title: Automated multi-objective calibration of biological agent-based simulations.
abstract: Computational agent-based simulation (ABS) is increasingly used to complement laboratory techniques in advancing our understanding of biological systems. Calibration, the identification of parameter values that align simulation with biological behaviours, becomes challenging as increasingly complex biological domains are simulated. Complex domains cannot be characterized by single metrics alone, rendering simulation calibration a fundamentally multi-metric optimization problem that typical calibration techniques cannot handle. Yet calibration is an essential activity in simulation-based science; the baseline calibration forms a control for subsequent experimentation and hence is fundamental in the interpretation of results. Here, we develop and showcase a method, built around multi-objective optimization, for calibrating ABSs against complex target behaviours requiring several metrics (termed objectives) to characterize. Multi-objective calibration (MOC) delivers those sets of parameter values representing optimal trade-offs in simulation performance against each metric, in the form of a Pareto front. We use MOC to calibrate a well-understood immunological simulation against both established a priori and previously unestablished target behaviours. Furthermore, we show that simulation-borne conclusions are broadly, but not entirely, robust to adopting baseline parameter values from different extremes of the Pareto front, highlighting the importance of MOC's identification of numerous calibration solutions. We devise a method for detecting overfitting in a multi-objective context, not previously possible, used to save computational effort by terminating MOC when no improved solutions will be found. MOC can significantly impact biological simulation, adding rigour to and speeding up an otherwise time-consuming calibration process and highlighting inappropriate biological capture by simulations that cannot be well calibrated. As such, it produces more accurate simulations that generate more informative biological predictions.
authors.affiliation: School of Life and Environmental Sciences, The University of Sydney, Camperdown, New South Wales, Australia Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia mark.read@sydney.edu.au.
authors.forename: Mark N
authors.identifier: 0000-0002-1481-4780
authors.initials: MN
authors.lastname: Read
authors.affiliation: Department of Electronics, University of York, York, UK.
authors.forename: Kieran
authors.initials: K
authors.lastname: Alden
authors.affiliation: Department of Computer Science, University of York, York, UK.
authors.forename: Louis M
authors.initials: LM
authors.lastname: Rose
authors.affiliation: Department of Electronics, University of York, York, UK.
authors.forename: Jon
authors.initials: J
authors.lastname: Timmis
mesh_terms: D001331:Automation; D002138:Calibration; D003198:Computer Simulation / Q000592:standards*; D008954:Models, Biological
keywords: agent-based simulation; calibration; computational biology; experimental autoimmune encephalomyelitis; multi-objective optimization