We make software available for our research. Note that it is not ‘production code’, it is often just a snapshot of the software used to produce the results in a particular paper. This makes it easier for other people to make comparisons and to reproduce our results.
MATweave
MATweave is a couple of tricks for integrating your MATLAB/Octave code into LaTeX documents.
Making Software Available
Really Reproducible Research in the Computational Sciences
I believe machine learning researchers should be making their software available at the same time they submit (or before) their papers to conference papers or journals, and I’ve carried out this practice since 2001. I wanted to put together the reasons why we should be doing this at some point, but it turns out that other researchers have already laid out reasons that pretty much match my own. So if you want to know why I (and why you should) make your code available that reproduces the figures in your papers please read this which was inspired by ideas of Jon Claerbout. See his white paper here.
Thanks to Kevin Murphy for pointing out these papers.
Neil Lawrence, 05 December 2005
Software on Github via the SheffieldML Group Repo
| Software | Author | Description |
|---|---|---|
| Python GPy Software on Github | Python Toolbox | GP, GP-LVM, Bayesian GP-LVM software and many other extentions from our group and range of collaborators. |
| MATLAB GPmat Software on Github | MATLAB Toolbox | IVM, GP and GP-LVM software and many other extentions from a range of collaborators. |
| C++ GPc Software on Github | C++ Toolbox | IVM, GP and GP-LVM software in C++. |
| R gprege Software on Github | R Toolbox | GP software in R. |
Repositories Available Under lawrennd
| package | description | |
|---|---|---|
| ambassadors14 | Sheffield Computer Science 2014 Cutler’s Ambassadors Programme for Schools | 0 github watchers |
| bfd | MATLAB code for Bayesian interpretation of Fisher’s discriminant | 0 github watchers |
| bibliography | Bibliography files | 0 github watchers |
| blf | MATLAB code for mean field theory for sigmoid belief networks from my PhD thesis. | 4 github watchers |
| chipdyno | Dynamical model for inference of transcription factor activities. | 1 github watchers |
| chipvar | Software for variational Inference of transcription factor activities in MATLAB. | 1 github watchers |
| collab | 3 github watchers | |
| data-readiness | Repo to store suggestions about data readiness levels. | 3 github watchers |
| datasets | MATLAB datasets repository. | 1 github watchers |
| dgplvm | Discriminative GP-LVM. | 2 github watchers |
| dimred | Dimensional reduction in MATLAB. | 3 github watchers |
| disimrank | Gene target ranking by driven input single input motif Matlab code. | 1 github watchers |
| drawing | MATLAB tools for drawing (originally with image labelling in mind). | 2 github watchers |
| drbook | Dimensionality Reduction for Machine Learning Book | 2 github watchers |
| dsschool- | Base repo containing barebones page for schools and workshops. | 0 github watchers |
| ensmlp | MATLAB Code for Variational Learning of Neural Networks | 3 github watchers |
| fgplvm | Faster GP-LVM software in MATLAB. | 31 github watchers |
| gca | Generalized Component Analysis MATLAB software. | 1 github watchers |
| gp | Gaussian process software in MATLAB. | 9 github watchers |
| gplvm | Deprecated MATLAB software for IVM Based GPLVM | 7 github watchers |
| gppmacros | 0 github watchers | |
| gpsim | Gaussian Process Single Input Motif software in MATLAB. | 1 github watchers |
| gpy-gallery | Notebook gallery for the GPy software. | 2 github watchers |
| gpy_examples | Examples for using the GPy software. | 0 github watchers |
| hgplvm | Hierarchical GP-LVM code in MATLAB | 5 github watchers |
| ivm | MATLAB software for the Informative Vector Machine. | 6 github watchers |
