Parameter Estimation and Uncertainty Quantification for Systems Biology Models

Mitra, Eshan David; Hlavacek, William Scott

doi:10.1016/j.coisb.2019.10.006

Title: Parameter Estimation and Uncertainty Quantification for Systems Biology Models

Abstract

Mathematical models can provide quantitative insights into immunoreceptor signaling, and other biological processes, but require parameterization and uncertainty quantification before reliable predictions become possible. We review currently available methods and software tools to address these problems. We consider gradient-based and gradient-free methods for point estimation of parameter values, and methods of profile likelihood, bootstrapping, and Bayesian inference for uncertainty quantification. We consider recent and potential future applications of these methods to systems-level modeling of immune-related phenomena.

Authors:

Mitra, Eshan David ^[1];

^[1]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Publication Date:: Wed Nov 06 00:00:00 EST 2019

Research Org.:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Org.:: National Institutes of Health (NIH); USDOE

OSTI Identifier:: 1574756

Report Number(s):: LA-UR-19-26245
Journal ID: ISSN 2452-3100; TRN: US2001141

Grant/Contract Number:: 89233218CNA000001

Resource Type:: Accepted Manuscript

Journal Name:: Current Opinion in Systems Biology

Additional Journal Information:: Journal Volume: 18; Journal ID: ISSN 2452-3100

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; immune cell signaling; biological modeling

Citation Formats


                    Mitra, Eshan David, and Hlavacek, William Scott. Parameter Estimation and Uncertainty Quantification for Systems Biology Models.  United States: N. p., 2019. 
Web.  doi:10.1016/j.coisb.2019.10.006.

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                    Mitra, Eshan David, & Hlavacek, William Scott. Parameter Estimation and Uncertainty Quantification for Systems Biology Models.  United States.  https://doi.org/10.1016/j.coisb.2019.10.006

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                    Mitra, Eshan David, and Hlavacek, William Scott. Wed .  
"Parameter Estimation and Uncertainty Quantification for Systems Biology Models".  United States.  https://doi.org/10.1016/j.coisb.2019.10.006.  https://www.osti.gov/servlets/purl/1574756.

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@article{osti_1574756,

  title        = {Parameter Estimation and Uncertainty Quantification for Systems Biology Models},

  author       = {Mitra, Eshan David and Hlavacek, William Scott},

  abstractNote = {Mathematical models can provide quantitative insights into immunoreceptor signaling, and other biological processes, but require parameterization and uncertainty quantification before reliable predictions become possible. We review currently available methods and software tools to address these problems. We consider gradient-based and gradient-free methods for point estimation of parameter values, and methods of profile likelihood, bootstrapping, and Bayesian inference for uncertainty quantification. We consider recent and potential future applications of these methods to systems-level modeling of immune-related phenomena.},

  doi          = {10.1016/j.coisb.2019.10.006},

  journal      = {Current Opinion in Systems Biology},

  number       = ,

  volume       = 18,

  place        = {United States},

  year         = {Wed Nov 06 00:00:00 EST 2019},

  month        = {Wed Nov 06 00:00:00 EST 2019}

}

Copy to clipboard

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Title: Parameter Estimation and Uncertainty Quantification for Systems Biology Models

Abstract

Citation Formats

T cell receptor signalling networks: branched, diversified and bounded journal, March 2013

B cell antigen receptor signaling 101 journal, July 2004

Molecular regulation of mast cell activation journal, June 2006

A Perspective on the Role of Computational Models in Immunology journal, April 2017

COPASI--a COmplex PAthway SImulator journal, October 2006

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems: Fig. 1. journal, July 2015

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks journal, January 2017

PESTO: Parameter EStimation TOolbox journal, October 2017

PyBioNetFit and the Biological Property Specification Language journal, September 2019

From word models to executable models of signaling networks using automated assembly journal, November 2017

INDRA-IPM: interactive pathway modeling using natural language with automated assembly journal, May 2019

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models journal, March 2003

BioNetGen 2.2: advances in rule-based modeling journal, July 2016

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems journal, January 2006

Stochastic Simulation of Chemical Kinetics journal, May 2007

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Efficient modeling, simulation and coarse-graining of biological complexity with NFsim journal, December 2010

A Limited Memory Algorithm for Bound Constrained Optimization journal, September 1995

Efficient gradient computation for dynamical models journal, September 2014

Correction: Lessons Learned from Quantitative Dynamical Modeling in Systems Biology journal, December 2013

Benchmark problems for dynamic modeling of intracellular processes journal, January 2019

Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets journal, December 2010

Identification of Nascent Memory CD8 T Cells and Modeling of Their Ontogeny journal, March 2017

FATODE: A Library for Forward, Adjoint, and Tangent Linear Integration of ODEs journal, January 2014

Adjoint Sensitivity Analysis for Differential-Algebraic Equations: The Adjoint DAE System and Its Numerical Solution journal, January 2003

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model journal, December 2018

Modeling for (physical) biologists: an introduction to the rule-based approach journal, July 2015

The gradient evolution algorithm: A new metaheuristic journal, September 2015

A survey on optimization metaheuristics journal, July 2013

Benchmarking optimization methods for parameter estimation in large kinetic models journal, August 2018

Differential Evolution – A Simple and Efficient Heuristic for global Optimization over Continuous Spaces journal, January 1997

Optimization by Simulated Annealing journal, May 1983

Enhanced parallel Differential Evolution algorithm for problems in computational systems biology journal, August 2015

A robust parallel algorithm of the particle swarm optimization method for large dimensional engineering problems journal, July 2015

Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy journal, January 2017

Phosphorylation Site Dynamics of Early T-cell Receptor Signaling journal, August 2014

Dynamic Optimization of Nonlinear Processes with an Enhanced Scatter Search Method journal, May 2009

A Simplex Method for Function Minimization journal, January 1965

A Parallel Implementation of the Simplex Function Minimization Routine journal, June 2007

Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle journal, January 2000

Integrative Analysis of Cell Cycle Control in Budding Yeast journal, August 2004

Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model journal, January 2013

Quantitative model analysis with diverse biological data: Applications in developmental pattern formation journal, July 2013

Model-Based Analysis for Qualitative Data: An Application in Drosophila Germline Stem Cell Regulation journal, March 2014

Using both qualitative and quantitative data in parameter identification for systems biology models journal, September 2018

Constraint-handling in nature-inspired numerical optimization: Past, present and future journal, December 2011

Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation journal, November 2017

Profile likelihood in systems biology journal, May 2013

Likelihood based observability analysis and confidence intervals for predictions of dynamic models journal, January 2012

Fast integration-based prediction bands for ordinary differential equation models journal, December 2015

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood journal, June 2009

Inference from Iterative Simulation Using Multiple Sequences journal, November 1992

COPASI and its applications in biotechnology journal, November 2017

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics journal, January 2014

Properties of cell death models calibrated and compared using Bayesian approaches journal, January 2013

Programming biological models in Python using PySB journal, January 2013

Analysis of a Generic Model of Eukaryotic Cell-Cycle Regulation journal, June 2006

Photoconversion and Nuclear Trafficking Cycles Determine Phytochrome A's Response Profile to Far-Red Light journal, September 2011

From START to FINISH: computational analysis of cell cycle control in budding yeast journal, December 2015

Effect of Spatial Inhomogeneities on the Membrane Surface on Receptor Dimerization and Signal Initiation journal, August 2016

Detailed Simulations of Cell Biology with Smoldyn 2.1 journal, March 2010

Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces journal, January 2008

Enhanced parallel Differential Evolution algorithm for problems in computational systems biology journal, August 2015

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model journal, December 2018

PyBioNetFit and the Biological Property Specification Language journal, September 2019

Molecular regulation of mast cell activation journal, June 2006

T cell receptor signalling networks: branched, diversified and bounded journal, March 2013

Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation journal, November 2017

Integrative Analysis of Cell Cycle Control in Budding Yeast journal, August 2004

Profile likelihood in systems biology journal, May 2013

Correction: Lessons Learned from Quantitative Dynamical Modeling in Systems Biology journal, December 2013

Model-Based Analysis for Qualitative Data: An Application in Drosophila Germline Stem Cell Regulation journal, March 2014

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks journal, January 2017

Selecting the Metric in Hamiltonian Monte Carlo preprint, January 2019

T cell receptor signalling networks: branched, diversified and bounded
journal, March 2013

B cell antigen receptor signaling 101
journal, July 2004

Molecular regulation of mast cell activation
journal, June 2006

A Perspective on the Role of Computational Models in Immunology
journal, April 2017

COPASI--a COmplex PAthway SImulator
journal, October 2006

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems: Fig. 1.
journal, July 2015

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
journal, January 2017

PESTO: Parameter EStimation TOolbox
journal, October 2017

PyBioNetFit and the Biological Property Specification Language
journal, September 2019

From word models to executable models of signaling networks using automated assembly
journal, November 2017

INDRA-IPM: interactive pathway modeling using natural language with automated assembly
journal, May 2019

