4,634 research outputs found

    Detecting semantic groups in MIP models

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    Advancing Dynamic Fault Tree Analysis

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    This paper presents a new state space generation approach for dynamic fault trees (DFTs) together with a technique to synthesise failures rates in DFTs. Our state space generation technique aggressively exploits the DFT structure --- detecting symmetries, spurious non-determinism, and don't cares. Benchmarks show a gain of more than two orders of magnitude in terms of state space generation and analysis time. Our approach supports DFTs with symbolic failure rates and is complemented by parameter synthesis. This enables determining the maximal tolerable failure rate of a system component while ensuring that the mean time of failure stays below a threshold

    Developing and applying heterogeneous phylogenetic models with XRate

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    Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog
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