Vasant Honavar

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We introduce Learn++, an algorithm for incremental training of neural network (NN) pattern classifiers. The proposed algorithm enables supervised NN paradigms, such as the multilayer perceptron (MLP), to accommodate new data, including examples that correspond to previously unseen classes. Furthermore, the algorithm does not require access to previously(More)
Practical pattern classi cation and knowledge discovery problems require selection of a subset of attributes or features (from a much larger set) to represent the patterns to be classi ed. This paper presents an approach to the multi-criteria optimization problem of feature subset selection using a genetic algorithm. Our experiments demonstrate the(More)
The identification and characterization of B-cell epitopes play an important role in vaccine design, immunodiagnostic tests, and antibody production. Therefore, computational tools for reliably predicting linear B-cell epitopes are highly desirable. We evaluated Support Vector Machine (SVM) classifiers trained utilizing five different kernel methods using(More)
RNA-protein interactions are vitally important in a wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses. We have developed a computational tool for predicting which amino acids of an RNA binding protein participate in RNA-protein interactions, using only the protein(More)
Glycosylation is one of the most complex post-translational modifications (PTMs) of proteins in eukaryotic cells. Glycosylation plays an important role in biological processes ranging from protein folding and subcellular localization, to ligand recognition and cell-cell interactions. Experimental identification of glycosylation sites is expensive and(More)
RNA-protein interactions (RPIs) play important roles in a wide variety of cellular processes, ranging from transcriptional and post-transcriptional regulation of gene expression to host defense against pathogens. High throughput experiments to identify RNA-protein interactions are beginning to provide valuable information about the complexity of RNA-protein(More)
In this paper, we propose a "bag of system calls" representation for intrusion detection in system call sequences and describe misuse and anomaly detection results with standard machine learning techniques on University of New Mexico (UNM) and MIT Lincoln Lab (MIT LL) system call sequences with the proposed representation. With the feature representation as(More)
Understanding the molecular details of protein-DNA interactions is critical for deciphering the mechanisms of gene regulation. We present a machine learning approach for the identification of amino acid residues involved in protein-DNA interactions. We start with a Naïve Bayes classifier trained to predict whether a given amino acid residue is a DNA-binding(More)
Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe RNABindR, a web-based server that identifies and displays RNA-binding residues in known protein-RNA complexes and predicts RNA-binding residues in proteins of unknown structure. RNABindR uses a distance cutoff to(More)