Chapter 6

Lecture Videos #

A Massive Open Online Course on Computational Systems Biology, which is in part, a basis for this book, is also available, through the Indian educational platforms, NPTEL (National Programme on Technology Enhanced Learning) and SWAYAM.

The lectures (including hands-on lab sessions), totalling over 30 hours of content, are also available on YouTube.

Chapter 6: Parameter estimation #

Parameter Estimation (12:45)

  • Biochemical Systems Theory
  • Optimisation: What is a good fit?

Parameter Estimation (16:59)

  • Setting up the Optimisation Problem

Parameter Estimation (20:06)

  • Data-driven Mechanistic Modelling: Flowchart

Methods for Parameter Estimation (23:57)

  • Introduction
  • Generic Recipe for Direct Search Algorithms

Direct Search Methods (23:14)

  • Stochastic Search Algorithms
  • Simulated Annealing
  • Genetic Algorithms

Genetic Algorithms (12:14)

  • Other Applications for GAs

Genetic Algorithms (21:02)

  • Representation Challenges & Examples
  • Some Illustrations

Other Evolutionary Algorithms (21:24)

  • Differential Evolution
  • Implementing EAs
  • When to use EAs?
  • Curse of Dimensionality

PyGMO (16:00)

  • Introduction to PyGMO
  • PyGMO Algorithms and Examples
  • Multi-objective Optimisation

Dynamic Modelling Recap (11:58)

Lab: Parameter Estimation (30:36)

  • Computing the Objective Function
  • \texttt{fminsearch}