248 research outputs found
Supervised Learning in Multilayer Spiking Neural Networks
The current article introduces a supervised learning algorithm for multilayer
spiking neural networks. The algorithm presented here overcomes some
limitations of existing learning algorithms as it can be applied to neurons
firing multiple spikes and it can in principle be applied to any linearisable
neuron model. The algorithm is applied successfully to various benchmarks, such
as the XOR problem and the Iris data set, as well as complex classifications
problems. The simulations also show the flexibility of this supervised learning
algorithm which permits different encodings of the spike timing patterns,
including precise spike trains encoding.Comment: 38 pages, 4 figure
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Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy
YesInfinium Human Methylation BeadChip is an array platform for complex evaluation of DNA methylation at an individual CpG locus in the human genome based on Illumina’s bead technology and is one of the most common techniques used in epigenome-wide association studies. Finding associations between epigenetic variation and phenotype is a significant challenge in biomedical research. The newest version, HumanMethylationEPIC, quantifies the DNA methylation level of 850,000 CpG sites, while the previous versions, HumanMethylation450 and HumanMethylation27, measured >450,000 and 27,000 loci, respectively. Although a number of bioinformatics tools have been developed to analyse this assay, they require some programming skills and experience in order to be usable.
Results
We have developed a pipeline for the Galaxy platform for those without experience aimed at DNA methylation analysis using the Infinium Human Methylation BeadChip. Our tool is integrated into Galaxy (http://galaxyproject.org), a web-based platform. This allows users to analyse data from the Infinium Human Methylation BeadChip in the easiest possible way.
Conclusions
The pipeline provides a group of integrated analytical methods wrapped into an easy-to-use interface. Our tool is available from the Galaxy ToolShed, GitHub repository, and also as a Docker image. The aim of this project is to make Infinium Human Methylation BeadChip analysis more flexible and accessible to everyone.Research Development Fund Publication Prize Award winner, May 2020
Exact exchange-correlation potential of a ionic Hubbard model with a free surface
We use Lanczos exact diagonalization to compute the exact
exchange-correlation (xc) potential of a Hubbard chain with large binding
energy ("the bulk") followed by a chain with zero binding energy ("the
vacuum"). Several results of density functional theory in the continuum
(sometimes controversial) are verified in the lattice. In particular we show
explicitly that the fundamental gap is given by the gap in the Kohn-Sham
spectrum plus a contribution due to the jump of the xc-potential when a
particle is added. The presence of a staggered potential and a nearest-neighbor
interaction V allows to simulate a ionic solid. We show that in the ionic
regime in the small hopping amplitude limit the xc-contribution to the gap
equals V, while in the Mott regime it is determined by the Hubbard U
interaction. In addition we show that correlations generates a new potential
barrier at the surface
An accessible proteogenomics informatics resource for cancer researchers
Proteogenomics has emerged as a valuable approach in cancer research, which integrates genomic and transcriptomic data with mass spectrometry–based proteomics data to directly identify expressed, variant protein sequences that may have functional roles in cancer. This approach is computationally intensive, requiring integration of disparate software tools into sophisticated workflows, challenging its adoption by nonexpert, bench scientists. To address this need, we have developed an extensible, Galaxy-based resource aimed at providing more researchers access to, and training in, proteogenomic informatics. Our resource brings together software from several leading research groups to address two foundational aspects of proteogenomics: (i) generation of customized, annotated protein sequence databases from RNA-Seq data; and (ii) accurate matching of tandem mass spectrometry data to putative variants, followed by filtering to confirm their novelty. Directions for accessing software tools and workflows, along with instructional documentation, can be found at z.umn.edu/canresgithub.publishedVersio
Improved Slater approximation to SIC-OEP
We propose a simplification of the Optimized Effective Potential (OEP)
applied to the Self Interaction Correction (SIC) scheme of Density Functional
Theory (DFT). The new scheme fulfills several key formal properties and turns
out to be both simple and accurate. We show examples of applications on model
molecules in terms of observables known to be especially sensitive to details
of the SIC-OEP approach.Comment: 3 figure
Random-phase approximation and its applications in computational chemistry and materials science
The random-phase approximation (RPA) as an approach for computing the
