Research on Justin's Homepage

Advances in the Inference of Chemical Reaction Networks from Time Series Data: A Systematic Survey

info@justinnk.net (Justin Noah Kreikemeyer) — Mon, 13 Apr 2026 10:27:55 +0200

Advances in the Inference of Chemical Reaction Networks from Time Series Data: A Systematic Survey.
Justin N. Kreikemeyer and Adelinde M. Uhrmacher. 2026. Preprint (03 2026).
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Self-Adaptive Simulation Models: A Case Study in Cell Biology

info@justinnk.net (Justin Noah Kreikemeyer) — Mon, 17 Nov 2025 00:00:00 +0200

Self-Adaptive Simulation Models: A Case Study in Cell Biology.
Pia Wilsdorf, Philipp Henning, Justin N. Kreikemeyer, Marcel Kliefoth, Simone Baltrusch, Adelinde M. Uhrmacher. In 29th International Symposium on Distributed Simulation and Real Time Applications (DS-RT), September 17-19, Prague, Czech Republic. IEEE, 1-8.
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Combining Natural Language and Time Series to Infer Reaction Networks

info@justinnk.net (Justin Noah Kreikemeyer) — Mon, 10 Nov 2025 00:00:00 +0100

Combining Natural Language and Time Series to Infer Reaction Networks.
Justin N. Kreikemeyer, Adelinde M. Uhrmacher. In 23rd International Conference on Computational Methods in Systems Biology (CMSB 2025), 10-12, Lyon, France. Eprint, not in proceedings.
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Using (Not-so) Large Language Models to Generate Simulation Models in a Formal DSL: A Study on Reaction Networks

info@justinnk.net (Justin Noah Kreikemeyer) — Sat, 01 Nov 2025 00:00:00 +0200

Using (Not-so) Large Language Models to Generate Simulation Models in a Formal DSL: A Study on Reaction Networks.
Justin N. Kreikemeyer, Miłosz Jankowski, Pia Wilsdorf, Adelinde M. Uhrmacher. 2025. ACM Transactions on Modeling and Computer Simulation 35, 4 (September 2025), 1-27.
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Synopsis: Using (Not-so) Large Language Models to Generate Simulation Models in a Formal DSL: A Study on Reaction Networks

info@justinnk.net (Justin Noah Kreikemeyer) — Mon, 23 Jun 2025 00:00:00 +0200

Synopsis: Using (Not-so) Large Language Models to Generate Simulation Models in a Formal DSL: A Study on Reaction Networks.
Justin N. Kreikemeyer, Miłosz Jankowski, Pia Wilsdorf, Adelinde M. Uhrmacher. In SIGSIM-PADS '25: 39th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, June 23-26, Santa Fe, NM, USA. Association for Computing Machinery, 56-57.
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Learning surrogate equations for the analysis of an agent-based cancer model

info@justinnk.net (Justin Noah Kreikemeyer) — Thu, 01 May 2025 00:00:00 +0200

Learning surrogate equations for the analysis of an agent-based cancer model.
Kevin Burrage, Pamela M. Burrage, Justin N. Kreikemeyer, Adelinde M. Uhrmacher, Hasitha N. Weerasinghe. 2025. Frontiers in Applied Mathematics and Statistics 11 (May 2025).
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Challenges and promises of self-adaptive simulation models

info@justinnk.net (Justin Noah Kreikemeyer) — Sun, 01 Dec 2024 00:00:00 +0200

Challenges and promises of self-adaptive simulation models.
Adelinde M. Uhrmacher, Pia Wilsdorf, and Justin N. Kreikemeyer. 2024. SIMULATION 100, 12 (December 2024), 1281-1295.
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Discovering Biochemical Reaction Models by Evolving Libraries

info@justinnk.net (Justin Noah Kreikemeyer) — Sun, 17 Nov 2024 00:00:00 +0200

Discovering Biochemical Reaction Models by Evolving Libraries.
[Received Best Paper Award]
J. N. Kreikemeyer, K. Burrage, A. M. Uhrmacher. In 22nd Conference on Computational Methods in Systems Biology (CMSB '24). Lecture Notes in Computer Science, vol. 14971, September 17 - 19, Pisa, Italy. Springer, Cham, 117-136.
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Learning Reaction Networks by Gradient Descent

