7,698 research outputs found
Towards the Design of Heuristics by Means of Self-Assembly
The current investigations on hyper-heuristics design have sprung up in two
different flavours: heuristics that choose heuristics and heuristics that
generate heuristics. In the latter, the goal is to develop a problem-domain
independent strategy to automatically generate a good performing heuristic for
the problem at hand. This can be done, for example, by automatically selecting
and combining different low-level heuristics into a problem specific and
effective strategy. Hyper-heuristics raise the level of generality on automated
problem solving by attempting to select and/or generate tailored heuristics for
the problem at hand. Some approaches like genetic programming have been
proposed for this. In this paper, we explore an elegant nature-inspired
alternative based on self-assembly construction processes, in which structures
emerge out of local interactions between autonomous components. This idea
arises from previous works in which computational models of self-assembly were
subject to evolutionary design in order to perform the automatic construction
of user-defined structures. Then, the aim of this paper is to present a novel
methodology for the automated design of heuristics by means of self-assembly
Boosting Haplotype Inference with Local Search
Abstract. A very challenging problem in the genetics domain is to infer haplotypes from genotypes. This process is expected to identify genes affecting health, disease and response to drugs. One of the approaches to haplotype inference aims to minimise the number of different haplotypes used, and is known as haplotype inference by pure parsimony (HIPP). The HIPP problem is computationally difficult, being NP-hard. Recently, a SAT-based method (SHIPs) has been proposed to solve the HIPP problem. This method iteratively considers an increasing number of haplotypes, starting from an initial lower bound. Hence, one important aspect of SHIPs is the lower bounding procedure, which reduces the number of iterations of the basic algorithm, and also indirectly simplifies the resulting SAT model. This paper describes the use of local search to improve existing lower bounding procedures. The new lower bounding procedure is guaranteed to be as tight as the existing procedures. In practice the new procedure is in most cases considerably tighter, allowing significant improvement of performance on challenging problem instances.
Paradigms for computational nucleic acid design
The design of DNA and RNA sequences is critical for many endeavors, from DNA nanotechnology, to PCR‐based applications, to DNA hybridization arrays. Results in the literature rely on a wide variety of design criteria adapted to the particular requirements of each application. Using an extensively studied thermodynamic model, we perform a detailed study of several criteria for designing sequences intended to adopt a target secondary structure. We conclude that superior design methods should explicitly implement both a positive design paradigm (optimize affinity for the target structure) and a negative design paradigm (optimize specificity for the target structure). The commonly used approaches of sequence symmetry minimization and minimum free‐energy satisfaction primarily implement negative design and can be strengthened by introducing a positive design component. Surprisingly, our findings hold for a wide range of secondary structures and are robust to modest perturbation of the thermodynamic parameters used for evaluating sequence quality, suggesting the feasibility and ongoing utility of a unified approach to nucleic acid design as parameter sets are refined further. Finally, we observe that designing for thermodynamic stability does not determine folding kinetics, emphasizing the opportunity for extending design criteria to target kinetic features of the energy landscape
Where Quantum Complexity Helps Classical Complexity
Scientists have demonstrated that quantum computing has presented novel
approaches to address computational challenges, each varying in complexity.
Adapting problem-solving strategies is crucial to harness the full potential of
quantum computing. Nonetheless, there are defined boundaries to the
capabilities of quantum computing. This paper concentrates on aggregating prior
research efforts dedicated to solving intricate classical computational
problems through quantum computing. The objective is to systematically compile
an exhaustive inventory of these solutions and categorize a collection of
demanding problems that await further exploration
Error Correction in DNA Computing: Misclassification and Strand Loss
We present a method of transforming an extract-based DNA computation that is error-prone into one that is relatively error-free. These improvements in error rates are achieved without the supposition of any improvements in the reliability of the underlying laboratory techniques. We assume that only two types of errors are possible: a DNA strand may be incorrectly processed or it may be lost entirely. We show to deal with each of these
errors individually and then analyze the tradeoff when both must be optimized simultaneously
Kernel Spectral Clustering and applications
In this chapter we review the main literature related to kernel spectral
clustering (KSC), an approach to clustering cast within a kernel-based
optimization setting. KSC represents a least-squares support vector machine
based formulation of spectral clustering described by a weighted kernel PCA
objective. Just as in the classifier case, the binary clustering model is
expressed by a hyperplane in a high dimensional space induced by a kernel. In
addition, the multi-way clustering can be obtained by combining a set of binary
decision functions via an Error Correcting Output Codes (ECOC) encoding scheme.
Because of its model-based nature, the KSC method encompasses three main steps:
training, validation, testing. In the validation stage model selection is
performed to obtain tuning parameters, like the number of clusters present in
the data. This is a major advantage compared to classical spectral clustering
where the determination of the clustering parameters is unclear and relies on
heuristics. Once a KSC model is trained on a small subset of the entire data,
it is able to generalize well to unseen test points. Beyond the basic
formulation, sparse KSC algorithms based on the Incomplete Cholesky
Decomposition (ICD) and , , Group Lasso regularization are
reviewed. In that respect, we show how it is possible to handle large scale
data. Also, two possible ways to perform hierarchical clustering and a soft
clustering method are presented. Finally, real-world applications such as image
segmentation, power load time-series clustering, document clustering and big
data learning are considered.Comment: chapter contribution to the book "Unsupervised Learning Algorithms
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