IMMAN: free software for information theory-based chemometric analysis

• Published in: Molecular diversity 2015-05, Vol.19 (2), p.305-319
• Main Authors: Urias, Ricardo W. Pino, Barigye, Stephen J., Marrero-Ponce, Yovani, García-Jacas, César R., Valdes-Martiní, José R., Perez-Gimenez, Facundo
• Format: Article
• Language: English
• Subjects: Algorithms; Biochemistry; Biomedical and Life Sciences; Full-Length Paper; Information management; Life Sciences; Metric system; Models, Theoretical; Organic Chemistry; Pharmacy; Polymer Sciences; Software; Theory
• ISSN: 1381-1991; 1573-501X
• DOI: 10.1007/s11030-014-9565-z

The features and theoretical background of a new and free computational program for chemometric analysis denominated IMMAN (acronym for I nformation theory-based Che M o M etrics AN alysis) are presented. This is multi-platform software developed in the Java programming language, designed with a remarkably user-friendly graphical interface for the computation of a collection of information-theoretic functions adapted for rank-based unsupervised and supervised feature selection tasks. A total of 20 feature selection parameters are presented, with the unsupervised and supervised frameworks represented by 10 approaches in each case. Several information-theoretic parameters traditionally used as molecular descriptors (MDs) are adapted for use as unsupervised rank-based feature selection methods. On the other hand, a generalization scheme for the previously defined differential Shannon’s entropy is discussed, as well as the introduction of Jeffreys information measure for supervised feature selection. Moreover, well-known information-theoretic feature selection parameters, such as information gain, gain ratio, and symmetrical uncertainty are incorporated to the IMMAN software ( http://mobiosd-hub.com/imman-soft/ ), following an equal-interval discretization approach. IMMAN offers data pre-processing functionalities, such as missing values processing, dataset partitioning, and browsing. Moreover, single parameter or ensemble (multi-criteria) ranking options are provided. Consequently, this software is suitable for tasks like dimensionality reduction, feature ranking, as well as comparative diversity analysis of data matrices. Simple examples of applications performed with this program are presented. A comparative study between IMMAN and WEKA feature selection tools using the Arcene dataset was performed, demonstrating similar behavior. In addition, it is revealed that the use of IMMAN unsupervised feature selection methods improves the performance of both IMMAN and WEKA supervised algorithms. Graphical abstract Graphic representation for Shannon’s distribution of MD calculating software.