LEGClust- a clustering algorithm based on layered entropic subgraphs

Detection of Replication Origin Sites in Herpesvirus Genomes by Clustering and Scoring of Palindromes with Quadratic Entropy Measures

Replication in herpesvirus genomes is a major concern of public health as they multiply rapidly during the lytic phase of infection that cause maximum damage to the host cells. Earlier research has established that sites of replication origin are dominated by high concentration of rare palindrome sequences of DNA. Computational methods are devised based on scoring to determine the concentration of palindromes. In this paper, we propose both extraction and localization of rare palindromes in an automated manner. Discrete Cosine Transform (DCT-II), a widely recognized image compression algorithm is utilized here to extract palindromic sequences based on their reverse complimentary symmetry property of existence. We formulate a novel approach to localize the rare palindrome clusters by devising a Minimum Quadratic Entropy (MQE) measure based on the Renyi's Quadratic Entropy (RQE) function. Experimental results over a large number of herpesvirus genomes show that the RQE based scoring of rare palindromes have higher order of sensitivity, and lesser false alarm in detecting concentration of rare palindromes and thereby sites of replication origin.

The MEE principle in data classification: a perceptron-based analysis

This letter focuses on the issue of whether risk functionals derived from information-theoretic principles, such as Shannon or Rényi's entropies, are able to cope with the data classification problem in both the sense of attaining the risk functional minimum and implying the minimum probability of error allowed by the family of functions implemented by the classifier, here denoted by min Pe. The analysis of this so-called minimization of error entropy (MEE) principle is carried out in a single perceptron with continuous activation functions, yielding continuous error distributions. In spite of the fact that the analysis is restricted to single perceptrons, it reveals a large spectrum of behaviors that MEE can be expected to exhibit in both theory and practice. In what concerns the theoretical MEE, our study clarifies the role of the parameters controlling the perceptron activation function (of the squashing type) in often reaching the minimum probability of error. Our study also clarifies the role of the kernel density estimator of the error density in achieving the minimum probability of error in practice.