9,002 research outputs found
A Distributed Dendritic Cell Algorithm for Big Data
In this work, we focus on the Dendritic Cell Algorithm (DCA), a bio-inspired classifier, and its limitation when coping with very large datasets. To overcome this limitation, we propose a novel distributed DCA version for data classification based on the MapReduce framework to distribute the functioning of this algorithm through a cluster of computing elements. Our experimental results show that our proposed distributed solution is suitable to enhance the performance of the DCA enabling the algorithm to be applied over big data classification problems.authorsversio
KInNeSS: A Modular Framework for Computational Neuroscience
Making use of very detailed neurophysiological, anatomical, and behavioral data to build biological-realistic computational models of animal behavior is often a difficult task. Until recently, many software packages have tried to resolve this mismatched granularity with different approaches. This paper presents KInNeSS, the KDE Integrated NeuroSimulation Software environment, as an alternative solution to bridge the gap between data and model behavior. This open source neural simulation software package provides an expandable framework incorporating features such as ease of use, scalabiltiy, an XML based schema, and multiple levels of granularity within a modern object oriented programming design. KInNeSS is best suited to simulate networks of hundreds to thousands of branched multu-compartmental neurons with biophysical properties such as membrane potential, voltage-gated and ligand-gated channels, the presence of gap junctions of ionic diffusion, neuromodulation channel gating, the mechanism for habituative or depressive synapses, axonal delays, and synaptic plasticity. KInNeSS outputs include compartment membrane voltage, spikes, local-field potentials, and current source densities, as well as visualization of the behavior of a simulated agent. An explanation of the modeling philosophy and plug-in development is also presented. Further developement of KInNeSS is ongoing with the ultimate goal of creating a modular framework that will help researchers across different disciplines to effecitively collaborate using a modern neural simulation platform.Center for Excellence for Learning Education, Science, and Technology (SBE-0354378); Air Force Office of Scientific Research (F49620-01-1-0397); Office of Naval Research (N00014-01-1-0624
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Error, reproducibility and sensitivity : a pipeline for data processing of Agilent oligonucleotide expression arrays
Background
Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples.
Results
We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2% of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log2 units ( 6% of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators.
Conclusions
This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells
Perspective: Organic electronic materials and devices for neuromorphic engineering
Neuromorphic computing and engineering has been the focus of intense research
efforts that have been intensified recently by the mutation of Information and
Communication Technologies (ICT). In fact, new computing solutions and new
hardware platforms are expected to emerge to answer to the new needs and
challenges of our societies. In this revolution, lots of candidates
technologies are explored and will require leveraging of the pro and cons. In
this perspective paper belonging to the special issue on neuromorphic
engineering of Journal of Applied Physics, we focus on the current achievements
in the field of organic electronics and the potentialities and specificities of
this research field. We highlight how unique material features available
through organic materials can be used to engineer useful and promising
bioinspired devices and circuits. We also discuss about the opportunities that
organic electronic are offering for future research directions in the
neuromorphic engineering field
The effects of polydispersity and metastability on crystal growth kinetics
We investigate the effect of metastable gas-liquid (G-L) separation on
crystal growth in a system of either monodisperse or slightly size-polydisperse
square well particles, using a simulation setup that allows us to focus on the
growth of a single crystal. Our system parameters are such that, inside the
metastable G-L binodal, a macroscopic layer of the gas phase "coats" the
crystal as it grows, consistent with experiment and theoretical free energy
considerations. Crucially, the effect of this metastable G-L separation on the
crystal growth rate depends qualitatively on whether the system is
polydisperse. We measure reduced polydispersity and qualitatively different
local size ordering in the crystal relative to the fluid, proposing that the
required fractionation is dynamically facilitated by the gas layer. Our results
show that polydispersity and metastability, both ubiquitous in soft matter,
must be considered in tandem if their dynamical effects are to be understood.Comment: Published in Soft Matter. DOI: 10.1039/C3SM27627
Neuro-memristive Circuits for Edge Computing: A review
The volume, veracity, variability, and velocity of data produced from the
ever-increasing network of sensors connected to Internet pose challenges for
power management, scalability, and sustainability of cloud computing
infrastructure. Increasing the data processing capability of edge computing
devices at lower power requirements can reduce several overheads for cloud
computing solutions. This paper provides the review of neuromorphic
CMOS-memristive architectures that can be integrated into edge computing
devices. We discuss why the neuromorphic architectures are useful for edge
devices and show the advantages, drawbacks and open problems in the field of
neuro-memristive circuits for edge computing
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