Publications of the CSL group2024
-
Proceedings. Preface. In: Computational Science – ICCS 2024. ISBN 9783031637599. III, pp. v-vi.
-
Article. Predicting early-stage coronary artery disease using machine learning and routine clinical biomarkers improved by augmented virtual data. European Heart Journal - Digital Health 5(5), pp. 542-550.
-
PhD Thesis. Platelet aggregation in complex vessel geometries. ISBN 9789464698121. Supervised by A. G. Hoekstra and G. Závodszky.
-
Proceedings. Plasma-Assisted Air Cleaning Decreases COVID-19 Infections in a Primary School. In: Computational Science – ICCS 2024. ISBN 9783031637728. IV, pp. 196-209.
-
Article. Physics informed data-driven near-wall modelling for lattice Boltzmann simulation of high Reynolds number turbulent flows. Communications Physics 7, 338.
-
Chapter. Natural Information Processing. In: Foundational Papers in Complexity Science. - Volume 4. ISBN 9781947864597, 9781947864559. pp. 2447-2532.
-
PhD Thesis. Modern advances in computational credit risk modelling. ISBN 9789464736298. Supervised by B. D. Kandhai and P. M. A. Sloot.
-
Article. Inferring Dealer Networks in the Foreign Exchange Market Using Conditional Transfer Entropy. Entropy 26(9), 738.
-
Article. Impact of increasing local economic capacity on reducing maritime logistics costs in island Province of eastern Indonesia. Transportation Research Interdisciplinary Perspectives 27, 101195.
-
Article. How social rewiring preferences bridge polarized communities. Chaos, Solitons and Fractals 180, 114594.
-
Proceedings. Higher Order Reasoning under Intent Uncertainty Reinforces the Hobbesian Trap. In: AAMAS '24. ISBN 9798400704864. p. 1066–1074.
-
Article. Global ranking of the sensitivity of interaction potential contributions within classical molecular dynamics force fields. npj Comput Mater 10, 87.
-
Chapter. Fractals and Chaos in the Hemodynamics of Intracranial Aneurysms. In: The Fractal Geometry of the Brain. ISBN 9783031476068. p. 397–412.
-
Article. FAIR compliant database development for human microbiome data samples. Frontiers in Cellular and Infection Microbiology 14, 1384809.
-
Article. Efficient Search Algorithms for Identifying Synergistic Associations in High-Dimensional Datasets. Entropy 26(11), 968.
-
Article. Dynamics in and dynamics of networks using DyNSimF. Journal of Computational Science 81, 102376.
-
Article. Digital twins of the Earth with and for humans. Communications earth & environment 5, 463.
-
Article. Data-driven reduced-order modelling for blood flow simulations with geometry-informed snapshots. Journal of computational Physics 497, 112639.
-
Article. Data-driven Lie point symmetry detection for continuous dynamical systems. Machine Learning: Science and Technology 5(1), 015037.
-
Article. Criminal organizations exhibit hysteresis, resilience, and robustness by balancing security and efficiency. Scientific Reports 14, 17678.
-
Proceedings. CrimeSeen: An Interactive Visualization Environment for Scenario Testing on Criminal Cocaine Networks. In: Computational Science – ICCS 2024. ISBN 9783031637599. III, pp. 195-204.
-
Article. Cooperative food bank: a collective insurance regime to govern food insecurity and nitrogen pollution under risk. Environmental Research Letters 19(8), 084057.
-
Article. Computation at the Cutting Edge of Science. Journal of Computational Science 81, 102379.
-
Article. Comparison of Flow Reduction Efficacy of Nominal and Oversized Flow Diverters Using a Novel Measurement-assisted in Silico Method. Clinical Neuroradiology 34(3), p. 675–684.
-
Article. Characterizing pedestrian contact interaction trajectories to understand spreading risk in human crowds. Journal of Computational Science 81, 102358.
-
Chapter. Cellular Blood Flow Modeling with HemoCell. In: High Performance Computing for Drug Discovery and Biomedicine . ISBN 9781071634493. pp. 351-368.
-
Article. Cascades Towards Noise-Induced Transitions on Networks Revealed Using Information Flows. Entropy 26(12), 1050.
-
Article. Carotid single- and dual-layer stents reduce the wall adhesion of platelets by influencing flow and cellular transport. Computers in Biology and Medicine 183, 109313.
-
Article. Bias in O-Information Estimation. Entropy 26(10), 837.
-
Article. Artificial Intelligence Must Be Made More Scientific. Journal of Chemical Information and Modeling 64(15), pp. 5739-5741.
-
Proceedings. Article Classification with Graph Neural Networks and Multigraphs. In: The 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024). ISBN 9782493814104. pp. 1539-1547.
-
Proceedings. Application of Generative Artificial Intelligence for Epidemic Modeling. In: 2024 Winter Simulation Conference (WSC 2024). ISBN 9798331534202. pp. 2727-2738.
-
Article. Anti-conformists catalyze societal transitions and facilitate the expression of evolving preferences. PNAS nexus 3(8), pgae302.
