1
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Martinson WD, Volkening A, Schmidtchen M, Venkataraman C, Carrillo JA. Linking discrete and continuous models of cell birth and migration. ROYAL SOCIETY OPEN SCIENCE 2024; 11:232002. [PMID: 39021774 PMCID: PMC11252671 DOI: 10.1098/rsos.232002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/10/2024] [Indexed: 07/20/2024]
Abstract
Self-organization of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, but analytical tractability often comes at the cost of biological intuition. Discrete models provide straightforward interpretations by tracking each individual yet can be computationally expensive. Alternatively, continuous models supply a large-scale perspective by representing the 'effective' dynamics of infinite agents, but their results are often difficult to translate into experimentally relevant insights. We address this challenge by quantitatively linking spatio-temporal dynamics of continuous models and individual-based data in settings with biologically realistic, time-varying cell numbers. Specifically, we introduce and fit scaling parameters in continuous models to account for discrepancies that can arise from low cell numbers and localized interactions. We illustrate our approach on an example motivated by zebrafish-skin pattern formation, in which we create a continuous framework describing the movement and proliferation of a single cell population by upscaling rules from a discrete model. Our resulting continuous models accurately depict ensemble average agent-based solutions when migration or proliferation act alone. Interestingly, the same parameters are not optimal when both processes act simultaneously, highlighting a rich difference in how combining migration and proliferation affects discrete and continuous dynamics.
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Affiliation(s)
| | | | - Markus Schmidtchen
- Institute of Scientific Computing, Technische Universität Dresden, Dresden, Germany
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2
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Fonseca LL, Böttcher L, Mehrad B, Laubenbacher RC. Surrogate modeling and control of medical digital twins. ARXIV 2024:arXiv:2402.05750v2. [PMID: 38827450 PMCID: PMC11142319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The vision of personalized medicine is to identify interventions that maintain or restore a person's health based on their individual biology. Medical digital twins, computational models that integrate a wide range of health-related data about a person and can be dynamically updated, are a key technology that can help guide medical decisions. Such medical digital twin models can be high-dimensional, multi-scale, and stochastic. To be practical for healthcare applications, they often need to be simplified into low-dimensional surrogate models that can be used for optimal design of interventions. This paper introduces surrogate modeling algorithms for the purpose of optimal control applications. As a use case, we focus on agent-based models (ABMs), a common model type in biomedicine for which there are no readily available optimal control algorithms. By deriving surrogate models that are based on systems of ordinary differential equations, we show how optimal control methods can be employed to compute effective interventions, which can then be lifted back to a given ABM. The relevance of the methods introduced here extends beyond medical digital twins to other complex dynamical systems.
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Affiliation(s)
- Luis L. Fonseca
- Laboratory for Systems Medicine, Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Lucas Böttcher
- Laboratory for Systems Medicine, Department of Medicine, University of Florida, Gainesville, FL, USA
- Department of Computational Science and Philosophy, Frankfurt School of Finance and Management, 60322 Frankfurt am Main, Germany
| | - Borna Mehrad
- Laboratory for Systems Medicine, Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Reinhard C. Laubenbacher
- Laboratory for Systems Medicine, Department of Medicine, University of Florida, Gainesville, FL, USA
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3
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Miles CE, McKinley SA, Ding F, Lehoucq RB. Inferring Stochastic Rates from Heterogeneous Snapshots of Particle Positions. Bull Math Biol 2024; 86:74. [PMID: 38740619 DOI: 10.1007/s11538-024-01301-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/20/2024] [Indexed: 05/16/2024]
Abstract
Many imaging techniques for biological systems-like fixation of cells coupled with fluorescence microscopy-provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics they intend to capture. These snapshot observations contain no information about individual trajectories, but still encode information about movement and demographic dynamics, especially when combined with a well-motivated biophysical model. The relationship between spatially evolving populations and single-moment representations of their collective locations is well-established with partial differential equations (PDEs) and their inverse problems. However, experimental data is commonly a set of locations whose number is insufficient to approximate a continuous-in-space PDE solution. Here, motivated by popular subcellular imaging data of gene expression, we embrace the stochastic nature of the data and investigate the mathematical foundations of parametrically inferring demographic rates from snapshots of particles undergoing birth, diffusion, and death in a nuclear or cellular domain. Toward inference, we rigorously derive a connection between individual particle paths and their presentation as a Poisson spatial process. Using this framework, we investigate the properties of the resulting inverse problem and study factors that affect quality of inference. One pervasive feature of this experimental regime is the presence of cell-to-cell heterogeneity. Rather than being a hindrance, we show that cell-to-cell geometric heterogeneity can increase the quality of inference on dynamics for certain parameter regimes. Altogether, the results serve as a basis for more detailed investigations of subcellular spatial patterns of RNA molecules and other stochastically evolving populations that can only be observed for single instants in their time evolution.
