programs, the average ti me requi red by the Omega test to determi ne the di recti on vectors for an array pai ri s less than 500 secs on a 12 MIPS workstati on. The Omega testi based on an extensi n of Four i0-Motzki var i ble eli937 ti n (aliB: r programmiA method) toi nteger programmi ng, and has worst

Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions

The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hashtable based methods has been developed, including MAQ, which is accurate, feature rich and fast enough

This note describes a separation-logic-based approach for the specification and verification of safety properties of pointer-manipulating imperative programs. The programmer may declare inductive datatypes and primitive recursive functions for specification. Verification proceeds by symbolic

This paper proposes a new algorithm for training support vector machines: Sequential Minimal Optimization, or SMO. Training a support vector machine requires the solution of a very large quadratic programming (QP) optimization problem. SMO breaks this large QP problem into a series of smallest

converging linear iteration can be cast as a semidefinite program, and therefore efficiently and globally solved. These optimal linear iterations are often substantially faster than several common heuristics that are based on the Laplacian of the associated graph. We show how problem structure can

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using tree

a larger impact on performance. Consequently, one must know the details of a computer architecture in order to design a fast algorithm. In this paper, we propose an adaptive FFT program that tunes the computation automatically for any particular hardware. We compared our program, called FFTW

need fast automatic attack detection and filtering mechanisms. In this paper we propose dynamic taint analysis for automatic detection and analysis of overwrite attacks, which include most types of exploits. This approach does not need source code or special compilation for the monitored program