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

Source code from other researchers          Old Q&T source code

   
NEW rPLS - Recursive weighted Partial least Squares for variable selection
NEW SCREAM - A novel method for multi-way regression problems with shifts and shape changes in one mode
NEW AutoChrome - Matlab toolbox for automatically finding the right PARAFAC2 model of e.g. GCMS data
NEW drEEM - Matlab toolbox supporting visualisation and PARAFAC of excitation emission matrices (EEMs)
NEW Chromatric Spatial Variance Toolbox, Matlab toolbox for RGB image analysis
NEW POLYS 2.0 - An open source software package for building 3D structures of polysaccharides
NEW PCA bootstrap - Bootstrap based Confidence Limits in Principal Component Analysis
NEW CMTF Toolbox - Coupled Matrix and Tensor Factorization for Matlab
NEW 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
  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.
  Extended Canonical Variates Analysis - a discrimination method for collinear data

by Lars Nørgaard, Rasmus Bro, Frank Westad, Søren Balling Engelsen
  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
  INDAFAC sparse implementation of Levenberg Marquadt algorithm for PARAFAC in Matlab
  PARALIND (aka restricted PARATUCk2) for modeling multi-way data with linear dependencies
  iToolbox (updated, extended version of the iPLS toolset)

Set of interval-based PLS and PCA routines for exploratory investigations.
  DTW and COW

Code for signal alignment by Dynamic Time Warping and/or Correlation Optimized Warping for Matlab
  SENSABLE

GUI for processing of sensor based data
 

Extended Multiplicative Signal Correction (EMSC) for MATLAB

EMSC/EISC signal correction

 

The N-way Toolbox for MATLAB  (matlab 7.3)

Procedures for fitting PARAFAC, Tucker, N-PLS and other N-way models.

  INCA

Imports and prepares fluorometric data from the PE-FLDM for use in MATLAB, e.g., The N-way Toolbox for MATLAB.
  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
  PARAFAC2 model for MATLAB 5.2

Save the file and type - help parafac2 - in MATLAB (Updated Jan 2003).
  Jackknifed PARAFAC

Jackknifing of PARAFAC models - Version 2.03 - self-contained (no need for the Nway Toolbox)
  MILES for MATLAB 5/6

Algorithm for fitting maximum likelihood models through least squares algorithms
  GEMANOVA model for MATLAB 5/6

Model for fitting multi-linear ANOVA models in MATLAB.
  The Missing Toolbox

Simple functions for handling missing values.
  Non-negativity constrained least squares regression

M-files for non-negativity constrained least squares regression.
  PARAFAC for complex-valued problems

Useful e.g. for problems in tele communication
  Uni-modality (and monotonic) constrained least squares regression

M-files for unimodality constrained least squares regression.
  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
  Multiblock Toolbox

M-files for various PCA- and PLS-like multiblock algorithms in MATLAB

 

 

Source Code from other researchers

  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)
  Image Analysis Toolbox IMAT (courtesy of Sensory Science, Department of Food Science, KVL)

Methods for extracting global features in images
  The Standard Dataset Object For Matlab (by Eigenvector)
  MVACDF, a multivariate data format standard

 

 

Old Q&T source code 

  Preferably use the N-way Toolbox above. The programs below are old versions 
  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)
  Multi-way PLS

Standalone M-files for multi-linear partial least squares regression (old version now covered by the N-way Toolbox)
  GUI iPLS (independent of Command Line iPLS)

Interval PLS for variable selection with optimization of interval width.
  PARAFAC

Models for estimating PARAFAC (old version now covered by the N-way Toolbox)
 

 


Contact rb@life.ku.dk in case of problems and questions to these pages

Use this link to other sources of MATLAB code