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Affiliation(s)
| | - Scott A McKinley
- Department of Mathematics, Tulane University, New Orleans, LA, USA
| | - Fangyuan Ding
- Departments of Biomedical Engineering, Developmental and Cell Biology, University of California, Irvine, Irvine, USA
| | - Richard B Lehoucq
- Discrete Math and Optimization, Sandia National Laboratories, Albuquerque, NM, USA
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4
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Simpson MJ, Murphy KM, McCue SW, Buenzli PR. Discrete and continuous mathematical models of sharp-fronted collective cell migration and invasion. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240126. [PMID: 39076824 PMCID: PMC11286127 DOI: 10.1098/rsos.240126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/22/2024] [Indexed: 07/31/2024]
Abstract
Mathematical models describing the spatial spreading and invasion of populations of biological cells are often developed in a continuum modelling framework using reaction-diffusion equations. While continuum models based on linear diffusion are routinely employed and known to capture key experimental observations, linear diffusion fails to predict well-defined sharp fronts that are often observed experimentally. This observation has motivated the use of nonlinear degenerate diffusion; however, these nonlinear models and the associated parameters lack a clear biological motivation and interpretation. Here, we take a different approach by developing a stochastic discrete lattice-based model incorporating biologically inspired mechanisms and then deriving the reaction-diffusion continuum limit. Inspired by experimental observations, agents in the simulation deposit extracellular material, which we call a substrate, locally onto the lattice, and the motility of agents is taken to be proportional to the substrate density. Discrete simulations that mimic a two-dimensional circular barrier assay illustrate how the discrete model supports both smooth and sharp-fronted density profiles depending on the rate of substrate deposition. Coarse-graining the discrete model leads to a novel partial differential equation (PDE) model whose solution accurately approximates averaged data from the discrete model. The new discrete model and PDE approximation provide a simple, biologically motivated framework for modelling the spreading, growth and invasion of cell populations with well-defined sharp fronts. Open-source Julia code to replicate all results in this work is available on GitHub.
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Affiliation(s)
- Matthew J. Simpson
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Keeley M. Murphy
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Scott W. McCue
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Pascal R. Buenzli
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
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5
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Böttcher L, Fonseca LL, Laubenbacher RC. Control of Medical Digital Twins with Artificial Neural Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585589. [PMID: 38562787 PMCID: PMC10983973 DOI: 10.1101/2024.03.18.585589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The objective of personalized medicine is to tailor interventions to an individual patient's unique characteristics. A key technology for this purpose involves medical digital twins, computational models of human biology that can be personalized and dynamically updated to incorporate patient-specific data collected over time. Certain aspects of human biology, such as the immune system, are not easily captured with physics-based models, such as differential equations. Instead, they are often multi-scale, stochastic, and hybrid. This poses a challenge to existing model-based control and optimization approaches that cannot be readily applied to such models. Recent advances in automatic differentiation and neural-network control methods hold promise in addressing complex control problems. However, the application of these approaches to biomedical systems is still in its early stages. This work introduces dynamics-informed neural-network controllers as an alternative approach to control of medical digital twins. As a first use case for this method, the focus is on agent-based models, a versatile and increasingly common modeling platform in biomedicine. The effectiveness of the proposed neural-network control method is illustrated and benchmarked against other methods with two widely-used agent-based model types. The relevance of the method introduced here extends beyond medical digital twins to other complex dynamical systems.
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6
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Bergman DR, Norton KA, Jain HV, Jackson T. Connecting Agent-Based Models with High-Dimensional Parameter Spaces to Multidimensional Data Using SMoRe ParS: A Surrogate Modeling Approach. Bull Math Biol 2023; 86:11. [PMID: 38159216 PMCID: PMC10757706 DOI: 10.1007/s11538-023-01240-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024]
Abstract
Across a broad range of disciplines, agent-based models (ABMs) are increasingly utilized for replicating, predicting, and understanding complex systems and their emergent behavior. In the biological and biomedical sciences, researchers employ ABMs to elucidate complex cellular and molecular interactions across multiple scales under varying conditions. Data generated at these multiple scales, however, presents a computational challenge for robust analysis with ABMs. Indeed, calibrating ABMs remains an open topic of research due to their own high-dimensional parameter spaces. In response to these challenges, we extend and validate our novel methodology, Surrogate Modeling for Reconstructing Parameter Surfaces (SMoRe ParS), arriving at a computationally efficient framework for connecting high dimensional ABM parameter spaces with multidimensional data. Specifically, we modify SMoRe ParS to initially confine high dimensional ABM parameter spaces using unidimensional data, namely, single time-course information of in vitro cancer cell growth assays. Subsequently, we broaden the scope of our approach to encompass more complex ABMs and constrain parameter spaces using multidimensional data. We explore this extension with in vitro cancer cell inhibition assays involving the chemotherapeutic agent oxaliplatin. For each scenario, we validate and evaluate the effectiveness of our approach by comparing how well ABM simulations match the experimental data when using SMoRe ParS-inferred parameters versus parameters inferred by a commonly used direct method. In so doing, we show that our approach of using an explicitly formulated surrogate model as an interlocutor between the ABM and the experimental data effectively calibrates the ABM parameter space to multidimensional data. Our method thus provides a robust and scalable strategy for leveraging multidimensional data to inform multiscale ABMs and explore the uncertainty in their parameters.
