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MEmilio v2.4.0 - A high performance Modular EpideMIcs simuLatIOn software

Authors: Bicker, Julia; Gerstein, Carlotta; Kerkmann, David; Korf, Sascha; Schmieding, René; Wendler, Anna; Zunker, Henrik; +19 Authors

MEmilio v2.4.0 - A high performance Modular EpideMIcs simuLatIOn software

Abstract

MEmilio implements various models for infectious disease dynamics, ranging from simple compartmental models to complex Integro-Differential and agent-based models. Its modular design enables the combination of different models with distinct mobility patterns. Through efficient implementation and parallelization in C++ and an easy-to-use python interface, MEmilio delivers cutting-edge and compute-intensive epidemiological models to broad range of applications and users, providing precise and high-resolution spatiotemporal infectious disease dynamics. MEmilio is continuously extended and is available open-source for community use. We here publish version 2.4.0, our most recent major release. v2.4.0 Changes Added features / functionality: Added generic country simulation that automatically downloads contact data for various countries from POLYMOD ODE/IDE-based models with hospitalization: Added possibility of death from hospitalization without intensive care Added ODE SEIR metapopulation model with implicit mobility Added Python bindings for ODE SEIR metapopulation model Added PyPI package for memilio-simulation Added Graph Neural Networks Added ODE model generator from yaml and toml template General changes: Improved functionality for DynamicNPIs Use of ContactMatrix instead of CustomIndexArray for contact rates of ABM Move output of examples to example_results Corrections: Corrected macOS import failure due to incorrect runtime library lookup (RPATH) Fixed typos and bugs in documentation Harmonized description of time series, infection states and other keywords in documentation Added ScalarType to code examples in the documentation Corrected use of the ABMs RNG after initialization Corrected operation to act only on current system state and not on result time series in SMM Minor changes: Build benchmarks in CI Switched to Doxysphinx Removed log outputs from testing Improved documentation of TypeSafe and derived types Extended documentation Build and test on MacOS Replaced the deprecated FetchContent_Populate and increased CMake minimum version to 3.18. For more details, see https://github.com/SciCompMod/memilio and our novel documentation: https://memilio.readthedocs.io/en/latest/

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