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ESTIpop: a computational tool to simulate and estimate parameters for continuous-time Markov branching processes.

James P Roney1, Jeremy Ferlic2,3, Franziska Michor2,3,4,5,6

  • 1Harvard College, Cambridge MA 02138, USA.

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Summary

ESTIpop is a new R package for simulating and estimating parameters in cell population dynamics using Markov branching processes. It offers faster, accurate simulations and parameter estimation for complex biological models.

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Area of Science:

  • Computational Biology
  • Mathematical Biology
  • Population Dynamics

Background:

  • Continuous-time Markov branching processes are essential for modeling cell populations.
  • Analytical parameter estimation becomes challenging with complex branching processes.
  • Efficient computational tools are needed for analyzing these models.

Purpose of the Study:

  • To introduce ESTIpop, an R package for simulating and estimating parameters of Markov branching processes.
  • To provide a computationally efficient alternative to existing methods for analyzing cell population dynamics.
  • To facilitate research in areas relying on branching process models.

Main Methods:

  • Parameter estimation using a likelihood function approximated by the Central Limit Theorem for multitype branching processes.
  • Simulation of branching processes with constant or time-dependent rates.
  • Implementation within an R package for user accessibility.

Main Results:

  • ESTIpop enables parameter estimation for complex branching processes where analytical methods fail.
  • Approximate simulation in ESTIpop is significantly faster than exact methods while maintaining accuracy.
  • The package provides a practical tool for researchers studying cell proliferation and related phenomena.

Conclusions:

  • ESTIpop offers a powerful and efficient solution for the analysis of continuous-time Markov branching processes.
  • The package democratizes the use of complex branching models in biological research.
  • ESTIpop is a valuable addition to the computational biology toolkit for population dynamics.