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Affiliation(s)
- Daniel R Bergman
- Department of Mathematics, University of Michigan, 530 Church Street, Ann Arbor, MI, 48109, USA
| | - Kerri-Ann Norton
- Computational Biology Laboratory, Computer Science Program, Bard College, 30 Campus Road, Annandale-on-Hudson, NY, 12504, USA
| | - Harsh Vardhan Jain
- Department of Mathematics & Statistics, University of Minnesota Duluth, 1117 University Drive, Duluth, MN, 55812, USA
| | - Trachette Jackson
- Department of Mathematics, University of Michigan, 530 Church Street, Ann Arbor, MI, 48109, USA.
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7
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Miles CE, McKinley SA, Ding F, Lehoucq RB. Inferring stochastic rates from heterogeneous snapshots of particle positions. ARXIV 2023:arXiv:2311.04880v1. [PMID: 37986720 PMCID: PMC10659442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Many imaging techniques for biological systems - like fixation of cells coupled with fluorescence microscopy - provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics they intend to capture. These snapshot observations contain no information about individual trajectories, but still encode information about movement and demographic dynamics, especially when combined with a well-motivated biophysical model. The relationship between spatially evolving populations and single-moment representations of their collective locations is well-established with partial differential equations (PDEs) and their inverse problems. However, experimental data is commonly a set of locations whose number is insufficient to approximate a continuous-in-space PDE solution. Here, motivated by popular subcellular imaging data of gene expression, we embrace the stochastic nature of the data and investigate the mathematical foundations of parametrically inferring demographic rates from snapshots of particles undergoing birth, diffusion, and death in a nuclear or cellular domain. Toward inference, we rigorously derive a connection between individual particle paths and their presentation as a Poisson spatial process. Using this framework, we investigate the properties of the resulting inverse problem and study factors that affect quality of inference. One pervasive feature of this experimental regime is the presence of cell-to-cell heterogeneity. Rather than being a hindrance, we show that cell-to-cell geometric heterogeneity can increase the quality of inference on dynamics for certain parameter regimes. Altogether, the results serve as a basis for more detailed investigations of subcellular spatial patterns of RNA molecules and other stochastically evolving populations that can only be observed for single instants in their time evolution.
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Affiliation(s)
| | | | - Fangyuan Ding
- Department of Biomedical Engineering, University of California, Irvine
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8
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Gyllingberg L, Sumpter DJT, Brännström Å. Finding analytical approximations for discrete, stochastic, individual-based models of ecology. Math Biosci 2023; 365:109084. [PMID: 37778619 DOI: 10.1016/j.mbs.2023.109084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/15/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023]
Abstract
Discrete time, spatially extended models play an important role in ecology, modelling population dynamics of species ranging from micro-organisms to birds. An important question is how 'bottom up', individual-based models can be approximated by 'top down' models of dynamics. Here, we study a class of spatially explicit individual-based models with contest competition: where species compete for space in local cells and then disperse to nearby cells. We start by describing simulations of the model, which exhibit large-scale discrete oscillations and characterize these oscillations by measuring spatial correlations. We then develop two new approximate descriptions of the resulting spatial population dynamics. The first is based on local interactions of the individuals and allows us to give a difference equation approximation of the system over small dispersal distances. The second approximates the long-range interactions of the individual-based model. These approximations capture demographic stochasticity from the individual-based model and show that dispersal stabilizes population dynamics. We calculate extinction probability for the individual-based model and show convergence between the local approximation and the non-spatial global approximation of the individual-based model as dispersal distance and population size simultaneously tend to infinity. Our results provide new approximate analytical descriptions of a complex bottom-up model and deepen understanding of spatial population dynamics.
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Affiliation(s)
| | - David J T Sumpter
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Åke Brännström
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden; Complexity Science and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami, Japan
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9
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Gyllingberg L, Birhane A, Sumpter DJT. The lost art of mathematical modelling. Math Biosci 2023:109033. [PMID: 37257641 DOI: 10.1016/j.mbs.2023.109033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
We provide a critique of mathematical biology in light of rapid developments in modern machine learning. We argue that out of the three modelling activities - (1) formulating models; (2) analysing models; and (3) fitting or comparing models to data - inherent to mathematical biology, researchers currently focus too much on activity (2) at the cost of (1). This trend, we propose, can be reversed by realising that any given biological phenomenon can be modelled in an infinite number of different ways, through the adoption of an pluralistic approach, where we view a system from multiple, different points of view. We explain this pluralistic approach using fish locomotion as a case study and illustrate some of the pitfalls - universalism, creating models of models, etc. - that hinder mathematical biology. We then ask how we might rediscover a lost art: that of creative mathematical modelling.
