Partial derivative automata formalized in Coq

In this paper we present a computer assisted proof of the correctness of a partial derivative automata construction from a regular expression within the Coq proof assistant. This proof is part of a for- malization of Kleene algebra and regular languages in Coq towards their usage in program certification.Fundação para a Ciência e Tecnologia (FCT) Program POSI, RESCUE (PTDC/EIA/65862/2006), SFRH/BD/33233/2007

A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer

We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organisms can be calculated in O(N+hM^2) time and O(N+M^2) space, where N is the number of organisms, $h$ is the height of the phylogeny, and M is the sum of family sizes. We apply the model to the evolution of gene content in Preoteobacteria using the gene families in the COG (Clusters of Orthologous Groups) database

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A suffix tree approach to anti-spam email filtering

We present an approach to email filtering based on the suffix tree data structure. A method for the scoring of emails using the suffix tree is developed and a number of scoring and score normalisation functions are tested. Our results show that the character level representation of emails and classes facilitated by the suffix tree can significantly improve classification accuracy when compared with the currently popular methods, such as naive Bayes. We believe the method can be extended to the classification of documents in other domains