Update by Michael: I've repurposed this ticket to collect various toy problems / benchmarks we might like to add at some point. Whenever someone decides a certain benchmark is necessary - and that they're going to implement it - we can make a separate ticket for that!
- Hass et al. (2018 pre-print) - Reaction-diffusion problems, Optimisation focus
- 20 biochemical reaction networks, all taken from literature & with real data.
- Note in discussion that log transform is good because convexity changes
- Villaverde et al. "BioPredyn" (2015) - All reaction-diffusion problems, Optimisation focus
- Problem B1: genome-wide kinetic model of S. cerevisiae
- Problem B2: dynamic model of the Central Carbon Metabolism of E. coli
- Problem B3: enzymatic and transcriptional regulation of the Central Carbon Metabolism of E. coli
- Problem B4: metabolic model of Chinese Hamster Ovary (CHO) cells
- Problem B5: signal transduction logic model
- Problem B6: the gap gene network of the vinegar fly, Drosophila melanogaster
- Ballnus et al (2017). - All reaction-diffusion problems, MCMC focus
- Very nice plots of the posterior (or a representative cut) for each problem
- M1 mRNA transfection
- M2 Bistable switch
- M3 Saturated growth
- M4 Biochemical system with Hopf bifurcation
- M5 Driven Van der Pol Oscillator
- M6 Lorenz Attractor
- Feroz & Skilling (2013) - Theoretical focus
- Rastrigin function,
- Himmelblau's function,
- multidimensional eggbox,
- Bayesian object detection case study.
- Wikipedia's list of optimisation test functions
Update by Michael: I've repurposed this ticket to collect various toy problems / benchmarks we might like to add at some point. Whenever someone decides a certain benchmark is necessary - and that they're going to implement it - we can make a separate ticket for that!