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Many scientific and Grid applications require high-speed circuits of guaranteed bandwidth for scheduled transfers. Offline optimization of dynamic scheduled bandwidth demands is an efficient way of finding the near-optimal solution to the bandwidth scheduling problem. In this paper, we propose a continuous and parallel optimization method to address the dynamic and deterministic bandwidth scheduling...
The identification of a differentially expressed set of genes in microarray data analysis is essential, both for novel onco-genic pathway identification, as well as for automated diagnostic purposes. This paper assesses the effectiveness of the Population-Based Incremental Learning (PBIL) algorithm in identifying a class differentiating gene set for sample classification. PBIL is based on iteratively...
Despite of being a very common task in bioinformatics, multiple sequence alignment is not a trivial matter. Arranging a set of molecular sequences to reveal their similarities and their differences is often hardened by the complexity and the size of the search space involved, which undermine the approaches that try to explore exhaustively the solution's search space. Due to its nature, Genetic Algorithms,...
Conditional random fields (CRFs) are undirected probabilistic graphical models that were introduced for solving sequence labeling and segmenting problems. CRFs have several advantages compared to other well understood and widely used techniques such as hidden Markov models (HMMs) or maximum entropy Markov models (MEMMs). Being a conditional model, it does not explicitly model the input data sequences...
In game theory, the traveler's dilemma (abbreviated TD) is a non-zero-sum game in which two players attempt to maximize their own payoff without deliberately willing to damage the opponent. In the classical formulation of this problem, game theory predicts that, if both players are purely rational, they will always choose the strategy corresponding to the Nash equilibrium for the game. However, when...
For biomedical researchers it is now possible to measure large numbers of DNA sequence variations across the human genome. Measuring hundreds of thousands of variations is now routine, but single variations which consistently predict an individual's risk of common human disease have proven elusive. Instead of single variants determining the risk of common human diseases, it seems more likely that...
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