Bridging the gap between mechanistic biological models and machine learning surrogates

IM Gherman, ZS Abdallah, W Pang… - PLoS Computational …, 2023 - journals.plos.org
Mechanistic models have been used for centuries to describe complex interconnected
processes, including biological ones. As the scope of these models has widened, so have …

Learning differential equation models from stochastic agent-based model simulations

JT Nardini, RE Baker… - Journal of the Royal …, 2021 - royalsocietypublishing.org
Agent-based models provide a flexible framework that is frequently used for modelling many
biological systems, including cell migration, molecular dynamics, ecology and epidemiology …

In silico design of recombinant multi-epitope vaccine against influenza A virus

A Maleki, G Russo, GA Parasiliti Palumbo… - BMC …, 2021 - Springer
Background Influenza A virus is one of the leading causes of annual mortality. The emerging
of novel escape variants of the influenza A virus is still a considerable challenge in the …

Applying optimal control theory to complex epidemiological models to inform real-world disease management

EH Bussell, CE Dangerfield… - … Transactions of the …, 2019 - royalsocietypublishing.org
Mathematical models provide a rational basis to inform how, where and when to control
disease. Assuming an accurate spatially explicit simulation model can be fitted to spread …

Deep reinforcement learning and simulation as a path toward precision medicine

BK Petersen, J Yang, WS Grathwohl… - Journal of …, 2019 - liebertpub.com
Traditionally, precision medicine involves classifying patients to identify subpopulations that
respond favorably to specific therapeutics. We pose precision medicine as a dynamic …

Delayed skeletal muscle repair following inflammatory damage in simulated agent-based models of muscle regeneration

S Khuu, JW Fernandez… - PLOS Computational …, 2023 - journals.plos.org
Healthy skeletal muscle undergoes repair in response to mechanically localised strains
during activities such as exercise. The ability of cells to transduce the external stimuli into a …

Examining the controllability of sepsis using genetic algorithms on an agent-based model of systemic inflammation

RC Cockrell, G An - PLoS computational biology, 2018 - journals.plos.org
Sepsis, a manifestation of the body's inflammatory response to injury and infection, has a
mortality rate of between 28%-50% and affects approximately 1 million patients annually in …

Trends in mathematical modeling of host–pathogen interactions

J Ewald, P Sieber, R Garde, SN Lang… - Cellular and Molecular …, 2020 - Springer
Pathogenic microorganisms entail enormous problems for humans, livestock, and crop
plants. A better understanding of the different infection strategies of the pathogens enables …

Near-optimal control of dynamical systems with neural ordinary differential equations

L Böttcher, T Asikis - Machine Learning: Science and Technology, 2022 - iopscience.iop.org
Near-optimal control of dynamical systems with neural ordinary differential equations -
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Predicting the artificial immunity induced by RUTI® vaccine against tuberculosis using universal immune system simulator (UISS)

M Pennisi, G Russo, G Sgroi, A Bonaccorso… - BMC …, 2019 - Springer
Background Tuberculosis (TB) represents a worldwide cause of mortality (it infects one third
of the world's population) affecting mostly developing countries, including India, and recently …