ViDaExpert
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ViDaExpert - is a software for multidimensional vectorial data visualization (ViDa stands for VIsualization of DAta).
Description
Development of ViDaExpert software is a continuous process which was started in 2000 by Dr. Andrei Zinovyev
for his PhD thesis
at the Institute
Of Computational Modeling of
Russian Academy of Science, was continued at IHES and
moved to Bioinformatics service of Institut Curie. For the moment, it is actively used by researchers
of Institut Curie for exploratory data analysis (mainly, microarray data).
ViDaExpert implements a number of methods for exploratory data analysis:
- Principal Components Analysis
- Weighted Principal Components Analysis
- Method of Elastic Maps for construction of Non-linear Principal Manifolds with Different Topologies
- PCA-based bi-plots
- Visualization of Functions by Coloring (non-linear analogue of bi-plots and visualization of density estimations)
- K-means clustering
- Hierarchical clustering
- Linear discriminant analysis
- Linear regression analysis
- Linear desicion tree construction machine
In ViDaExpert there is a well-developed set of tools to browse, annotate and mark datapoints with colors, shapes and sizes.
ViDaExpert is equiped with fast and convenient OpenGL-based 3D-viewer, which creates an integrative environment
for exploratory data analysis.
ViDaExpert was shown to be a useful tool, in particular, in analysis of microarray data. There are special
panels integrated to support analysis of microarray data (for example, dot-plots).
In the nearest future we plan to integrate into ViDaExpert several data analysis techniques, including
a version of Independent Component Analysis.
Screenshots
References
- Gorban A.N., Pitenko A., Zinovyev A. ViDaExpert: user-friendly tool for nonlinear visualization and analysis of multidimensional vectorial data. ArXiv:1406.5550
- Gorban A.N., Zinovyev A. 2010. Principal manifolds and graphs in practice: from molecular biology to dynamical systems. Int J Neural Syst 20(3):219-32. PDF
- Gorban A.N. and Zinovyev A. Principal Graphs and Manifolds. In Handbook of Research on Machine Learning Applications and Trends: Algorithms, Methods and Techniques (eds. Olivas E.S., Guererro J.D.M., Sober M.M., Benedito J.R.M., Lopes A.J.S.). Information Science Reference, September 4, 2009. PDF
- Gorban A.N,, Zinovyev A. Elastic Principal Graphs and Manifolds and their Practical Applications. Computing, 2005 (PDF)
- Zinovyev A.. Method And Software For Fast Construction Of Principal Manifolds Approximations. (PDF)
- Gorban A.N., Zinovyev A. Visualization of Data by Method of Elastic Maps and Its Applications in Genomics, Economics and Sociology. (PDF)
- Gorban A.N., Zinovyev A. and Wunsch D. Application of the method of elastic maps in analysis of genetic texts. (PDF)
- Zinovyev A. Visualization of Multidimensional Data (in Russian). Krasnoyasrk: KGTU Publ., 2000, 168 p. PDF
You can also have a look at the following Powerpoint presentation:
- Non-linear Principal Manifolds - elastic maps approach. (PPT)
VidaExpert tool was also used in the following publicaitons:
- Boss, G.J. and Kozloski, J.R. and Pickover, C.A. and Sand, A.R. (2014) Multi-dimensional channel directories. US Patent App. 14/030,521.
- Zinovyev A. (2011) Data visualization in political and social sciences.
International Encyclopedia of Political Science (eds. Badie, B.,
Berg-Schlosser, D., Morlino, L. A.), SAGE Publications, arXiv:1008.1188
- Resta M. (2010) Portfolio optimization through elastic maps: Some evidence
from the Italian stock exchange. Knowledge-Based Intelligent Information and
Engineering Systems, B. Apolloni, R.J. Howlett and L. Jain (eds.), Lecture Notes in
Computer Science 4693, Springer: Berlin – Heidelberg, 635-641.
- Gorban A., Popova T., Zinovyev A. Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences. In Silico Biology, 2005 (HTML)
- Carbone A., Kepes F., Zinovyev A. Codon Bias Signatures, Organization of Microorganisms in Codon Space, and Lifestyle. Mol.Biol.Evol., 2005 (PDF)
- Carbone A., Zinovyev A., Kepes F. Codon Adaptation Index as a measure of dominating codon bias. Bioinformatics, 2003 (PDF)
- Gorban A., Zinovyev A., Popova T. Seven Clusters In Genomic Triplet Distributions. In Silico Biology, 2003 (PDF)
Method of elastic maps is also used in development of VIMIDA Java-applet.
Documentation
Here you can find several tutorials to start with ViDaExpert.
Here is a detailed video tutorial, in Russian language: (zipped file , 500M).
Look also at the description of elmap method.
Implementation
ViDaExpert was implemented in Borland Delphi version 5. The installation does not require any additional
libraries.
Downloads
Contact
Bioinformatics service of Instiute of Curie
Dr. Andrei Zinovyev
VidaExpert v1.2 executable (only Windows)