info@justinnk.net (Justin Noah Kreikemeyer) — Sat, 16 Nov 2024 00:00:00 +0100

Learning Reaction Networks by Gradient Descent.
Justin N. Kreikemeyer, Philipp Andelfinger, Adelinde M. Uhrmacher. In 22nd International Conference on Computational Methods in System Biology (CMSB 2024), 16-18, Pisa, Italy. Eprint, not in proceedings.
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Automatic Gradient Estimation for Calibrating Crowd Models with Discrete Decision Making

info@justinnk.net (Justin Noah Kreikemeyer) — Fri, 28 Jun 2024 00:00:00 +0100

Automatic Gradient Estimation for Calibrating Crowd Models with Discrete Decision Making.
Philipp Andelfinger, Justin N. Kreikemeyer. In Computational Science – ICCS 2024. Lecture Notes in Computer Science, vol. 14836, July 2 - 4, Malaga, Spain. Springer, Cham, 227-241.
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Towards Learning Stochastic Population Models by Gradient Descent

info@justinnk.net (Justin Noah Kreikemeyer) — Mon, 24 Jun 2024 00:00:00 +0200

Towards Learning Stochastic Population Models by Gradient Descent.
Justin N. Kreikemeyer, Philipp Andelfinger, Adelinde M. Uhrmacher. In Proceedings of the 38th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (SIGSIM-PADS '24), June 24-26, Atlanta, GA, USA. Association for Computing Machinery, New York, NY, USA, 88-92.
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Smoothing Methods for Automatic Differentiation Across Conditional Branches

info@justinnk.net (Justin Noah Kreikemeyer) — Wed, 01 Nov 2023 00:00:00 +0200

Smoothing Methods for Automatic Differentiation Across Conditional Branches.
Justin N. Kreikemeyer, Philipp Andelfinger. 2023. IEEE Access 11, 143190-143211.
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Tensor-Based Smooth Execution of Stochastic Agent-Based Simulations

info@justinnk.net (Justin Noah Kreikemeyer) — Sun, 01 Jan 2023 00:00:00 +0200

Tensor-Based Smooth Execution of Stochastic Agent-Based Simulations.
[Received INFO.RO award for best master thesis 2022/2023]
Justin N. Kreikemeyer. Master's thesis.
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Inferring Dependency Graphs for Agent-Based Models Using Aspect-Oriented Programming

info@justinnk.net (Justin Noah Kreikemeyer) — Sun, 12 Dec 2021 00:00:00 +0200

Inferring Dependency Graphs for Agent-Based Models Using Aspect-Oriented Programming.
Justin N. Kreikemeyer, Till Köster, Adelinde M. Uhrmacher, Tom Warnke. In 2021 Winter Simulation Conference (WSC), December 12-15, Phoenix, AZ, USA. IEEE, 1-12.
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Inferring Dependency Graphs for Agent-Based Models using Aspect-Oriented Programming

info@justinnk.net (Justin Noah Kreikemeyer) — Fri, 01 Jan 2021 00:00:00 +0200

Inferring Dependency Graphs for Agent-Based Models using Aspect-Oriented Programming.
[Received INFO.RO award for best bachelor thesis 2020/2021]
Justin N. Kreikemeyer. Bachelor's thesis.
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Probing the Performance of the Edinburgh Bike Sharing System using SSTL

info@justinnk.net (Justin Noah Kreikemeyer) — Mon, 15 Jun 2020 00:00:00 +0200

Probing the Performance of the Edinburgh Bike Sharing System using SSTL.
Justin N. Kreikemeyer, Jane Hillston, Adelinde Uhrmacher. In Proceedings of the 2020 ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (SIGSIM PADS '20), June 15-17, Miami, FL, USA. ACM, New York, NY, USA, 141-152.
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