FOkin is an object-oriented MATLAB toolbox for the analysis of kinetic data from systems of first-order reactions, typically obtained by spectroscopic experiments. Instead of the conventional multi-exponential fitting, FOkin applies the methods of sparse modeling (lasso, group-lasso and elastic net) for the prediction of the kinetic parameters. The hyperparameters controlling the model selection are automatically determined by a machine-learning procedure based on cross-validation and Bayesian optimization. The details of the applied methods are described in [1].
Download the content of the repository and add the Code folder as a path to your MATLAB environment.
See the FOkin User Guide.pdf file in the Documentation folder. Example programs reproducing the figures and tables presented in [1] are available in the Examples folder.
- Zimányi L, Sipos Á, Sarlós F, Nagypál R, Groma GI. ‘Machine-learning model selection and parameter estimation from kinetic data of complex first-order reaction systems’, PLoS One, in press.
For comments and questions please contact: Géza I. Groma, Institute of Biophysics, Biological Research Centre, Szeged, Hungary, email: geza DOT groma AT brc DOT hu.