-
Article. An in silico modeling approach to understanding the dynamics of the post-burn immune response. Frontiers in Immunology 15, 1303776.
-
Article. Alcohol consumption as a socially contagious phenomenon in the Framingham Heart Study social network. Scientific Reports 14, 4499.
-
Article. Adaptive foraging of pollinators fosters gradual tipping under resource competition and rapid environmental change. PLoS Computational Biology 20, e1011762.
-
Article. A static replication approach for callable interest rate derivatives. Quantitative Finance 24(3-4), pp. 409-432.
-
Article. A data-driven agent-based model of primary school segregation in Amsterdam. Journal of Mathematical Sociology 48(3), pp. 362-392.
-
Proceedings. A Three-Dimensional Fluid-Structure Interaction Model for Platelet Aggregates Based on Porosity-Dependent Neo-Hookean Material. In: Computational Science – ICCS 2024. ISBN 9783031637834. VII, pp. 48-62.
-
Proceedings. 3D-LEX v1.0. In: 11th Workshop on the Representation and Processing of Sign Languages: Evaluation of Sign Language Resources (sign-lang@LREC-COLING 2024). ISBN 9782493814302. pp. 290-301.
2023
-
Proceedings. Visualization Techniques and Tools for Developing Digital Twins of Ecosystems. In: Proceedings, 2023 IEEE SmartWorld, Ubiquitous Intelligence & Computing, Autonomous & Trust Vehicles, Scalable Computing and Communications, Digital Twin, Privacy Computing and Data Security, Metaverse. ISBN 9798350319804. pp. 225-232.
-
Article. Using picoliter droplet deposition to track clonal competition in adherent and organoid cancer cell cultures. Scientific Reports 13, 18832.
-
Article. Using network analysis to identify leverage points based on causal loop diagrams leads to false inference. Scientific Reports 13(1), 21046.
-
Article. Unitary partitioning and the contextual subspace variational quantum eigensolver. Physical Review Research 5(1), 013095.
-
Proceedings. Understanding the Dynamics of the Proliferative Phase in Local Burn Wound Healing. In: Proceedings : 2023 IEEE International Conference on Bioinformatics and Biomedicine. ISBN 9798350337488. pp. 3676-3683.
-
Article. Understanding multimorbidity requires sign-disease networks and higher-order interactions, a perspective. Frontiers in Systems Biology 3, 1155599.
-
Proceedings. Toxicity in Evolving Twitter Topics. In: Computational Science – ICCS 2023. ISBN 9783031360275. IV, pp. 40-54.
-
Article. Towards evolutionary predictions: Current promises and challenges. Evolutionary Applications 16(1), pp. 3-21.
-
Article. The relationship between cognitive functioning and psychopathology in patients with psychiatric disorders. Psychological Medicine 53(2), pp. 476-485.
-
Article. The evolution of forecasting for decision-making in dynamic environments. Collective Intelligence 2(4).
-
Article. The dynamics of corruption under an optional external supervision service. Applied Mathematics and Computation 457, 128172.
-
Article. The computational planet. Journal of Computational Science 72, 102102.
-
Article. Testing hypotheses on the calcification in scleractinian corals using a spatio-temporal model that shows a high degree of robustness. Journal of Theoretical Biology 561(21), 111382.
-
Article. TIES 2.0: A dual-topology open source relative binding free energy builder with web portal. Journal of Chemical Information and Modeling 63(3), pp. 718-724.
-
Article. Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nature Communications 14, 3630.
-
Article. Simulating the multicausality of Alzheimer's disease with system dynamics. Alzheimer's & Dementia 19(6), pp. 2633-2654.
-
Proceedings. Simulating Initial Steps of Platelet Aggregate Formation in a Cellular Blood Flow Environment. In: Computational Science – ICCS 2023. ISBN 9783031360244. III, pp. 323-336.
-
Article. Reduced Plasticity in Coupling Strength in the Aging SCN Clock as Revealed by Kuramoto Modeling. Journal of biological rhythms 38(5), pp. 461-475.
-
Article. Promises and pitfalls of computational modelling for insurgency conflicts. The Journal of Defense Modeling and Simulation: Applications, Methodology, Technology 20(3), pp. 333-350.
-
Proceedings. Professional and 21st Century Skills for Data Driven Digital Economy. In: 2023 IEEE Global Engineering Education Conference (EDUCON). ISBN 9798350399431. pp. 847-854.
-
Proceedings. Preface. In: Computational Science – ICCS 2023. ISBN 9783031359958. I, pp. v-vi.
-
Proceedings. Preface. In: Computational Science – ICCS 2023. ISBN 9783031360213. II, pp. v-vi.
-
Proceedings. Preface. In: Computational Science – ICCS 2023. ISBN 9783031360305. V, pp. v-vi.
-
Proceedings. Preface. In: Computational Science – ICCS 2023. ISBN 9783031360275. IV, pp. v-vi.
-
Proceedings. Preface. In: Computational Science – ICCS 2023. ISBN 9783031360244. III, pp. v-vi.
-
Article. Periodic orbits in chaotic systems simulated at low precision. Scientific Reports 13, 11410.
