8,105 research outputs found

    "Going back to our roots": second generation biocomputing

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    Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin

    Rough sets, their extensions and applications

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    Rough set theory provides a useful mathematical foundation for developing automated computational systems that can help understand and make use of imperfect knowledge. Despite its recency, the theory and its extensions have been widely applied to many problems, including decision analysis, data-mining, intelligent control and pattern recognition. This paper presents an outline of the basic concepts of rough sets and their major extensions, covering variable precision, tolerance and fuzzy rough sets. It also shows the diversity of successful applications these theories have entailed, ranging from financial and business, through biological and medicine, to physical, art, and meteorological

    Using numerical plant models and phenotypic correlation space to design achievable ideotypes

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    Numerical plant models can predict the outcome of plant traits modifications resulting from genetic variations, on plant performance, by simulating physiological processes and their interaction with the environment. Optimization methods complement those models to design ideotypes, i.e. ideal values of a set of plant traits resulting in optimal adaptation for given combinations of environment and management, mainly through the maximization of a performance criteria (e.g. yield, light interception). As use of simulation models gains momentum in plant breeding, numerical experiments must be carefully engineered to provide accurate and attainable results, rooting them in biological reality. Here, we propose a multi-objective optimization formulation that includes a metric of performance, returned by the numerical model, and a metric of feasibility, accounting for correlations between traits based on field observations. We applied this approach to two contrasting models: a process-based crop model of sunflower and a functional-structural plant model of apple trees. In both cases, the method successfully characterized key plant traits and identified a continuum of optimal solutions, ranging from the most feasible to the most efficient. The present study thus provides successful proof of concept for this enhanced modeling approach, which identified paths for desirable trait modification, including direction and intensity.Comment: 25 pages, 5 figures, 2017, Plant, Cell and Environmen

    Error Metrics for Learning Reliable Manifolds from Streaming Data

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    Spectral dimensionality reduction is frequently used to identify low-dimensional structure in high-dimensional data. However, learning manifolds, especially from the streaming data, is computationally and memory expensive. In this paper, we argue that a stable manifold can be learned using only a fraction of the stream, and the remaining stream can be mapped to the manifold in a significantly less costly manner. Identifying the transition point at which the manifold is stable is the key step. We present error metrics that allow us to identify the transition point for a given stream by quantitatively assessing the quality of a manifold learned using Isomap. We further propose an efficient mapping algorithm, called S-Isomap, that can be used to map new samples onto the stable manifold. We describe experiments on a variety of data sets that show that the proposed approach is computationally efficient without sacrificing accuracy

    Fuzzy-Rough Sets Assisted Attribute Selection

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    Attribute selection (AS) refers to the problem of selecting those input attributes or features that are most predictive of a given outcome; a problem encountered in many areas such as machine learning, pattern recognition and signal processing. Unlike other dimensionality reduction methods, attribute selectors preserve the original meaning of the attributes after reduction. This has found application in tasks that involve datasets containing huge numbers of attributes (in the order of tens of thousands) which, for some learning algorithms, might be impossible to process further. Recent examples include text processing and web content classification. AS techniques have also been applied to small and medium-sized datasets in order to locate the most informative attributes for later use. One of the many successful applications of rough set theory has been to this area. The rough set ideology of using only the supplied data and no other information has many benefits in AS, where most other methods require supplementary knowledge. However, the main limitation of rough set-based attribute selection in the literature is the restrictive requirement that all data is discrete. In classical rough set theory, it is not possible to consider real-valued or noisy data. This paper investigates a novel approach based on fuzzy-rough sets, fuzzy rough feature selection (FRFS), that addresses these problems and retains dataset semantics. FRFS is applied to two challenging domains where a feature reducing step is important; namely, web content classification and complex systems monitoring. The utility of this approach is demonstrated and is compared empirically with several dimensionality reducers. In the experimental studies, FRFS is shown to equal or improve classification accuracy when compared to the results from unreduced data. Classifiers that use a lower dimensional set of attributes which are retained by fuzzy-rough reduction outperform those that employ more attributes returned by the existing crisp rough reduction method. In addition, it is shown that FRFS is more powerful than the other AS techniques in the comparative study
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