Algorithms
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.
The following software are …..
| Name | Description | Download |
|---|---|---|
| SIT | Shift-invariant trilinear tensor model - a faster alternative to PARAFAC2 (sometimes) | Get the data |
| Simulated GC-MS | GC-MS datasets are simulated over short retention-time intervals | Get the data |
| AHIMBU | Automatic hierarchical classification model builder (AHIMBU). An automated tool for complex classification. Check the paper heremodels. | Check the paper - check the code (requires PLS_Toolbox) |
| Multiblock Toolbox | M-files for various PCA- and PLS-like multiblock algorithms in MATLAB | Get the code |
| PARADISe | Resolving untargeted GC-MS data | Get the code |
| 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 | Get the code |
| Uni-modality (and monotonic) constrained least squares regression | M-files for unimodality constrained least squares regression. | Get the code |
| PARAFAC for complex-valued problems | Useful e.g. for problems in tele communication | |
| Non-negativity constrained least squares regression | M-files for non-negativity constrained least squares regression. | Get the code |
| The Missing Toolbox | Simple functions for handling missing values. | Get the code |
| GEMANOVA model for MATLAB 5/6 | Model for fitting multi-linear ANOVA models in MATLAB. | Get the code |
| MILES for MATLAB 5/6 | Algorithm for fitting maximum likelihood models through least squares algorithms | Get the code |
| Jackknifed PARAFAC | Jackknifing of PARAFAC models - Version 2.03 - self-contained (no need for the Nway Toolbox) | Get the code |
| PARAFAC2 model for MATLAB 5.2 | Save the file and type - help parafac2 - in MATLAB (Updated Jan 2003). | Get the code |
| 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 | Get the code |
| INCA | Imports and prepares fluorometric data from the PE-FLDM for use in MATLAB, e.g., The N-way Toolbox for MATLAB. | Get the code |
| The N-way Toolbox for MATLAB | (matlab 7.3) Procedures for fitting PARAFAC, Tucker, N-PLS and other N-way models. | Get the code |
| Extended Multiplicative Signal Correction (EMSC) for MATLAB | EMSC/EISC signal correction | Get the code |
| SENSABLE | GUI for processing of sensor based data | Get the code |
| DTW and COW | Code for signal alignment by Dynamic Time Warping and/or Correlation Optimized Warping for Matlab | Get the code |
| iToolbox | (updated, extended version of the iPLS toolset) Set of interval-based PLS and PCA routines for exploratory investigations. | Get the code |
| PARALIND | (aka restricted PARATUCk2) for modeling multi-way data with linear dependencies | Get the code |
| INDAFAC | sparse implementation of Levenberg Marquadt algorithm for PARAFAC in Matlab | Get the code |
| 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 | |
| Extended Canonical Variates Analysis | a discrimination method for collinear data by Lars Nørgaard, Rasmus Bro, Frank Westad, Søren Balling Engelsen | Get the algorithm |
| 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. | Get the code |
| EEMSCAT | is a tool for removing scatter from EEMs and for interpolating values in the removed areas. | |
| Clustering | is a tool for performing interactive two- and multi-way clustering. | Get the code |
| CONLOAD | for calculating correlation loadings and congruence loadings for two-way and multi-way models | Get the code |
| iCDF | a freeware function to import netCDF files from GC-MS, LC-MS etc. software in MATLAB | Get the code |
| Signflip | a freeware function to correct for sign ambiguity in SVD/PCA (MATLAB) | |
| Rotation of PCA models | a freeware function to rotate and counterotate scores or loadings (MATLAB - uses PLS_Toolbox) | Get the code |
| DOMFluor | Characterizing dissolved organic matter fluorescence with parallel factor analysis. | Get the code |
| icoshift | An ultra rapid and versatile tool for the alignment of spectral datasets | Get the code |
| EEMizer | automatically determine the appropriate PARAFAC model for EEM data | Get the code |
| SMR | Sparse matrix regression for coclustering | Get the code |
| FDOMFLuor | FDOMcorr Toolbox by Kate Murphy. Simplify and automate correction of DOM EEM data | Get the code |
| Loads2Chrom | identify modelled peaks from GC-MS datasets. | Get the code |
| FastChrom | Processing of chromatographic data | Get the code |
| NSIMCA | Multi-way classification | Get the code |
| CMTF Toolbox | Coupled Matrix and Tensor Factorization for Matlab | Get the code |
| PCA bootstrap | Bootstrap based Confidence Limits in Principal Component Analysis | Get the code |
| POLYS 2.0 | An open source software package for building 3D structures of polysaccharides | Get the code |
| Chromatric Spatial Variance Toolbox | Matlab toolbox for RGB image analysis | |
| drEEM | Matlab toolbox supporting visualisation and PARAFAC of excitation emission matrices (EEMs) | Get the code |
| AutoChrome | Matlab toolbox for automatically finding the right PARAFAC2 model of e.g. GCMS data | Get the code |
| SCREAM | A novel method for multi-way regression problems with shifts and shape changes in one mode | Get the code |
| rPLS | Recursive weighted Partial least Squares for variable selection | Get the code |
| Spiderplots | Visual presentation of factor loadings | Get the code |
| SPCA | Sparse Principal Component Analysis | Get the code |
| SPARAFAC | Sparse (non-negative) PARAFAC | Get the code |
| HYPERTOOLS | Tools for hyperspectral analysis |
This software are form other researchers
| Name | Code by | Download |
|---|---|---|
| MVACDF, a multivariate data format standard | Get the code | |
| The Standard Dataset Object for Matlab | Eigenvector | |
| Image Analysis Toolbox IMAT | courtesy of Sensory Science, Department of Food Science, KVL | Get the code |
| The PLS-Genetic Algorithm Toolbox | courtesy of Riccardo Leardi - University of Genoa, Italy | Get the code |
| MATLAB Tensor Classes for Fast Algorithm Prototyping | B. Bader & T. Kolda | |
| iToolbox GUI 1.01 | Dr. Giorgio Luciano | Get the code |
| Multi-way VIP for multi-way variable selection | M. Cocchi and coworkers | |
| FPDC Probabilistic clustering. | Cristina Torora | Get the code |
| Multi-way PLS regression for R. | Casey Kneale |
This software are some old stuff
| Name | Description | Download |
|---|---|---|
| PARAFAC | Models for estimating PARAFAC (old version now covered by the N-way Toolbox) | Get the code |
| GUI iPLS | (independent of Command Line iPLS) Interval PLS for variable selection with optimization of interval width. | Get the code |
| Multi-way PLS | Standalone M-files for multi-linear partial least squares regression (old version now covered by the N-way Toolbox) | Get the code |
| Three-way Procedures with a three-way dataset | Tucker, PARAFAC, GRAM, RAFA and misc. 2nd order models with a test data set (old version now covered by the N-way Toolbox) | Get the code |