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Affiliation(s)
| | - Abeba Birhane
- Mozilla Foundation, 2 Harrison Street, Suite 175, San Francisco, CA 94105, USA
| | - David J T Sumpter
- Department of Information Technology, Uppsala University, Box 337, Uppsala, SE-751 05, Sweden.
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10
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Pilosof S. Conceptualizing microbe-plasmid communities as complex adaptive systems. Trends Microbiol 2023:S0966-842X(23)00025-2. [PMID: 36822952 DOI: 10.1016/j.tim.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/29/2022] [Accepted: 01/23/2023] [Indexed: 02/24/2023]
Abstract
Plasmids shape microbial communities' diversity, structure, and function. Nevertheless, we lack a mechanistic understanding of how community structure and dynamics emerge from local microbe-plasmid interactions and coevolution. Addressing this gap is challenging because multiple processes operate simultaneously at multiple levels of organization. For example, immunity operates between a plasmid and a cell, but incompatibility mechanisms regulate coexistence between plasmids. Conceptualizing microbe-plasmid communities as complex adaptive systems is a promising approach to overcoming these challenges. I illustrate how agent-based evolutionary modeling, extended by network analysis, can be used to quantify the relative importance of local processes governing community dynamics. These theoretical developments can advance our understanding of plasmid ecology and evolution, especially when combined with empirical data.
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Affiliation(s)
- Shai Pilosof
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel.
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11
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Supekar R, Song B, Hastewell A, Choi GPT, Mietke A, Dunkel J. Learning hydrodynamic equations for active matter from particle simulations and experiments. Proc Natl Acad Sci U S A 2023; 120:e2206994120. [PMID: 36763535 PMCID: PMC9963139 DOI: 10.1073/pnas.2206994120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 01/12/2023] [Indexed: 02/11/2023] Open
Abstract
Recent advances in high-resolution imaging techniques and particle-based simulation methods have enabled the precise microscopic characterization of collective dynamics in various biological and engineered active matter systems. In parallel, data-driven algorithms for learning interpretable continuum models have shown promising potential for the recovery of underlying partial differential equations (PDEs) from continuum simulation data. By contrast, learning macroscopic hydrodynamic equations for active matter directly from experiments or particle simulations remains a major challenge, especially when continuum models are not known a priori or analytic coarse graining fails, as often is the case for nondilute and heterogeneous systems. Here, we present a framework that leverages spectral basis representations and sparse regression algorithms to discover PDE models from microscopic simulation and experimental data, while incorporating the relevant physical symmetries. We illustrate the practical potential through a range of applications, from a chiral active particle model mimicking nonidentical swimming cells to recent microroller experiments and schooling fish. In all these cases, our scheme learns hydrodynamic equations that reproduce the self-organized collective dynamics observed in the simulations and experiments. This inference framework makes it possible to measure a large number of hydrodynamic parameters in parallel and directly from video data.
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Affiliation(s)
- Rohit Supekar
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Boya Song
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Alasdair Hastewell
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Gary P. T. Choi
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Alexander Mietke
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
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12
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Lusseau D, Kindt-Larsen L, van Beest FM. Emergent interactions in the management of multiple threats to the conservation of harbour porpoises. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 855:158936. [PMID: 36152860 DOI: 10.1016/j.scitotenv.2022.158936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/09/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
Human activities at sea are intensifying and diversifying. This is leading to more complex interactions of anthropogenic impacts requiring adaptable management interventions to mitigate their cumulative effects on biodiversity conservation and restoration objectives. Bycatch remains the dominant conservation threat for coastal cetaceans. Additionally, the indirect impact of repeated exposure to disturbances, particularly acoustic disturbances, can affect cetacean population growth and therefore conservation objectives. Pingers are used to ensonify nets to provide an effective mitigation of bycatch risk. As those become more prevalent across fisheries at risk to catch for example harbour porpoises, pingers become contributors to the anthropogenic noise landscape which may affect the vital rates of this species as well. Currently, we do not know how to best balance pinger prevalence to minimise both bycatch rate and the population consequences of acoustic disturbance (PCoD). Here we use an agent-based model to determine how pinger prevalence in nets can be adjusted to minimise bycatch rate and noise disturbance propagating to affect population growth for harbour porpoises. We show that counter-intuitively bycatch rate can increase at lower pinger prevalence. When ecological conditions are such that PCOD can emerge, higher prevalence of pingers can lead to indirect effects on population growth. This would result from condition-mediated decreased reproductive potential. Displacing fishing effort, via time-area closure, can be an effective mitigation strategy in these circumstances. These findings have important implications for current management plans which, for practical consideration, may lead to lower overall pinger prevalence at sea. This study also shows that estimating the reproductive potential of the species should be incorporated in bycatch monitoring programmes. We now need to better understand how physiological condition affect reproductive decisions and behavioural responses to noise in cetaceans to better appraise and estimate the cumulative impacts of bycatch and its mitigations.
