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Professional Profile & Research

Portrait of Justin Kreikemeyer.

Justin N. Kreikemeyer

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I build methods that turn measured data into models humans can read. Given observations of how a system changed over time and prior knowledge, my work develops methods to automatically propose a mechanism that explains them: a set of interaction rules that can be inspected and simulated over time. This is in contrast to the opaque, phenomenological models typically produced by deep learning. It also supports otherwise very time-intensive manual modeling with an automated search, guided by data and expert knowledge.

I am currently a research associate and PhD candidate with the Modeling and Simulation Chair at the University of Rostock, Germany. I plan to defend my PhD in Q2 2027.

Recent News

September 2026
Excited to attend the 13th Heidelberg Laureate Forum.
July 2026
Paper accepted and to be presented in December at WSC'26: Visual Interactive Inference of Chemical Reaction Networks From Time-Series Data. In the meantime, you can try it yourself with our interactive webapp.
June 2026
Chaired the PhD Colloquium at the 40th ACM SIGSIM PADS in Vienna, Austria together with Steffen Straßburger. Learned about digital humanism at the pre-conference and a social event together with DigHum2026.
March 2026
New Preprint: Advances in the Inference of Chemical Reaction Networks from Time Series Data: A Systematic Survey (currently under review).

Curriculum Vitae

Positions

2023 – today
Research Associate, University of Rostock.as part of my PhD at the Modeling and Simulation Chair, Institute for Visual and Analytic Computing.
2021
Part-time intern, PlanetAI GmbH, Rostock.Image classification with convolutional neural networks in TensorFlow; cloud deployment with Terraform and Kubernetes.
2019 – 2020
Research Assistant, University of Edinburgh.On "Modeling Edinburgh's Mobility During the Festival". Built and validated a stochastic model of the Edinburgh cycle hire scheme using spatio-temporal model-checking and the process algebra CARMA, supervised by Jane Hillston; this became my first paper.

Education

2023 – today
PhD Computer Science, University of Rostock.Fields: simulation, machine learning, systems biology. Advisor: Adelinde M. Uhrmacher. Targeting a defense date in Q2 2027.
2021 – 2023
M.Sc. Computer Science, University of Rostock.Thesis on simulation-based optimization and parallel simulation, advised by Philipp Andelfinger.
2017 – 2021
B.Sc. Computer Science, University of Rostock.Thesis on stochastic discrete-event simulation, advised by Tom Warnke.

Teaching & Supervision

2023 – today
Tutoring for introductory lectures and master-level seminarsimperative programming; algorithms and data structures; seminar on simulation and machine learning; special lecture on differentiable simulation.
2023 – today
Thesis supervision of bachelor's and master's theses.Supervised four Bachelor's theses and three Master's theses.
2018 – 2019
Tutor in the Junior Studies Program, which gives high-school students a first taste of university.Algorithms and Data Structures; Functional Programming; Complexity and Formal Languages.

Awards

2024
Best Paper Award at CMSB '24.22nd International Conference on Computational Methods in Systems Biology.
2024
Best Master's Thesis 2022/23.Awarded by Informatik-Forum Rostock e.V.
2021
Best Bachelor's Thesis 2020/21.Awarded by Informatik-Forum Rostock e.V.
2020 – 2021
Deutschlandstipendium scholarship.Awarded by the University of Rostock.
2017
DPG Abiturpreis for outstanding performance in physics.Awarded by the German Physical Society.

Participation in the Academic System

2025 – 2026
PhD Colloquium Co-Chair, ACM SIGSIM PADS.
2024 – 2026
Reviewer, ACM SIGSIM PADS.review of papers, PhD colloquium contributions, and for the ACM reproducibility initiative.
ongoing
Student member of ACM and ACM SIGSIM.
Want more details or prefer a PDF? My full CV and references are available upon request.

Skills & Tools
MethodsAutomatic differentiation and gradient estimation, stochastic simulation, simulation-based optimization and inference, system identification, sparse regression, evolutionary algorithms, LLM fine-tuning, Chemical Reaction Network modeling.
PracticeReproducible research artifacts (open code on GitHub, archival on Zenodo, ACM reproducibility initiative), scientific writing, LaTeX typesetting and publishing, Unix command line, Linux native, agentic AI workflows for coding & academic research.
Programming LanguagesProficient programmer with lots of experience in Python. Some experience with C, Java, Julia, C++, CUDA, Haskell (in descending order of last usage).
Natural LanguagesGerman (first language), English.
Research

Modeling and simulation often runs forwards: you write down a mechanism, then compute how it behaves over time. I work on the inverse problem: going from data back to the mechanism. This is much harder, because both the structure of the model and its parameters are unknown and the inverse mapping is not unique. It is part the emerging field of “AI for Science”, where AI is meant in its original, broad sense and large language models are just one small subclass. My dissertation focuses on the concrete instance of automated modeling of chemical reaction networks given time-series data.

My current research interests are:

My main interest is in developing new methods, and I’m always happy to go into the theory as well where the problem calls for it. I’m also interested in interdisciplinary applications of the methods I develop or, even better, being inspired by interdisciplinary problems. Currently, my focus is on systems biology, where chemical reaction networks are a de-facto standard modeling formalism.

Chronological Publication List

This list includes everything in chronological order, including unpublished posters and reviews for the ACM reproducibility initiative. You can see the article type below each entry. The code, data and other artifacts associated with my publications can usually be found on GitHub and/or Zenodo and are also linked below. You may click on “more” to reveal abstracts and sometimes further information on an entry.

2026

Interactive Visual Inference of Chemical Reaction Networks From Time-Series Data.
Justin N. Kreikemeyer, Glenn Skrzypczak, Christian Tominski, Adelinde M. Uhrmacher. In Proceedings of the Winter Simulation Conference (WSC '26), December 6-9, Glasgow, Scotland. Accepted, to appear.
conference paper | bib| artifacts| git| more
RCR Report for the Paper: "On the Modelling of Aggregated Behaviour for Simulation: An Event–Based Architecture".
Justin Noah Kreikemeyer. In SIGSIM-PADS '26: 40th ACM SIGSIM International Conference on Principles of Advanced Discrete Simulation, June 24-26, Vienna, Austria. Association for Computing Machinery, 204-207.
reproducibility review | pdf | doi| bib| more
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).
preprint | pdf | doi| bib| more

2025

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.
conference paper | doi| bib| artifacts| more
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.
conference poster | pdf| bib| more
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.
journal article | pdf | doi| bib| artifacts| git| more
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.
extended abstract | pdf | doi| bib| more
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).
journal article | pdf | doi| bib| artifacts| git| more

2024

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.
journal article | doi| bib| more
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.
conference paper | pdf | doi| bib| artifacts| git| more
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.
conference poster | pdf| bib| more
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.
conference paper | pdf | doi| bib| git| more
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.
conference paper | pdf | doi| bib| more

2023

Smoothing Methods for Automatic Differentiation Across Conditional Branches.
Justin N. Kreikemeyer, Philipp Andelfinger. 2023. IEEE Access 11, 143190-143211.
journal article | pdf | doi| bib| artifacts| git| more

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.
thesis | bib| more

2021

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.
conference paper | doi| bib| git| more
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.
thesis | bib| git| more

2020

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.
conference paper | pdf | doi| bib| artifacts| git| more