3196759
Low-complexity algorithms for sequencing jobs with a fixed number of job-classes
In this paper we consider the problem of scheduling n jobs such that makespan is minimized. It is assumed that the jobs can be divided into K job-classes and that the change-over time between two consecutive jobs depends on the job-classes to which the two jobs belong. In this setting, we discuss the one machine scheduling problem with arbitrary processing times and the parallel machines scheduling problem with identical processing times. In both cases it is assumed that the number of job-classes K is fixed. By using an appropriate integer programming formulation with a fixed number of variables and constraints, it is shown that these two problems are solvable in polynomial time. For the one machine scheduling case it is shown that the complexity of our algorithm is linear in the number of jobs n. Moreover, if the problem is encoded according to the high multiplicity model of Hochbaum and Shamir, the time complexity of the algorithm is shown to be a polynomial in log n. In the parallel machine scheduling case, it is shown that if the number of machines is fixed the same results hold.
96314
On the long-step path-following method for semidefinite programming
It has been shown in various recent research reports that the analysis of short-step primal-dual path following algorithms for linear programming can be nicely generalized to semidefinite programming. However, the analysis of long-step path-following algorithms for semidefinite programming appeared to be less straightforward. For such an algorithm, Monteiro (1997) obtained an O(n^1^.^5log(1/@e)) iteration bound for obtaining an @e-optimal solution, where n is the order of the semidefinite decision variable. In this paper, we propose to use a different search direction, viz. the so-called V-space direction. It is shown that this modification reduces the iteration complexity to O(nlog(1/@e)). Independently, Monteiro and Y. Zhang obtained a similar result using Nesterov-Todd directions.
9519800
Turbulent Decay and Mixing of Accelerated Inhomogeneous Flows Via a Feature Based Analysis
In this paper, we focus on the late time turbulence of an accelerated inhomogeneous flow environment, which is a generalization of the Richtmyer--Meshkov environment. The numerical investigation is based on two-dimensional (2D) compressible Euler simulation, which is initiated by a shock wave hitting a gas layer (curtain). Although our unforced study is based on the intrinsic numerical dissipation, we observe excellent agreement with the previous decay analysis on 2D viscous isotropic homogeneous turbulence at inertial range [J. R. Chasnov, Phys. Fluids, 9 (1997), pp. 171--180]. The baroclinic circulation in our environment plays a major role in the mass transport and mixing. The mass-transport induced density gradient intensification, in turn, enhances the circulation baroclinically and provides an intrinsic forcing at intermediate to high wave number range. With the assistance of a computer graphics based feature extraction and tracking algorithm, we address quantitatively the spatial and temporal diffusivity of the mixing zone. We study and compare both the slow/fast/slow and fast/slow/fast cases to illustrate heuristically the correlation of mass and momentum diffusivity.
40464778
A model for compressing probabilities in belief networks
Probabilistic reasoning with belief (Bayesian) networks is based on conditional probability matrices. Thus it suffers from NP-hard implementations. In particular, the amount of probabilistic information necessary for the computations is often overwhelming. So, compressing the conditional probability table is one of the most important issues faced by the probabilistic reasoning community. Santos suggested an approach (called linear potential functions) for compressing the information from a combinatorial amount to roughly linear in the number of random variable assignments. However, much of the information in Bayesian networks, in which there are no linear potential functions, would be fitted by polynomial approximating functions rather than by reluctantly linear functions. For this reason, we construct a polynomial method to compress the conditional probability table in this paper. We evaluated the proposed technique, and our experimental results demonstrate that the approach is efficient and promising.
3022359
CVSSearch: searching through source code using CVS comments
CVSSearch is a tool that searches for fragments of source code by using CVS comments. CVS is a version control system that is widely used in the open source community. Our search tool takes advantage of the fact that a CVS comment typically describes the lines of code involved in the commit and this description will typically hold for many future versions. In other words, CVSSearch allows one to better search the most recent version of the code by looking at previous versions to better understand the current version. In this paper we describe our algorithm for mapping CVS comments to the corresponding source code, present a search tool based on this technique, and discuss preliminary feedback.
31017610
Structural Alignment of Pseudoknotted RNA
In this paper, we address the problem of discovering novel non-coding RNA (ncRNA) using primary sequence, and secondary structure conservation, focusing on ncRNA families with pseudo-knotted structures. Our main technical result is an efficient algorithm for computing an optimum structural alignment of an RNA sequence against a genomic substring. This algorithm finds two applications. First, by scanning a genome, we can identify novel (homologous) pseudoknotted ncRNA, and second, we can infer the secondary structure of the target aligned sequence. We test an implementation of our algorithm (Pal), and show that it has near-perfect behavior for predicting the structure of many known pseudoknots. Additionally, it can detect the true homologs with high sensitivity and specificity in controlled tests. We also use Pal to search entire viral genome and mouse genome for novel homologs of some viral, and eukaryotic pseudoknots respectively. In each case, we have found strong support for novel homologs.
11213421
Consensus Folding of Unaligned RNA Sequences Revisited
As one of the earliest problems in computational biology, RNA secondary structure prediction (sometimes referred to as "RNA folding") problem has attracted attention again, thanks to the recent discoveries of many novel non-coding RNA molecules. The two common approaches to this problem are de novo prediction of RNA secondary structure based on energy minimization and the consensus folding approach (computing the common secondary structure for a set of unaligned RNA sequences). Consensus folding algorithms work well when the correct seed alignment is part of the input to the problem. However, seed alignment itself is a challenging problem for diverged RNA families. In this paper, we propose a novel framework to predict the common secondary structure for unaligned RNA sequences. By matching putative stacks in RNA sequences, we make use of both primary sequence information and thermodynamic stability for prediction at the same time. We show that our method can predict the correct common RNA secondary structures even when we are given only a limited number of unaligned RNA sequences, and it outperforms current algorithms in sensitivity and accuracy.