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Affiliation(s)
- David Lusseau
- National Institute for Aquatic Resources, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - Lotte Kindt-Larsen
- National Institute for Aquatic Resources, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Floris M van Beest
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
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13
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Jain HV, Norton KA, Prado BB, Jackson TL. SMoRe ParS: A novel methodology for bridging modeling modalities and experimental data applied to 3D vascular tumor growth. Front Mol Biosci 2022; 9:1056461. [PMID: 36619168 PMCID: PMC9816661 DOI: 10.3389/fmolb.2022.1056461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Multiscale systems biology is having an increasingly powerful impact on our understanding of the interconnected molecular, cellular, and microenvironmental drivers of tumor growth and the effects of novel drugs and drug combinations for cancer therapy. Agent-based models (ABMs) that treat cells as autonomous decision-makers, each with their own intrinsic characteristics, are a natural platform for capturing intratumoral heterogeneity. Agent-based models are also useful for integrating the multiple time and spatial scales associated with vascular tumor growth and response to treatment. Despite all their benefits, the computational costs of solving agent-based models escalate and become prohibitive when simulating millions of cells, making parameter exploration and model parameterization from experimental data very challenging. Moreover, such data are typically limited, coarse-grained and may lack any spatial resolution, compounding these challenges. We address these issues by developing a first-of-its-kind method that leverages explicitly formulated surrogate models (SMs) to bridge the current computational divide between agent-based models and experimental data. In our approach, Surrogate Modeling for Reconstructing Parameter Surfaces (SMoRe ParS), we quantify the uncertainty in the relationship between agent-based model inputs and surrogate model parameters, and between surrogate model parameters and experimental data. In this way, surrogate model parameters serve as intermediaries between agent-based model input and data, making it possible to use them for calibration and uncertainty quantification of agent-based model parameters that map directly onto an experimental data set. We illustrate the functionality and novelty of Surrogate Modeling for Reconstructing Parameter Surfaces by applying it to an agent-based model of 3D vascular tumor growth, and experimental data in the form of tumor volume time-courses. Our method is broadly applicable to situations where preserving underlying mechanistic information is of interest, and where computational complexity and sparse, noisy calibration data hinder model parameterization.
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Affiliation(s)
- Harsh Vardhan Jain
- Department of Mathematics and Statistics, University of Minnesota Duluth, Duluth, MN, United States
| | - Kerri-Ann Norton
- Reem and Kayden Center for Science and Computation, Computational Biology Laboratory, Computer Science Program, Bard College, Annandale-on-Hudson, NY, United States
| | | | - Trachette L. Jackson
- Department of Mathematics, University of Michigan, Ann Arbor, MI, United States,*Correspondence: Trachette L. Jackson,
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14
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Sánchez JM, Rodríguez JP, Espitia HE. Bibliometric analysis of publications discussing the use of the artificial intelligence technique agent-based models in sustainable agriculture. Heliyon 2022; 8:e12005. [DOI: 10.1016/j.heliyon.2022.e12005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/21/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
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15
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Johnston ST, Faria M. Equation learning to identify nano-engineered particle-cell interactions: an interpretable machine learning approach. NANOSCALE 2022; 14:16502-16515. [PMID: 36314284 DOI: 10.1039/d2nr04668g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Designing nano-engineered particles capable of the delivery of therapeutic and diagnostic agents to a specific target remains a significant challenge. Understanding how interactions between particles and cells are impacted by the physicochemical properties of the particle will help inform rational design choices. Mathematical and computational techniques allow for details regarding particle-cell interactions to be isolated from the interwoven set of biological, chemical, and physical phenomena involved in the particle delivery process. Here we present a machine learning framework capable of elucidating particle-cell interactions from experimental data. This framework employs a data-driven modelling approach, augmented by established biological knowledge. Crucially, the model of particle-cell interactions learned by the framework can be interpreted and analysed, in contrast to the 'black box' models inherent to other machine learning approaches. We apply the framework to association data for thirty different particle-cell pairs. This library of data contains both adherent and suspension cell lines, as well as a diverse collection of particles. We consider hyperbranched polymer and poly(methacrylic acid) particles, from 6 nm to 1032 nm in diameter, with small molecule, monoclonal antibody, and peptide surface functionalisations. Despite the diverse nature of the experiments, the learned models of particle-cell interactions for each particle-cell pair are remarkably consistent: out of 2048 potential models, only four unique models are learned. The models reveal that nonlinear saturation effects are a key feature governing particle-cell interactions. Further, the framework provides robust estimates of particle performance, which facilitates quantitative evaluation of particle design choices.