-
Article. Optimization of institutional incentives for cooperation in structured populations. Journal of the Royal Society Interface 20(199), 20220653.
-
Article. Multivariate continuous-time autoregressive moving-average processes on cones. Stochastic Processes and their Applications 162, pp. 299-337.
-
Article. Multi-unit building address geocoding: An approach without indoor location reference data. Transactions in GIS 27(1), pp. 57-83.
-
Proceedings. Modelling the Interplay Between Chronic Stress and Type 2 Diabetes On-Set. In: Computational Science – ICCS 2023. ISBN 9783031360206. II, pp. 330-338.
-
Proceedings. Modeling mechanisms of school segregation and policy interventions: A complexity perspective. In: International Conference on Computational Science. pp. 74-89.
-
Article. Measure cross-sectoral structural similarities from financial networks. Scientific Reports 13, 7124.
-
Proceedings. Manifold Analysis for High-Dimensional Socio-Environmental Surveys. In: Computational Science – ICCS 2023. ISBN 9783031360275. IV, pp. 25-39.
-
Article. Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand-Protein Interactions and Allostery in SARS-CoV-2 Targets. Journal of Chemical Theory and Computation 19(11), pp. 3359-3378.
-
Article. Learning Lie Group Symmetry Transformations with Neural Networks. Proceedings of Machine Learning Research 221, pp. 50-59.
-
Article. Large-scale molecular dynamics elucidates the mechanics of reinforcement in graphene-based composites. Advanced materials 35(35), e2302237.
-
Article. Inverse uncertainty quantification of a mechanical model of arterial tissue with surrogate modelling. Reliability Engineering & System Safety 238, 109393.
-
Article. Intrinsic fluctuations of reinforcement learning promote cooperation. Scientific Reports 13, 1309.
-
Article. Initial platelet aggregation in the complex shear environment of a punctured vessel model. Physics of Fluids 35(7), 071904.
-
Proceedings. Improving the Resiliency of Decentralized Crowdsourced Blockchain Oracles. In: Computational Science – ICCS 2023. ISBN 9783031359958. I, pp. 3-17.
-
Article. Improving Article Classification with Edge-Heterogeneous Graph Neural Networks.
-
Article. Image-based flow simulation of platelet aggregates under different shear rates. PLoS Computational Biology 19(7), e1010965.
-
Article. High-Content and High-Throughput Clonogenic Survival Assay Using Fluorescence Barcoding. Cancers 15(19), 4772.
-
Article. High resolution simulation of basilar artery infarct and flow within the circle of Willis. Scientific Reports 13, 21665.
-
Proceedings. Global Sensitivity Analysis Using Polynomial Chaos Expansion on the Grassmann Manifold. In: Computational Science – ICCS 2023. ISBN 9783031360305. V, pp. 583-597.
-
Article. FabSim3: An automation toolkit for verified simulations using high performance computing. Computer Physics Communications 283, 108596.
-
Article. Exploring the potential impact of multi-factor precision interventions in Alzheimer's disease with system dynamics. Journal of Biomedical Informatics 145, 104462.
-
Article. Ensemble-Based Approaches Ensure Reliability and Reproducibility. Journal of Chemical Information and Modeling 63(22), pp. 6959-6963.
-
Proceedings. Empowering Machine Learning Development with Service-Oriented Computing Principles. In: Service-Oriented Computing - 17th Symposium and Summer School, SummerSOC 2023, Revised Selected Papers. ISBN 9783031457289. pp. 24-44.
-
Article. Embracing complexity in sepsis. Critical Care 27, 102.
-
Article. Development and performance of a HemeLB GPU code for human-scale blood flow simulation. Computer Physics Communications 282(108548), 108548.
-
Proceedings. Data Integration Landscapes. In: Computational Science – ICCS 2023. ISBN 9783031359958. I, pp. 494-508.
-
Article. Cooperative behaviour at public electric vehicle charging stations. Travel Behaviour and Society 32, 100572.
-
PhD Thesis. Computational models of emergent organisation in conflict environments. ISBN 9789464731811. Supervised by P. M. A. Sloot, T. M. van Engers, and A. I. Barros.
-
Article. Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions. Journal of Chemical Theory and Computation 19(21), pp. 7846-7860.
-
Proceedings. Characterization of Pedestrian Contact Interaction Trajectories. In: Computational Science – ICCS 2023. ISBN 9783031359958. I, pp. 18-32.
-
Article. Capitalized value of evolving flood risks discount and nature-based solution premiums on property prices. Ecological Economics 205, 107682.
-
Proceedings. Building a Fine-Grained Analytical Performance Model for Complex Scientific Simulations. In: Parallel Processing and Applied Mathematics. ISBN 9783031304422. I, pp. 183-196.
-
Article. Branching archaeocyaths as ecosystem engineers during the Cambrian radiation. Geobiology 21(1), pp. 66-85.
-
Article. Benchmarking noisy intermediate scale quantum error mitigation strategies for ground state preparation of the HCl molecule. Physical Review Research 5(4), 043054.