Guidelines for benchmarking of optimization approaches for fitting mathematical models

07/08/2019
by   Clemens Kreutz, et al.
University of Freiburg
0

Insufficient performance of optimization approaches for fitting of mathematical models is still a major bottleneck in systems biology. In this manuscript, the reasons and methodological challenges are summarized as well as their impact in benchmark studies. Important aspects for increasing evidence of outcomes of benchmark analyses are discussed. Based on general guidelines for benchmarking in computational biology, a collection of tailored guidelines is presented for performing informative and unbiased benchmarking of optimization-based fitting approaches. Comprehensive benchmark studies based on these recommendations are urgently required for establishing of a robust and reliable methodology for the systems biology community.

READ FULL TEXT
12/03/2018

Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently ...
01/19/2023

The Lost Art of Mathematical Modelling

We provide a critique of mathematical biology in light of rapid developm...
07/07/2020

Benchmarking in Optimization: Best Practice and Open Issues

This survey compiles ideas and recommendations from more than a dozen re...
07/29/2014

A CUDA-Based Real Parameter Optimization Benchmark

Benchmarking is key for developing and comparing optimization algorithms...
12/23/2020

The necessity and power of random, under-sampled experiments in biology

A vast array of transformative technologies developed over the past deca...
03/29/2022

A review of heath economic evaluation practice in the Netherlands: are we moving forward?

In 2016, the Dutch National Health Care Institute issued new guidelines ...

Please sign up or login with your details

Forgot password? Click here to reset