| kappenball | Code for the Kappenball game and other code from my 2012 lecture on uncertainty. | 2 github watchers |
| kern | Kernel toolbox for MATLAB. | 5 github watchers |
| kpca | MATLAB Software for missing data in KPCA. | 2 github watchers |
| lamd | Python scripts for turning markdown into talks. | 2 github watchers |
| makeparts | Make files to move across to lamd | 0 github watchers |
| meu | MATLAB code for maximum entropy unfolding. | 1 github watchers |
| mgplvm | Mixtures of GP-LVM models in MATLAB. | 3 github watchers |
| mi2013 | Machines and Intelligence 2013 | 0 github watchers |
| mlai | Software for lectures on machine learning. | 3 github watchers |
| mlai2012 | Machine Learning and Adaptive Intelligence, 2012 | 0 github watchers |
| mlai2013 | Machine Learning and Adaptive Intelligence 2013 | 1 github watchers |
| mlai2014 | Machine Learning and Adaptive Intelligence Module 2013-2014 | 3 github watchers |
| mlai2015 | Machine learning and adaptive intelligence module for 2015. | 23 github watchers |
| mlai2018 | Machine learning and adaptive intelligence module for 2018. | 7 github watchers |
| mltools | Machine learning tools in MATLAB | 8 github watchers |
| mocap | Matlab software for processing motion capture files. | 56 github watchers |
| mtivm | Multitask IVM software in MATLAB. | 2 github watchers |
| ncca | MATLAB Code for non-consolidating CCA. | 3 github watchers |
| ncnm | Null category noise model for semi-supervised learning. | 1 github watchers |
| ndlpy | Neil’s python files for scripts. | 0 github watchers |
| ndlutil | General utilities for MATLAB. | 3 github watchers |
| neurips2014 | Notebooks for managing NeurIPS 2014 and analysing the NeurIPS experiment. | 11 github watchers |
| nips2016 | Papers presented from the NIPS 2016 conference. | 0 github watchers |
| nkfd | MATLAB Code for Kernel linear discriminant analysis with Noisy Labels. | 2 github watchers |
| noise | Noise models implemented in MATLAB. | 1 github watchers |
| nppca | MATLAB code for PCA in data with heteroschedastic noise. Originally targeted at gene expression analysis. | 3 github watchers |
| old_talks | Talks from Neil Lawrence | 52 github watchers |
| optimi | MATLAB helper functions and constraint functions for optimization. | 1 github watchers |
| oxford | MATLAB demos first created for a tutorial at Oxford University. | 1 github watchers |
| plot2svg | Save MATLAB plots as svg files | 1 github watchers |
| ppa | Probabilistic Point Assimilation: Variational Inference Software for Gaussian Processes. | 2 github watchers |
| prior | prior distributions in MATLAB. | 1 github watchers |
| rca | Residual Component Analysis software in MATLAB. | 3 github watchers |
| rochol | Rank one Cholesky update in MATLAB. | 1 github watchers |
| sdlfmgp | Switching dynamic latent force model Gaussian processes code in MATLAB. | 1 github watchers |
| sgplvm | Shared GP-LVM model in MATLAB. | 7 github watchers |
| slides | Storage of slides from talks. | 0 github watchers |
| spectral | MATLAB Software for assessing the number of clusters in Spectral Clustering. | 5 github watchers |
| synth | MATLAB software for speech synthesis through eigenvoices. | 3 github watchers |
| talks | Talks from Neil Lawrence | 0 github watchers |
| vargplvm | Variational Bayesian GP-LVM model in MATLAB. | 12 github watchers |
| vis | Variational Importance Sampler | 2 github watchers |
Code Restructuring
Code is currently being restructured to update git repos with old SVN and CVS history.
MATLAB/Octave Toolkits
These toolboxes make use of the core functionality in the GPmat toolbox. To download these software packages you need to register, the packages are freely available for academic use, you must seek a license for commercial use. Follow instructions on the sites to access the software. Some will be merged into the core toolbox over time. They tend to reflect more recent research innovations than the core material.
Older Toolboxes