A benchmark suite of intracellular Boolean model variants and multiscale simulations for computational biology
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- June 17, 2026
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✨ NEW PRERINT ✨ PHYSIBENCH – A BENCHMARK SUITE OF INTRACELLULAR BOOLEAN MODEL VARIANTS AND MULTISCALE SIMULATIONS FOR COMPUTATIONAL BIOLOGY
📜 Preprint: https://arxiv.org/abs/2606.18215
🔗 GitHub repository: https://github.com/smilies-polito/PhysiBench
Are you a researcher in computational biology or scientific machine learning in search of executable, reproducible, and diverse simulation benchmarks?
Take a look at our #PhysiBench, a controlled in silico resource designed to support the development and evaluation of computational methods for systems biology, including:
⏭️ 612 executable intracellular Boolean regulatory network variants compatible with the PhysiBoSS/PhysiCell multiscale simulation framework;
🎲 120,000 time-resolved stochastic multiscale simulations generated from 60 selected models under controlled stimulation protocols and initial conditions.
The resource is designed for tasks such as #surrogateModeling, #dataDriven inference, #optimizationViaSimulation, and #parameterEstimation, supporting comparative benchmarking. PhysiBench aims to help the community develop more robust, comparable, and reusable methods for computational biology.
A big thank you to all co-authors, Marco Masera, Riccardo Smeriglio, Alessandro Savino, and Stefano Di Carlo, for the work, collaboration, and dedication behind this project, and to the SMILIES Polito Research Group for the inspiring scientific environment and continuous support.
Many thanks to Laurence Calzone, Vincent NOËL, and Marco Ruscone from the #PhysiCell development team, who took the time to share very useful feedback on this work, helping the team improve it and present it more effectively to the research community.
Masera, M., Smeriglio, R., Bardini, R., Savino, A., & Di Carlo, S. (2026). A benchmark suite of intracellular Boolean model variants and multiscale simulations for computational biology [Preprint]. arXiv. https://lnkd.in/dnhStxt7
#SMILIESPoliTO #ComputationalBiology #SystemsBiology #MultiscaleModeling #BooleanNetworks #PhysiCell #PhysiBoSS #Benchmarking #SurrogateModeling #SimulationBasedOptimization #OpenScience
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