Department of Food Science
Faculty of Science
University of Copenhagen
Algorithms and source code
IMPORTANT: all downloadable material listed on these pages - appended by specifics mentioned under the individual headers/chapters - is available for public use. Please note that while great care has been taken, the software, code and data are provided "as is" and that Q&T, LIFE, KU does not accept any responsibility or liability.
MATLAB source code from Q&T
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| NEW | GS-PARAFAC2 - a new approach to line search implemented for the PARAFAC2 algorithm |
| HYPERTOOLS - tools for hyperspectral analysis --> New version with GUI available the 1st of August | |
| sparafac - Sparse (non-negative) PARAFAC | |
| spca - Sparse Principal Component Analysis | |
| spiderplots - Visual presentation of factor loadings | |
| rPLS - Recursive weighted Partial least Squares for variable selection | |
| SCREAM - A novel method for multi-way regression problems with shifts and shape changes in one mode | |
| AutoChrome - Matlab toolbox for automatically finding the right PARAFAC2 model of e.g. GCMS data | |
| drEEM - Matlab toolbox supporting visualisation and PARAFAC of excitation emission matrices (EEMs) | |
| Chromatric Spatial Variance Toolbox, Matlab toolbox for RGB image analysis | |
| POLYS 2.0 - An open source software package for building 3D structures of polysaccharides | |
| PCA bootstrap - Bootstrap based Confidence Limits in Principal Component Analysis | |
| CMTF Toolbox - Coupled Matrix and Tensor Factorization for Matlab | |
| NSIMCA - Multi-way classification | |
| FastChrom - Processing of chromatographic data | |
| Loads2Chrom - identify modelled peaks from GC-MS datasets. | |
| FDOMFLuor - FDOMcorr Toolbox by Kate Murphy. Simplify and automate correction of DOM EEM data | |
| SMR - Sparse matrix regression for coclustering | |
| EEMizer - automatically determine the appropriate PARAFAC model for EEM data | |
| UPDATE | icoshift - An ultra rapid and versatile tool for the alignment of spectral datasets |
| DOMFluor - Characterizing dissolved organic matter fluorescence with parallel factor analysis. | |
| Rotation of PCA models - a freeware function to rotate and counterotate scores or loadings (MATLAB - uses PLS_Toolbox) | |
| Signflip - a freeware function to correct for sign ambiguity in SVD/PCA (MATLAB) | |
| iCDF - a freeware function to import netCDF files from GC-MS, LC-MS etc. software in MATLAB | |
| CONLOAD for calculating correlation loadings and congruence loadings for two-way and multi-way models | |
| Clustering is a tool for performing interactive two- and multi-way clustering. | |
| EEMSCAT is a tool for removing scatter from EEMs and for interpolating values in the removed areas. | |
| CuBatch is a graphical user interface based on the Matlab environment that can be employed for the analysis and the handling of the most disparate types of data. | |
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Extended Canonical Variates Analysis - a discrimination method for collinear data by Lars Nørgaard, Rasmus Bro, Frank Westad, Søren Balling Engelsen |
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Rayleigh scatter correcting PARAFAC of EEM data from "First order Rayleigh scatter as a separate component in the decomposition of fluorescence landscapes", Rinnan, Booksh, Bro Analytica Chimica Acta, Volume 537, Issues 1-2, 29 April 2005, Pages 349-358 |
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| INDAFAC sparse implementation of Levenberg Marquadt algorithm for PARAFAC in Matlab | |
| PARALIND (aka restricted PARATUCk2) for modeling multi-way data with linear dependencies | |
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iToolbox (updated, extended version of the iPLS toolset) Set of interval-based PLS and PCA routines for exploratory investigations. |
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DTW and COW Code for signal alignment by Dynamic Time Warping and/or Correlation Optimized Warping for Matlab |
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SENSABLE GUI for processing of sensor based data |
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Extended Multiplicative Signal Correction (EMSC) for MATLAB |
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The N-way Toolbox for MATLAB (matlab 7.3) |
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INCA Imports and prepares fluorometric data from the PE-FLDM for use in MATLAB, e.g., The N-way Toolbox for MATLAB. |
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Low-field NMR toolbox (Version 3.0 including simplified use by Power-SLICING) Contains algorithms for exponential fitting, phase correction of quadrature data and SLICING |
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PARAFAC2 model for MATLAB 5.2 Save the file and type - help parafac2 - in MATLAB (Updated Jan 2003). |
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Jackknifed PARAFAC Jackknifing of PARAFAC models - Version 2.03 - self-contained (no need for the Nway Toolbox) |
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MILES for MATLAB 5/6 Algorithm for fitting maximum likelihood models through least squares algorithms |
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GEMANOVA model for MATLAB 5/6 Model for fitting multi-linear ANOVA models in MATLAB. |
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The Missing Toolbox Simple functions for handling missing values. |
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Non-negativity constrained least squares regression M-files for non-negativity constrained least squares regression. |
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PARAFAC for complex-valued problems Useful e.g. for problems in tele communication |
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Uni-modality (and monotonic) constrained least squares regression M-files for unimodality constrained least squares regression. |
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Routine for calculating normalized 2D radial pair distributions Calculations used in paper "The mean hydration of carbohydrates as studied by normalized 2-D radial pair distributions" in Journal of Molecular Graphics and Modeling |
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Multiblock Toolbox M-files for various PCA- and PLS-like multiblock algorithms in MATLAB |
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Source Code from other researchers |
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| Multi-way PLS regression for R. Code by Casey Kneale | |
| FPDC Probabilistic clustering. Code by Cristina Torora | |
| Multi-way VIP for multi-way variable selection. Code by M. Cocchi and coworkers | |
| iToolbox GUI 1.01 including manual by Dr. Giorgio Luciano, Department of Chemistry, University of Genoa, Italy | |
| MATLAB Tensor Classes for Fast Algorithm Prototyping by B. Bader & T. Kolda | |
| The PLS-Genetic Algorithm Toolbox (courtesy of Riccardo Leardi - University of Genoa, Italy) | |
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Image Analysis Toolbox IMAT (courtesy of Sensory Science, Department of Food Science, KVL) Methods for extracting global features in images |
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| The Standard Dataset Object For Matlab (by Eigenvector) | |
| MVACDF, a multivariate data format standard | |
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Old Q&T source code |
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| Preferably use the N-way Toolbox above. The programs below are old versions | |
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Three-way Procedures with a three-way data set Tucker, PARAFAC, GRAM, RAFA and misc. 2nd order models with a test data set (old version now covered by the N-way Toolbox) |
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Multi-way PLS Standalone M-files for multi-linear partial least squares regression (old version now covered by the N-way Toolbox) |
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GUI iPLS (independent of Command Line iPLS) Interval PLS for variable selection with optimization of interval width. |
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PARAFAC Models for estimating PARAFAC (old version now covered by the N-way Toolbox) |
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Contact rb@life.ku.dk in case of problems and questions to these pages |
Use this link to other sources of MATLAB code |