"Simulation of Scientific Experiments with Generative Models"
Stepan Veretennikov, Koen Minartz, Vlado Menkovski, Burcu Gumuscu, Jan de Boer
Lecture Notes in Computer Science (April 2022)
"VAE-CE: Visual Contrastive Explanation Using Disentangled VAEs"
Yoeri Poels, Vlado Menkovski
Lecture Notes in Computer Science (April 2022)