Validation of nonlinear PCA

Linear principal component analysis (PCA) can be extended to a nonlinear PCA by using artificial neural networks. But the benefit of curved components requires a careful control of the model complexity. Moreover, standard techniques for model selection, including cross-validation and more generally the use of an independent test set, fail when applied to nonlinear PCA because of its inherent unsupervised characteristics. This paper presents a new approach for validating the complexity of nonlinear PCA models by using the error in missing data estimation as a criterion for model selection. It is motivated by the idea that only the model of optimal complexity is able to predict missing values with the highest accuracy. While standard test set validation usually favours over-fitted nonlinear PCA models, the proposed model validation approach correctly selects the optimal model complexity.Comment: 12 pages, 5 figure

A New Kilohertz Gravitational-Wave Feature from Rapidly Rotating Core-Collapse Supernovae

We present self-consistent three-dimensional core-collapse supernova simulations of a rotating $20M_\odot$ progenitor model with various initial angular velocities from $0.0$ to $4.0$ rad s$^{-1}$ using a smoothed particle hydrodynamics code, SPHYNX, and a grid-based hydrodynamics code, FLASH. We identify two strong gravitational-wave features, with peak frequencies of $\sim300$ Hz and $\sim1.3$ kHz in the first $100$ ms postbounce. We demonstrate that these two features are associated with the $m=1$ deformation from the proto-neutron star (PNS) modulation induced by the low-$T/|W|$ instability, regardless of the simulation code. The $300$ Hz feature is present in models with an initial angular velocity between $1.0$ and $4.0$ rad s$^{-1}$, while the $1.3$ kHz feature is present only in a narrower range, from $1.5$ to $3.5$ rad s$^{-1}$. We show that the $1.3$ kHz signal originates from the high-density inner core of the PNS, and the $m=1$ deformation triggers a strong asymmetric distribution of electron anti-neutrinos. In addition to the $300$ Hz and $1.3$ kHz features, we also observe one weaker but noticeable gravitational-wave feature from higher-order modes in the range between $1.5$ and $3.5$ rad s$^{-1}$. Its peak frequency is around $800$ Hz initially and gradually increases to $900-1000$ Hz. Therefore, in addition to the gravitational bounce signal, the detection of the $300$ Hz, $1.3$ kHz, the higher-order mode, and even the related asymmetric emission of neutrinos, could provide additional diagnostics to estimate the initial angular velocity of a collapsing core.Comment: 20 pages, 14 figures,. Accepted for publication in the Astrophysical Journa

Expected Shannon entropy and Shannon differentiation between subpopulations for neutral genes under the finite island model

<div><p>Shannon entropy <i>H</i> and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information (“Shannon differentiation”) between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (<i>Sturnus vulgaris</i>) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.</p></div

Bulkier glass formability enhanced by minor alloying additions

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Photoacid behaviour in a fluorinated green fluorescent protein chromophore:Ultrafast formation of anion and zwitterion states

The photophysics of the chromophore of the green fluorescent protein in Aequorea victoria (avGFP) are dominated by an excited state proton transfer reaction. In contrast the photophysics of the same chromophore in solution are dominated by radiationless decay, and photoacid behaviour is not observed. Here we show that modification of the pKa of the chromophore by fluorination leads to an excited state proton transfer on an extremely fast (50 fs) time scale. Such a fast rate suggests a barrierless proton transfer and the existence of a pre-formed acceptor site in the aqueous solution, which is supported by solvent and deuterium isotope effects. In addition, at lower pH, photochemical formation of the elusive zwitterion of the GFP chromophore is observed by means of an equally fast excited state proton transfer from the cation. The significance of these results for understanding and modifying the properties of fluorescent proteins are discusse

Early Outbreak of 2009 Influenza A (H1N1) in Mexico Prior to Identification of pH1N1 Virus

10.1371/journal.pone.0023853PLoS ONE68