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Affiliation(s)
- Stuart T Johnston
- School of Mathematics and Statistics, The University of Melbourne, Victoria, Australia.
| | - Matthew Faria
- Department of Biomedical Engineering, The University of Melbourne, Victoria, Australia
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16
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Messenger DA, Bortz DM. Learning mean-field equations from particle data using WSINDy. PHYSICA D. NONLINEAR PHENOMENA 2022; 439:133406. [PMID: 37476028 PMCID: PMC10358825 DOI: 10.1016/j.physd.2022.133406] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
We develop a weak-form sparse identification method for interacting particle systems (IPS) with the primary goals of reducing computational complexity for large particle number N and offering robustness to either intrinsic or extrinsic noise. In particular, we use concepts from mean-field theory of IPS in combination with the weak-form sparse identification of nonlinear dynamics algorithm (WSINDy) to provide a fast and reliable system identification scheme for recovering the governing stochastic differential equations for an IPS when the number of particles per experiment N is on the order of several thousands and the number of experiments M is less than 100. This is in contrast to existing work showing that system identification for N less than 100 and M on the order of several thousand is feasible using strong-form methods. We prove that under some standard regularity assumptions the scheme converges with rate O ( N - 1 ∕ 2 ) in the ordinary least squares setting and we demonstrate the convergence rate numerically on several systems in one and two spatial dimensions. Our examples include a canonical problem from homogenization theory (as a first step towards learning coarse-grained models), the dynamics of an attractive-repulsive swarm, and the IPS description of the parabolic-elliptic Keller-Segel model for chemotaxis. Code is available at https://github.com/MathBioCU/WSINDy_IPS.
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Affiliation(s)
- Daniel A. Messenger
- Department of Applied Mathematics, University of Colorado Boulder, 11 Engineering Dr, Boulder, CO 80309, USA
| | - David M. Bortz
- Department of Applied Mathematics, University of Colorado Boulder, 11 Engineering Dr, Boulder, CO 80309, USA
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17
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Jørgensen ACS, Ghosh A, Sturrock M, Shahrezaei V. Efficient Bayesian inference for stochastic agent-based models. PLoS Comput Biol 2022; 18:e1009508. [PMID: 36197919 PMCID: PMC9576090 DOI: 10.1371/journal.pcbi.1009508] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/17/2022] [Accepted: 09/21/2022] [Indexed: 11/14/2022] Open
Abstract
The modelling of many real-world problems relies on computationally heavy simulations of randomly interacting individuals or agents. However, the values of the parameters that underlie the interactions between agents are typically poorly known, and hence they need to be inferred from macroscopic observations of the system. Since statistical inference rests on repeated simulations to sample the parameter space, the high computational expense of these simulations can become a stumbling block. In this paper, we compare two ways to mitigate this issue in a Bayesian setting through the use of machine learning methods: One approach is to construct lightweight surrogate models to substitute the simulations used in inference. Alternatively, one might altogether circumvent the need for Bayesian sampling schemes and directly estimate the posterior distribution. We focus on stochastic simulations that track autonomous agents and present two case studies: tumour growths and the spread of infectious diseases. We demonstrate that good accuracy in inference can be achieved with a relatively small number of simulations, making our machine learning approaches orders of magnitude faster than classical simulation-based methods that rely on sampling the parameter space. However, we find that while some methods generally produce more robust results than others, no algorithm offers a one-size-fits-all solution when attempting to infer model parameters from observations. Instead, one must choose the inference technique with the specific real-world application in mind. The stochastic nature of the considered real-world phenomena poses an additional challenge that can become insurmountable for some approaches. Overall, we find machine learning approaches that create direct inference machines to be promising for real-world applications. We present our findings as general guidelines for modelling practitioners.
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Affiliation(s)
| | | | - Marc Sturrock
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Vahid Shahrezaei
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
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18
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Messenger DA, Wheeler GE, Liu X, Bortz DM. Learning anisotropic interaction rules from individual trajectories in a heterogeneous cellular population. J R Soc Interface 2022; 19:20220412. [PMCID: PMC9554727 DOI: 10.1098/rsif.2022.0412] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Interacting particle system (IPS) models have proven to be highly successful for describing the spatial movement of organisms. However, it is challenging to infer the interaction rules directly from data. In the field of equation discovery, the weak-form sparse identification of nonlinear dynamics (WSINDy) methodology has been shown to be computationally efficient for identifying the governing equations of complex systems from noisy data. Motivated by the success of IPS models to describe the spatial movement of organisms, we develop WSINDy for the second-order IPS to learn equations for communities of cells. Our approach learns the directional interaction rules for each individual cell that in aggregate govern the dynamics of a heterogeneous population of migrating cells. To sort a cell according to the active classes present in its model, we also develop a novel ad hoc classification scheme (which accounts for the fact that some cells do not have enough evidence to accurately infer a model). Aggregated models are then constructed hierarchically to simultaneously identify different species of cells present in the population and determine best-fit models for each species. We demonstrate the efficiency and proficiency of the method on several test scenarios, motivated by common cell migration experiments.