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
journal, March 2003

BioNetGen 2.2: advances in rule-based modeling
journal, July 2016

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
journal, January 2006

Stochastic Simulation of Chemical Kinetics
journal, May 2007

Generalizing Gillespie’s Direct Method to Enable Network-Free Simulations
journal, March 2018

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim
journal, December 2010

A Limited Memory Algorithm for Bound Constrained Optimization
journal, September 1995

Efficient gradient computation for dynamical models
journal, September 2014

Correction: Lessons Learned from Quantitative Dynamical Modeling in Systems Biology
journal, December 2013

Benchmark problems for dynamic modeling of intracellular processes
journal, January 2019

Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets
journal, December 2010

Identification of Nascent Memory CD8 T Cells and Modeling of Their Ontogeny
journal, March 2017

FATODE: A Library for Forward, Adjoint, and Tangent Linear Integration of ODEs
journal, January 2014

Adjoint Sensitivity Analysis for Differential-Algebraic Equations: The Adjoint DAE System and Its Numerical Solution
journal, January 2003

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model
journal, December 2018

Modeling for (physical) biologists: an introduction to the rule-based approach
journal, July 2015

The gradient evolution algorithm: A new metaheuristic
journal, September 2015

A survey on optimization metaheuristics
journal, July 2013

Benchmarking optimization methods for parameter estimation in large kinetic models
journal, August 2018

Differential Evolution – A Simple and Efficient Heuristic for global Optimization over Continuous Spaces
journal, January 1997

Optimization by Simulated Annealing
journal, May 1983

Enhanced parallel Differential Evolution algorithm for problems in computational systems biology
journal, August 2015

A robust parallel algorithm of the particle swarm optimization method for large dimensional engineering problems
journal, July 2015

Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy
journal, January 2017

Phosphorylation Site Dynamics of Early T-cell Receptor Signaling
journal, August 2014

Dynamic Optimization of Nonlinear Processes with an Enhanced Scatter Search Method
journal, May 2009

A Simplex Method for Function Minimization
journal, January 1965

A Parallel Implementation of the Simplex Function Minimization Routine
journal, June 2007

Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle
journal, January 2000

Integrative Analysis of Cell Cycle Control in Budding Yeast
journal, August 2004

Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model
journal, January 2013

Quantitative model analysis with diverse biological data: Applications in developmental pattern formation
journal, July 2013

Model-Based Analysis for Qualitative Data: An Application in Drosophila Germline Stem Cell Regulation
journal, March 2014

Using both qualitative and quantitative data in parameter identification for systems biology models
journal, September 2018

Constraint-handling in nature-inspired numerical optimization: Past, present and future
journal, December 2011

Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation
journal, November 2017

Profile likelihood in systems biology
journal, May 2013

Likelihood based observability analysis and confidence intervals for predictions of dynamic models
journal, January 2012

Fast integration-based prediction bands for ordinary differential equation models
journal, December 2015

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
journal, June 2009

Inference from Iterative Simulation Using Multiple Sequences
journal, November 1992

COPASI and its applications in biotechnology
journal, November 2017

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics
journal, January 2014

Properties of cell death models calibrated and compared using Bayesian approaches
journal, January 2013

Programming biological models in Python using PySB
journal, January 2013

Analysis of a Generic Model of Eukaryotic Cell-Cycle Regulation
journal, June 2006

Photoconversion and Nuclear Trafficking Cycles Determine Phytochrome A's Response Profile to Far-Red Light
journal, September 2011

From START to FINISH: computational analysis of cell cycle control in budding yeast
journal, December 2015

Effect of Spatial Inhomogeneities on the Membrane Surface on Receptor Dimerization and Signal Initiation
journal, August 2016

Detailed Simulations of Cell Biology with Smoldyn 2.1
journal, March 2010

Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces
journal, January 2008

Enhanced parallel Differential Evolution algorithm for problems in computational systems biology
journal, August 2015

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model
journal, December 2018

PyBioNetFit and the Biological Property Specification Language
journal, September 2019

Molecular regulation of mast cell activation
journal, June 2006

T cell receptor signalling networks: branched, diversified and bounded
journal, March 2013

Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation
journal, November 2017

Integrative Analysis of Cell Cycle Control in Budding Yeast
journal, August 2004

Profile likelihood in systems biology
journal, May 2013

Correction: Lessons Learned from Quantitative Dynamical Modeling in Systems Biology
journal, December 2013

Model-Based Analysis for Qualitative Data: An Application in Drosophila Germline Stem Cell Regulation
journal, March 2014

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
journal, January 2017

Selecting the Metric in Hamiltonian Monte Carlo
preprint, January 2019