pyMKM: An Open-Source Python Package for Microdosimetric Kinetic Model Calculation in Research and Clinical Applications

Among existing radiobiological models, the MKM and its extensions (SMK and OSMK) have demonstrated strong predictive capabilities but remain computationally demanding. To address this, we present pyMKM v0.1.0, an open-source Python package for the generation of microdosimetric tables and radiobiolog...

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Published in:	Computation Vol. 13; no. 11; p. 264
Main Authors:	Magro, Giuseppe, Pavanello, Vittoria, Jia, Yihan, Grevillot, Loïc, Glimelius, Lars, Mairani, Andrea
Format:	Journal Article
Language:	English
Published:	Basel MDPI AG 01.11.2025
Subjects:	Accuracy Energy Errors hadrontherapy Hypoxia linear energy transfer microdosimetric kinetic model Open source software open-source python package Radiation therapy relative biological effectiveness
ISSN:	2079-3197, 2079-3197
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Abstract	Among existing radiobiological models, the MKM and its extensions (SMK and OSMK) have demonstrated strong predictive capabilities but remain computationally demanding. To address this, we present pyMKM v0.1.0, an open-source Python package for the generation of microdosimetric tables and radiobiological quantities based on these models. The package includes modules for track structure integration, saturation and stochastic corrections, oxygen modulation, and survival fraction computation. Validation was conducted against multiple published datasets across various ion species, LET values, and cell lines under both normoxic and hypoxic conditions. Quantitative comparisons showed high agreement with reference data, with average log errors typically below 0.06 and symmetric mean absolute percentage errors under 2%. The software achieved full unit test coverage and successful execution across multiple Python versions through continuous integration workflows. These results confirm the numerical accuracy, structural robustness, and reproducibility of pyMKM. The package provides a transparent, modular, and extensible tool for microdosimetric modeling in support of radiobiological studies, Monte Carlo-based dose calculation, and biologically guided treatment planning.
AbstractList	Among existing radiobiological models, the MKM and its extensions (SMK and OSMK) have demonstrated strong predictive capabilities but remain computationally demanding. To address this, we present pyMKM v0.1.0, an open-source Python package for the generation of microdosimetric tables and radiobiological quantities based on these models. The package includes modules for track structure integration, saturation and stochastic corrections, oxygen modulation, and survival fraction computation. Validation was conducted against multiple published datasets across various ion species, LET values, and cell lines under both normoxic and hypoxic conditions. Quantitative comparisons showed high agreement with reference data, with average log errors typically below 0.06 and symmetric mean absolute percentage errors under 2%. The software achieved full unit test coverage and successful execution across multiple Python versions through continuous integration workflows. These results confirm the numerical accuracy, structural robustness, and reproducibility of pyMKM. The package provides a transparent, modular, and extensible tool for microdosimetric modeling in support of radiobiological studies, Monte Carlo-based dose calculation, and biologically guided treatment planning.
Audience	Academic
Author	Magro, Giuseppe Pavanello, Vittoria Jia, Yihan Grevillot, Loïc Mairani, Andrea Glimelius, Lars
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SubjectTerms	Accuracy Energy Errors hadrontherapy Hypoxia linear energy transfer microdosimetric kinetic model Open source software open-source python package Radiation therapy relative biological effectiveness
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Title	pyMKM: An Open-Source Python Package for Microdosimetric Kinetic Model Calculation in Research and Clinical Applications
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