The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect phylogeny model allowing persistent characters, that is characters can be gained and lost at most once. We define a natural generalization of the P-PP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained P-PP (CP-PP). Based on a graph formulation of the CP-PP problem, we are able to provide a polynomial time solution for the CP-PP problem for matrices having an empty conflict-graph. In particular we show that all such matrices admit a persistent perfect phylogeny in the unconstrained case. Using this result, we develop a parameterized algorithm for solving the CP-PP problem where the parameter is the number of characters. A preliminary experimental analysis of the algorithm shows that it performs efficiently and it may analyze real haplotype data not conforming to the classical perfect phylogeny model.
A new notion of Security Boundary is introduced to model multilevel security policies in the scenario of mobile systems, within Cardelli and Gordon's "pure" Mobile Ambients calculus. Information leakage may be expressed in terms of the possibility for a hostile ambient to access confidential data that are not protected inside a security boundary. A control flow analysis is defined, as a refinement of the Hansen-Jensen-Nielsons's CFA, that allows to properly capture boundary crossings. In this way, direct information leakage may be statically detected.
A multilevel security policy is considered in the scenario of mobile systems, and modeled within "pure" Mobile Ambients calculus, in which no communication channels are present and the only possible actions are represented by the moves performed by mobile processes. The information flow property of interest is defined in terms of the possibility for a confidential ambient/data to move outside a security boundary. In a previous paper, we gave a very simple syntactic property that is sufficient to imply the absence of unwanted information flows. In this paper, a control flow analysis is defined, as a refinement of the Hansen-Jensen-Nielsons's CFA, that allows to capture boundary crossings with better accuracy.
No abstract
This article describes an approach for the automated verification of mobile systems. Mobile systems are characterized by the explicit notion of location (e.g., sites where they run) and the ability to execute at different locations, yielding a number of security issues. To this aim, we formalize mobile systems as Labeled Kripke Structures, encapsulating the notion of location net that describes the hierarchical nesting of the threads constituting the system. Then, we formalize a generic security-policy specification language that includes rules for expressing and manipulating the code location. In contrast to many other approaches, our technique supports both access control and information flow specification. We developed a prototype framework for model checking of mobile systems. It works directly on the program code (in contrast to most traditional process-algebraic approaches that can model only limited details of mobile systems) and uses abstraction-refinement techniques, based also on location abstractions, to manage the program state space. We experimented with a number of mobile code benchmarks by verifying various security policies. The experimental results demonstrate the validity of the proposed mobile system modeling and policy specification formalisms and highlight the advantages of the model checking-based approach, which combines the validation of security properties with other checks, such as the validation of buffer overflows.
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