TopoBARTMAP

About

This repository provides Topological Biclustering ARTMAP MATLAB (TopoBARTMAP) package. TopoBARTMAP is a biclustering algorithm that combines TopoART with BARTMAP to produce a topological algorithm.

Quick Start

Installation

Clone the code to needed folder and add to the path in MATLAB, ```

addpath("Classes","Evaluation","Functions"); ```

Requirements

This package requires the CVAP: Cluster Validity Analysis Platform MATLAB package available on MATLAB Central as a dependency. Please add the path to the CVAP in MATLAB. addpath("/path/To/CVAP");

Usage

Input Data: The data is assumed to be a matrix of shape #observationsX#features, ie., features/genes are assumed to be the columns, whilst observations are assumed to be rows. This is representation of data is different from how most gene expression data sets are stored in Gene Expression Omnibus (GEO), where data is a matrix of shape #genesX#observations.

Classes: If ground truth is available for the observations, then the clustering performance can be evaluated using external cluter validity index Adujsted Rand Index. In absence of labels, then the clustering performance can be evaluated using internal cluster validity indices like Davies-Bouldin. Please refer to CVAP for further details.

Please add path to Classes, Functions, Evaluation, CVAP, and Data to ensure that the source files are available for the compiler. This can be done as following.

With classes

An example run file, run_TopoBARTMAP.m is provided in Functions to use with gene expression data from GEO. This run file assumes data is of shape #genesX#observations. run_TopoBARTMAP returns an instance of TopoBARTMAP and the indices value. Please check the run_TopoBARTMAP for details on the settings.

```

[y,TBM] = run_TopoBARTMAP(settings, data, classes); ```

Without classes

An example run file, runTopoBARTMAPUnsupervised.m is provided in Functions to use with gene expression data from GEO. This run file assumes data is of shape #genesX#observations. runTopoBARTMAPUnsupervised returns an instance of TopoBARTMAP and the indices value. The default cluster validity index is set to Davies-Bouldin. Please check the runTopoBARTMAPUnsupervised for details on the settings.

```

[y,TBM] = runTopoBARTMAPUnsupervised(settings, data); ```

Citing

If you use TopoBARTMAP in your research, please cite the TopoBARTMAP paper.

Yelugam, R., da Silva, L.E.B. and Wunsch II, D.C., 2023. Topological biclustering ARTMAP for identifying within bicluster relationships. Neural Networks, 160, pp.34-49.

In BibTeX format:

tex @article{YELUGAM202334, title = {Topological biclustering ARTMAP for identifying within bicluster relationships}, journal = {Neural Networks}, volume = {160}, pages = {34-49}, year = {2023}, issn = {0893-6080}, doi = {https://doi.org/10.1016/j.neunet.2022.12.010}, url = {https://www.sciencedirect.com/science/article/pii/S0893608022005020}, author = {Raghu Yelugam and Leonardo Enzo {Brito da Silva} and Donald C. {Wunsch II}}, keywords = {Biclustering, Topological data analysis, Adaptive resonance theory (ART), Gene expression, Gene Co-expression} }