title: Variable-length positional modeling for biological sequence classification.
abstract: Selecting the most informative features in supervised biological classification problems is a decisive pre-processing step for two main reasons: (1) to deal with the dimensionality reduction problem, and (2) to ascribe biological meaning to the underlying feature interactions. This paper presents a filter-based feature selection method that is suitable for positional modeling of biological sequences. The basic motivation is the problem of using a positional model of fixed length that sub-optimally describes biological sequences in a specific classification problem. The core filtering criterion is the F-score and the source features are the positional probabilities describing variable-length interactions among residues. The proposed method was evaluated on human splice sites classification using a linear SVM classifier. The method yields to superior classification accuracy compared to the individual positional models, while it maintains the space complexity of the individual models, in a time-efficient way and independently of the classifier.
authors.affiliation: Lab. of Medical Informatics, Aristotle University of Thessaloniki, Greece.
authors.forename: Andigoni
authors.initials: A
authors.lastname: Malousi
authors.forename: Ioanna
authors.initials: I
authors.lastname: Chouvarda
authors.forename: Vassilis
authors.initials: V
authors.lastname: Koutkias
authors.forename: Sofia
authors.initials: S
authors.lastname: Kouidou
authors.forename: Nicos
authors.initials: N
authors.lastname: Maglaveras
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017421:Sequence Analysis / Q000379:methods*