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Affiliation(s)
- Daniel A. Messenger
- Department of Applied Mathematics, University of Colorado, Boulder, CO 80309-0526, USA
| | - Graycen E. Wheeler
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0526, USA
| | - Xuedong Liu
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0526, USA
| | - David M. Bortz
- Department of Applied Mathematics, University of Colorado, Boulder, CO 80309-0526, USA
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19
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Bergman D, Sweis RF, Pearson AT, Nazari F, Jackson TL. A global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues. iScience 2022; 25:104387. [PMID: 35637730 PMCID: PMC9142654 DOI: 10.1016/j.isci.2022.104387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 03/30/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Agent-based models (ABMs) are a natural platform for capturing the multiple time and spatial scales in biological processes. However, these models are computationally expensive, especially when including molecular-level effects. The traditional approach to simulating this type of multiscale ABM is to solve a system of ordinary differential equations for the molecular events per cell. This significantly adds to the computational cost of simulations as the number of agents grows, which contributes to many ABMs being limited to around10 5 cells. We propose an approach that requires the same computational time independent of the number of agents. This speeds up the entire simulation by orders of magnitude, allowing for more thorough explorations of ABMs with even larger numbers of agents. We use two systems to show that the new method strongly agrees with the traditionally used approach. This computational strategy can be applied to a wide range of biological investigations.
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Affiliation(s)
- Daniel Bergman
- Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Randy F. Sweis
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, 5841 S Maryland Avenue, MC 2115, Chicago, IL 60605, USA
| | - Alexander T. Pearson
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, 5841 S Maryland Avenue, MC 2115, Chicago, IL 60605, USA
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20
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Martina-Perez S, Simpson MJ, Baker RE. Bayesian uncertainty quantification for data-driven equation learning. Proc Math Phys Eng Sci 2021; 477:20210426. [PMID: 35153587 PMCID: PMC8548080 DOI: 10.1098/rspa.2021.0426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/30/2021] [Indexed: 12/27/2022] Open
Abstract
Equation learning aims to infer differential equation models from data. While a number of studies have shown that differential equation models can be successfully identified when the data are sufficiently detailed and corrupted with relatively small amounts of noise, the relationship between observation noise and uncertainty in the learned differential equation models remains unexplored. We demonstrate that for noisy datasets there exists great variation in both the structure of the learned differential equation models and their parameter values. We explore how to exploit multiple datasets to quantify uncertainty in the learned models, and at the same time draw mechanistic conclusions about the target differential equations. We showcase our results using simulation data from a relatively straightforward agent-based model (ABM) which has a well-characterized partial differential equation description that provides highly accurate predictions of averaged ABM behaviours in relevant regions of parameter space. Our approach combines equation learning methods with Bayesian inference approaches so that a quantification of uncertainty can be given by the posterior parameter distribution of the learned model.
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Affiliation(s)
| | - Matthew J Simpson
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Ruth E Baker
- Mathematical Institute, University of Oxford, Oxford, UK
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21
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Thiem TN, Kemeth FP, Bertalan T, Laing CR, Kevrekidis IG. Global and local reduced models for interacting, heterogeneous agents. CHAOS (WOODBURY, N.Y.) 2021; 31:073139. [PMID: 34340348 DOI: 10.1063/5.0055840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Large collections of coupled, heterogeneous agents can manifest complex dynamical behavior presenting difficulties for simulation and analysis. However, if the collective dynamics lie on a low-dimensional manifold, then the original agent-based model may be approximated with a simplified surrogate model on and near the low-dimensional space where the dynamics live. Analytically identifying such simplified models can be challenging or impossible, but here we present a data-driven coarse-graining methodology for discovering such reduced models. We consider two types of reduced models: globally based models that use global information and predict dynamics using information from the whole ensemble and locally based models that use local information, that is, information from just a subset of agents close (close in heterogeneity space, not physical space) to an agent, to predict the dynamics of an agent. For both approaches, we are able to learn laws governing the behavior of the reduced system on the low-dimensional manifold directly from time series of states from the agent-based system. These laws take the form of either a system of ordinary differential equations (ODEs), for the globally based approach, or a partial differential equation (PDE) in the locally based case. For each technique, we employ a specialized artificial neural network integrator that has been templated on an Euler time stepper (i.e., a ResNet) to learn the laws of the reduced model. As part of our methodology, we utilize the proper orthogonal decomposition (POD) to identify the low-dimensional space of the dynamics. Our globally based technique uses the resulting POD basis to define a set of coordinates for the agent states in this space and then seeks to learn the time evolution of these coordinates as a system of ODEs. For the locally based technique, we propose a methodology for learning a partial differential equation representation of the agents; the PDE law depends on the state variables and partial derivatives of the state variables with respect to model heterogeneities. We require that the state variables are smooth with respect to model heterogeneities, which permit us to cast the discrete agent-based problem as a continuous one in heterogeneity space. The agents in such a representation bear similarity to the discretization points used in typical finite element/volume methods. As an illustration of the efficacy of our techniques, we consider a simplified coupled neuron model for rhythmic oscillations in the pre-Bötzinger complex and demonstrate how our data-driven surrogate models are able to produce dynamics comparable to the dynamics of the full system. A nontrivial conclusion is that the dynamics can be equally well reproduced by an all-to-all coupled and by a locally coupled model of the same agents.
