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We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP. SignalP consists of two different predictors based on neural network and hidden Markov model algorithms, where both components have been updated. Motivated by the idea

Abstract. The Nelder–Mead simplex algorithm, first published in 1965, is an enormously popular direct search method for multidimensional unconstrained minimization. Despite its widespread use, essentially no theoretical results have been proved explicitly for the Nelder–Mead algorithm. This paper

The R-tree, one of the most popular access methods for rectangles, is based on the heuristic optimization of the area of the enclosing rectangle in each inner node. By running numerous experiments in a standardized testbed under highly varying data, queries and operations, we were able to design

. These networks have been widely used for both prediction and classification in many different areas. Although the most popular method for training these networks is backpropagation, other optimization methods such as tabu search have been applied to solve this problem. This chapter describes two training

In this article, we present an overview of methods for sequential simulation from posterior distributions. These methods are of particular interest in Bayesian filtering for discrete time dynamic models that are typically nonlinear and non-Gaussian. A general importance sampling framework

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We describe new algorithms for training tagging models, as an alternative to maximum-entropy models or conditional random fields (CRFs). The algorithms rely on Viterbi decoding of training examples, combined with simple additive updates. We describe theory justifying the algorithms through a modification of the proof of convergence of the perceptron algorithm for classification problems. We give experimental results on part-of-speech tagging and base noun phrase chunking, in both cases showing improvements over results for a maximum-entropy tagger.

A new access meth d, called M-tree, is proposed to organize and search large data sets from a generic "metric space", i.e. whE4 object proximity is only defined by a distance function satisfyingth positivity, symmetry, and triangle inequality postulates. We detail algorith[ for insertion of objects and split management, whF h keep th M-tree always balanced - severalheralvFV split alternatives are considered and experimentally evaluated. Algorithd for similarity (range and k-nearest neigh bors) queries are also described. Results from extensive experimentationwith a prototype system are reported, considering as th performance criteria th number of page I/O's and th number of distance computations. Th results demonstratethm th Mtree indeed extendsth domain of applicability beyond th traditional vector spaces, performs reasonably well inhE[94Kv#E44V[vh data spaces, and scales well in case of growing files. 1

distortion--robustness tradeoffs than currently popular spread-spectrum and low-bit(s) modulation methods. Furthermore, we show that for some important classes of probabilistic models, DC-QIM is optimal (capacity-achieving) and regular QIM is near-optimal. These include both additive white Gaussian noise