8,105 research outputs found
"Going back to our roots": second generation biocomputing
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
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
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
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
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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