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Affiliation(s)
- Thomas N Thiem
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Felix P Kemeth
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Tom Bertalan
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Carlo R Laing
- School of Natural and Computational Sciences, Massey University, 0632 Auckland, New Zealand
| | - Ioannis G Kevrekidis
- Department of Applied Mathematics and Statistics, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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22
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Jiang Q, Fu X, Yan S, Li R, Du W, Cao Z, Qian F, Grima R. Neural network aided approximation and parameter inference of non-Markovian models of gene expression. Nat Commun 2021; 12:2618. [PMID: 33976195 PMCID: PMC8113478 DOI: 10.1038/s41467-021-22919-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/07/2021] [Indexed: 02/03/2023] Open
Abstract
Non-Markovian models of stochastic biochemical kinetics often incorporate explicit time delays to effectively model large numbers of intermediate biochemical processes. Analysis and simulation of these models, as well as the inference of their parameters from data, are fraught with difficulties because the dynamics depends on the system's history. Here we use an artificial neural network to approximate the time-dependent distributions of non-Markovian models by the solutions of much simpler time-inhomogeneous Markovian models; the approximation does not increase the dimensionality of the model and simultaneously leads to inference of the kinetic parameters. The training of the neural network uses a relatively small set of noisy measurements generated by experimental data or stochastic simulations of the non-Markovian model. We show using a variety of models, where the delays stem from transcriptional processes and feedback control, that the Markovian models learnt by the neural network accurately reflect the stochastic dynamics across parameter space.
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Affiliation(s)
- Qingchao Jiang
- grid.28056.390000 0001 2163 4895Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, China
| | - Xiaoming Fu
- grid.28056.390000 0001 2163 4895Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, China ,grid.4305.20000 0004 1936 7988School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland UK
| | - Shifu Yan
- grid.28056.390000 0001 2163 4895Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, China
| | - Runlai Li
- grid.4280.e0000 0001 2180 6431Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Wenli Du
- grid.28056.390000 0001 2163 4895Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, China
| | - Zhixing Cao
- grid.28056.390000 0001 2163 4895Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, China ,grid.28056.390000 0001 2163 4895State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Feng Qian
- grid.28056.390000 0001 2163 4895Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, China
| | - Ramon Grima
- grid.4305.20000 0004 1936 7988School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland UK
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23
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Hywood JD, Rice G, Pageon SV, Read MN, Biro M. Detection and characterization of chemotaxis without cell tracking. J R Soc Interface 2021; 18:20200879. [PMID: 33715400 PMCID: PMC8086846 DOI: 10.1098/rsif.2020.0879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/15/2021] [Indexed: 02/06/2023] Open
Abstract
Swarming has been observed in various biological systems from collective animal movements to immune cells. In the cellular context, swarming is driven by the secretion of chemotactic factors. Despite the critical role of chemotactic swarming, few methods to robustly identify and quantify this phenomenon exist. Here, we present a novel method for the analysis of time series of positional data generated from realizations of agent-based processes. We convert the positional data for each individual time point to a function measuring agent aggregation around a given area of interest, hence generating a functional time series. The functional time series, and a more easily visualized swarming metric of agent aggregation derived from these functions, provide useful information regarding the evolution of the underlying process over time. We extend our method to build upon the modelling of collective motility using drift-diffusion partial differential equations (PDEs). Using a functional linear model, we are able to use the functional time series to estimate the drift and diffusivity terms associated with the underlying PDE. By producing an accurate estimate for the drift coefficient, we can infer the strength and range of attraction or repulsion exerted on agents, as in chemotaxis. Our approach relies solely on using agent positional data. The spatial distribution of diffusing chemokines is not required, nor do individual agents need to be tracked over time. We demonstrate our approach using random walk simulations of chemotaxis and experiments investigating cytotoxic T cells interacting with tumouroids.
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Affiliation(s)
- Jack D. Hywood
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Gregory Rice
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Canada
| | - Sophie V. Pageon
- EMBL Australia, Single Molecule Science node, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Mark N. Read
- School of Computer Science & Charles Perkins Centre, University of Sydney, Sydney, Australia
| | - Maté Biro
- EMBL Australia, Single Molecule Science node, School of Medical Sciences, University of New South Wales, Sydney, Australia
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