electronic correlation energy is reviewed. After a brief account of its basic
concept and historical development, the paper is devoted to the theoretical
formulations of RPA, and its applications to realistic systems. With several
illustrating applications, we discuss the implications of RPA for computational
chemistry and materials science. The computational cost of RPA is also
addressed which is critical for its widespread use in future applications. In
addition, current correction schemes going beyond RPA and directions of further
development will be discussed.Comment: 25 pages, 11 figures, published online in J. Mater. Sci. (2012
Assessment of correlation energies based on the random-phase approximation
The random-phase approximation to the ground state correlation energy (RPA)
in combination with exact exchange (EX) has brought Kohn-Sham (KS) density
functional theory one step closer towards a universal, "general purpose first
principles method". In an effort to systematically assess the influence of
several correlation energy contributions beyond RPA, this work presents
dissociation energies of small molecules and solids, activation energies for
hydrogen transfer and non-hydrogen transfer reactions, as well as reaction
energies for a number of common test sets. We benchmark EX+RPA and several
flavors of energy functionals going beyond it: second-order screened exchange
(SOSEX), single excitation (SE) corrections, renormalized single excitation
(rSE) corrections, as well as their combinations. Both the single excitation
correction as well as the SOSEX contribution to the correlation energy
significantly improve upon the notorious tendency of EX+RPA to underbind.
Surprisingly, activation energies obtained using EX+RPA based on a KS reference
alone are remarkably accurate. RPA+SOSEX+rSE provides an equal level of
accuracy for reaction as well as activation energies and overall gives the most
balanced performance, which makes it applicable to a wide range of systems and
chemical reactions.Comment: 14 pages, 5 figures, full articl
The impact of acute nutritional interventions on the plasma proteome
Context: Humans respond profoundly to changes in diet, while nutrition and environment have a great impact on population health. It is therefore important to deeply characterize the human nutritional responses. Objective: Endocrine parameters and the metabolome of human plasma are rapidly responding to acute nutritional interventions such as caloric restriction or a glucose challenge. It is less well understood whether the plasma proteome would be equally dynamic, and whether it could be a source of corresponding biomarkers. Methods: We used high-throughput mass spectrometry to determine changes in the plasma proteome of i) 10 healthy, young, male individuals in response to 2 days of acute caloric restriction followed by refeeding; ii) 200 individuals of the Ely epidemiological study before and after a glucose tolerance test at 4 time points (0, 30, 60, 120 minutes); and iii) 200 random individuals from the Generation Scotland study. We compared the proteomic changes detected with metabolome data and endocrine parameters. Results: Both caloric restriction and the glucose challenge substantially impacted the plasma proteome. Proteins responded across individuals or in an individual-specific manner. We identified nutrient-responsive plasma proteins that correlate with changes in the metabolome, as well as with endocrine parameters. In particular, our study highlights the role of apolipoprotein C1 (APOC1), a small, understudied apolipoprotein that was affected by caloric restriction and dominated the response to glucose consumption and differed in abundance between individuals with and without type 2 diabetes. Conclusion: Our study identifies APOC1 as a dominant nutritional responder in humans and highlights the interdependency of acute nutritional response proteins and the endocrine system
Morphometrical analysis of transbronchial cryobiopsies
The recent introduction of bronchoscopically recovered cryobiopsy of lung tissue has opened up new possibilities in the diagnosis of neoplastic and non-neoplastic lung diseases in various aspects. Most notably the morphological diagnosis of peripheral lung biopsies promises to achieve a better yield with a high quality of specimens. To better understand this phenomenon, its diagnostic options and perspectives, this study morphometrically compares 15 cryobiopsies and 18 transbronchial forceps biopsies of peripheral lung tissue a priori without considering clinical hit ratio or integration of results in the clinical diagnostic processing. Cryotechnically harvested specimens were significantly larger (mean: 17.1 ± 10.7 mm2 versus 3.8 ± 4.0 mm2) and contained alveolar tissue more often. If present, the alveolar part in cryobiopsies exceeded the one of forceps biopsies. The alveolar tissue of crybiopsy specimens did not show any artefacts. Based on these results cryotechnique seems to open up new perspectives in bronchoscopic diagnosis of lung disease
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