Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Multicompartment Models: Overview01:14

Multicompartment Models: Overview

311
Multicompartment models are mathematical constructs that depict how drugs are distributed and eliminated within the body. They segment the body into several compartments, symbolizing various physiological or anatomical areas connected through drug transfer processes such as absorption, metabolism, distribution, and elimination.
These models offer a more comprehensive representation of drug behavior in the body than one-compartment models. They accommodate the complexity of drug distribution,...
311
Mechanistic Models: Overview of Compartment Models01:21

Mechanistic Models: Overview of Compartment Models

209
Mechanistic models, a category encompassing both physiological and compartmental modeling, differ from empirical models' approaches to incorporating known factors about the systems being modeled. Empirical models describe data with minimal assumptions, while mechanistic models aim to provide a robust description of available data by specifying assumptions and integrating known factors about the system. Compartmental analysis is a key example of a mechanistic model in pharmacokinetics and...
209
Mechanistic Models: Compartment Models in Individual and Population Analysis01:23

Mechanistic Models: Compartment Models in Individual and Population Analysis

114
Mechanistic models are utilized in individual analysis using single-source data, but imperfections arise due to data collection errors, preventing perfect prediction of observed data. The mathematical equation involves known values (Xi), observed concentrations (Ci), measurement errors (εi), model parameters (ϕj), and the related function (ƒi) for i number of values. Different least-squares metrics quantify differences between predicted and observed values. The ordinary least...
114
Model Approaches for Pharmacokinetic Data: Distributed Parameter Models01:06

Model Approaches for Pharmacokinetic Data: Distributed Parameter Models

150
Pharmacokinetic models are mathematical constructs that represent and predict the time course of drug concentrations in the body, providing meaningful pharmacokinetic parameters. These models are categorized into compartment, physiological, and distributed parameter models.
The distributed parameter models are specifically designed to account for variations and differences in some drug classes. This model is particularly useful for assessing regional concentrations of anticancer or...
150
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

134
Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
134
The Two-State Receptor Model01:29

The Two-State Receptor Model

2.7K
The two-state receptor model explains a drug's interaction with receptors, such as G protein-coupled receptors and ligand-gated ion channels, to induce or inhibit a biological response. When no natural ligands are present, a receptor exists in an equilibrium of inactive (Ri) and active (Ra) conformations. The inactive form does not produce a response, while the active form generates a basal effect known as constitutive activity.
The binding affinity of a drug determines its interaction with...
2.7K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Learning the temporal evolution of multivariate densities via normalizing flows.

Chaos (Woodbury, N.Y.)·2022
Same author

Interpolating between bumps and chimeras.

Chaos (Woodbury, N.Y.)·2021
Same author

Initializing LSTM internal states via manifold learning.

Chaos (Woodbury, N.Y.)·2021
Same author

Particles to partial differential equations parsimoniously.

Chaos (Woodbury, N.Y.)·2021
Same author

Moving bumps in theta neuron networks.

Chaos (Woodbury, N.Y.)·2020
Same author

On learning Hamiltonian systems from data.

Chaos (Woodbury, N.Y.)·2020

Related Experiment Video

Updated: Oct 26, 2025

The HoneyComb Paradigm for Research on Collective Human Behavior
06:48

The HoneyComb Paradigm for Research on Collective Human Behavior

Published on: January 19, 2019

9.6K

Global and local reduced models for interacting, heterogeneous agents.

Thomas N Thiem1, Felix P Kemeth2, Tom Bertalan3

  • 1Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA.

Chaos (Woodbury, N.Y.)
|August 3, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces a data-driven method to simplify complex agent-based models by finding low-dimensional dynamics. The approach successfully creates reduced models, either ordinary differential equations or partial differential equations, that accurately capture system behavior.

More Related Videos

The Spatial Memory Game: Testing the Relationship Between Spatial Language, Object Knowledge, and Spatial Cognition
05:15

The Spatial Memory Game: Testing the Relationship Between Spatial Language, Object Knowledge, and Spatial Cognition

Published on: February 19, 2018

11.0K
A Networked Desktop Virtual Reality Setup for Decision Science and Navigation Experiments with Multiple Participants
06:28

A Networked Desktop Virtual Reality Setup for Decision Science and Navigation Experiments with Multiple Participants

Published on: August 26, 2018

6.1K

Related Experiment Videos

Last Updated: Oct 26, 2025

The HoneyComb Paradigm for Research on Collective Human Behavior
06:48

The HoneyComb Paradigm for Research on Collective Human Behavior

Published on: January 19, 2019

9.6K
The Spatial Memory Game: Testing the Relationship Between Spatial Language, Object Knowledge, and Spatial Cognition
05:15

The Spatial Memory Game: Testing the Relationship Between Spatial Language, Object Knowledge, and Spatial Cognition

Published on: February 19, 2018

11.0K
A Networked Desktop Virtual Reality Setup for Decision Science and Navigation Experiments with Multiple Participants
06:28

A Networked Desktop Virtual Reality Setup for Decision Science and Navigation Experiments with Multiple Participants

Published on: August 26, 2018

6.1K

Area of Science:

  • Complex Systems Science
  • Computational Neuroscience
  • Data-Driven Modeling

Background:

  • Simulating large, coupled, heterogeneous agent systems is computationally challenging due to complex emergent dynamics.
  • Low-dimensional manifolds may govern the collective behavior of such systems, allowing for simplified surrogate models.
  • Analytical identification of these simplified models is often intractable.

Purpose of the Study:

  • To present a data-driven coarse-graining methodology for discovering reduced surrogate models from agent-based systems.
  • To develop both globally based (ODE) and locally based (PDE) reduced models.
  • To demonstrate the efficacy of these methods using a coupled neuron model.

Main Methods:

  • Proper Orthogonal Decomposition (POD) to identify the low-dimensional dynamics manifold.
  • Development of globally based models using POD coordinates to learn ordinary differential equations (ODEs).
  • Development of locally based models learning partial differential equations (PDEs) in heterogeneity space, utilizing artificial neural network integrators (ResNet-templated).

Main Results:

  • Learned reduced models (ODEs and PDEs) directly from agent-based system time series data.
  • Demonstrated that both globally and locally coupled surrogate models can accurately reproduce complex dynamics.
  • Validated the methodology on a simplified coupled neuron model exhibiting rhythmic oscillations.

Conclusions:

  • Data-driven coarse-graining effectively discovers simplified surrogate models for complex agent-based systems.
  • The methodology yields accurate ODEs (global) or PDEs (local) representing system dynamics on a low-dimensional manifold.
  • Both all-to-all coupled and locally coupled reduced models can achieve comparable predictive performance.