1,180 research outputs found
Random Costs in Combinatorial Optimization
The random cost problem is the problem of finding the minimum in an
exponentially long list of random numbers. By definition, this problem cannot
be solved faster than by exhaustive search. It is shown that a classical
NP-hard optimization problem, number partitioning, is essentially equivalent to
the random cost problem. This explains the bad performance of heuristic
approaches to the number partitioning problem and allows us to calculate the
probability distributions of the optimum and sub-optimum costs.Comment: 4 pages, Revtex, 2 figures (eps), submitted to PR
Comparative Methods for Gene Structure Prediction in Homologous Sequences
The increasing number of sequenced genomes motivates the use of evolutionary patterns to detect genes. We present a series of comparative methods for gene finding in homologous prokaryotic or eukaryotic sequences. Based on a model of legal genes and a similarity measure between genes, we find the pair of legal genes of maximum similarity. We develop methods based on genes models and alignment based similarity measures of increasing complexity, which take into account many details of real gene structures, e.g. the similarity of the proteins encoded by the exons. When using a similarity measure based on an exiting alignment, the methods run in linear time. When integrating the alignment and prediction process which allows for more fine grained similarity measures, the methods run in quadratic time. We evaluate the methods in a series of experiments on synthetic and real sequence data, which show that all methods are competitive but that taking the similarity of the encoded proteins into account really boost the performance
Digging deeper - A new data mining workflow for improved processing and interpretation of high resolution GC-Q-TOF MS data in archaeological research
Treatment of severe alcoholic hepatitis: A systematic review
Severe alcoholic hepatitis is the most severe form of alcohol-related liver disease. Corticosteroids remain the first choice of treatment. However, they are only effective in a subset of patients and are associated with an increased infection risk. Furthermore, nonresponders to corticosteroids have a poor prognosis with a mortality of 70% over 6 months. As such, there is a high need for a more personalized use of corticosteroids and the development and identification of alternative therapeutic strategies. In this review, we summarize the recent and ongoing randomized controlled trials concerning the treatment of severe alcoholic hepatitis
From in-vitro genetic alteration to in-vivo NMR imaging, a unique animal model of depression
International audienc
Optimal combinations of imperfect objects
We address the question of how to make best use of imperfect objects, such as
defective analog and digital components. We show that perfect, or near-perfect,
devices can be constructed by taking combinations of such defects. Any
remaining objects can be recycled efficiently. In addition to its practical
applications, our `defect combination problem' provides a novel generalization
of classical optimization problems.Comment: 4 pages, 3 figures, minor change
Slider—maximum use of probability information for alignment of short sequence reads and SNP detection
Motivation: A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce a new alignment approach (Slider) that reduces the alignment problem space by utilizing each read base's probabilities given in the prb files
Entropy-based analysis of the number partitioning problem
In this paper we apply the multicanonical method of statistical physics on
the number-partitioning problem (NPP). This problem is a basic NP-hard problem
from computer science, and can be formulated as a spin-glass problem. We
compute the spectral degeneracy, which gives us information about the number of
solutions for a given cost and cardinality . We also study an extension
of this problem for partitions. We show that a fundamental difference on
the spectral degeneracy of the generalized () NPP exists, which could
explain why it is so difficult to find good solutions for this case. The
information obtained with the multicanonical method can be very useful on the
construction of new algorithms.Comment: 6 pages, 4 figure
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