This page is for information relating to my MPhil thesis project, titled "A Comparison of Parallel Global Optimisation Algorithms for Reverse Engineering Gene Networks".
The project involved compared the performance of optimisation algorithms (the Parallel Lam Simulated Annealing algorithm, and a Parallel Evolutionary Strategy that I developed). The algorithms were used to fit a model of a gap gene network in the early Drosophila embryo to high-resolution spatio-temporal gene expression data. The Parallel ES was found to be more reliable and faster than the Parallel SA.
My project supervisor was Yogi Jaeger.
A PDF copy is available here
There are two separate programs, one for the Parallel ES and one for Lam SA. The code I used is modified from the code used by Jaeger (2004) and Fomekong-Nanfack (2007) for SA and ES respectively. Follow the instructions below to install both programs.
Parallel Evolutionary Strategy
Parallel Lam Simulated Annealing
Note that the extra SA code only adds time-stamping to the logs, and is used to produce descent curves.
The data-set used in the thesis is available here, in the file format that both programs accept.
J. Jaeger et al (2004) Dynamic control of positional information in the early Drosophila embryo. Nature, 430(6997):368-371 PDF
Y. Fomekong-Nanfack et al (2007) Efficient parameter estimation for spatio-temporal models of pattern formation: case study of Drosophila melanogaster. Bioinformatics, 23(24):3356-3363 Link
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