Software

Particle Swarm Optimiser Matlab code: PSOPC.zip
Citeation: S.He, Q. H. Wu, J. Y. Wen, J. R. Saunders and R. C. Paton, "A particle swarm optimizer with passive congregation", BioSystems, 78 (1-3): 135-147, Dec 2004.

Group Search Optimiser Matlab code: GSO.zip
Citeation: S. He, Q. H. Wu, and J. R. Saunders. "Group search optimizer - an optimization algorithm inspired by animal searching behaviour". IEEE Transaction on Evolutionary Computation. 13(5): 973-990, Oct 2009.

Smooth Nonlinar Energy Operator peak detection Matlab code: SourceCode-for-Proteomics.zip
Citeation: S. He, X. Li, M. R. Viant and X. Yao. "Profiling mass spectrometry proteomics data using Smoothed Nonlinear Energy Operator and Bayesian Additive Regression Trees". Proteomics, 9 (17): 4176-4191, Sep 2009.

Java Multi-objective Optimisation Library and source code: MOO.zip
Citeation: T. White and S. He. "An Empirical Comparison of Several Recent Multi-Objective Evolutionary Algorithms". Artificial Intelligence Applications and Innovations Conference (AIAI) 2012.

Disease Module Extraction (DiME):
DiME webpage with source code and user guide
Citeation: Y. Liu, D. A. Tennant, Z. Zhu, J. K. Heath, X. Yao, S. He, "DiME: a scalable disease module identification algorithm with application to glioma progression". Plos One, Feb. 2014

Multi-platform Unbiased optimisation of Spectrometry via Closed Loop Experimentation (MUSCLE):
MUSCLE project webpage
Citeation: J. Bradbury, G. Genta-Jouve, J. W. Allwood, W. B. Dunn, R. Goodacre, J. D. Knowles, S. He, M. R. Viant, "MUSCLE: Automated Multi-objective Evolutionary Optimisation of Targeted LC-MS/MS Analysis". Bioinformatics, online first Dec. 2014

Robust twin boosting for feature selection Matlab code: TReBFSMatlab.zip
Citeation: S. He, H. Chen, Z. Zhu, D. G. Ward, H. J. Cooper, M. R. Viant, J. K. Heath, X. Yao "Robust twin boosting for feature selection from high-dimensional omics data with label noise". Information Sciences, 291, 2015.