Joint Tensor Factorization and Outlying Slab Suppression with Applications

We consider factoring low-rank tensors in the presence of outlying slabs. This problem is important in practice, because data collected in many real-world applications, such as speech, fluorescence, and some social network data, fit this paradigm. Prior work tackles this problem by iteratively selecting a fixed number of slabs and fitting, a procedure which may not converge. We formulate this problem from a group-sparsity promoting point of view, and propose an alternating optimization framework to handle the corresponding $\ell_p$ ($0<p\leq 1$) minimization-based low-rank tensor factorization problem. The proposed algorithm features a similar per-iteration complexity as the plain trilinear alternating least squares (TALS) algorithm. Convergence of the proposed algorithm is also easy to analyze under the framework of alternating optimization and its variants. In addition, regularization and constraints can be easily incorporated to make use of \emph{a priori} information on the latent loading factors. Simulations and real data experiments on blind speech separation, fluorescence data analysis, and social network mining are used to showcase the effectiveness of the proposed algorithm

SWEEPFINDER2: Increased sensitivity, robustness, and flexibility

SweepFinder is a popular program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection, as well as increased flexibility that enables the user to examine genomic regions in greater detail and to specify a fixed distance between test sites. Moreover, SweepFinder2 enables the use of invariant sites for sweep detection, increasing both its power and precision relative to SweepFinder

The mind, the lab, and the field: Three kinds of populations in scientific practice

Scientists use models to understand the natural world, and it is important not to conflate model and nature. As an illustration, we distinguish three different kinds of populations in studies of ecology and evolution: theoretical, laboratory, and natural populations, exemplified by the work of R.A. Fisher, Thomas Park, and David Lack, respectively. Biologists are rightly concerned with all three types of populations. We examine the interplay between these different kinds of populations, and their pertinent models, in three examples: the notion of “effective” population size, the work of Thomas Park on /Tribolium/ populations, and model-based clustering algorithms such as /Structure/. Finally, we discuss ways to move safely between three distinct population types while avoiding confusing models and reality

Controlling the potential landscape and normal modes of ion Coulomb crystals by a standing wave optical potential

Light-induced control of ions within small Coulomb crystals is investigated. By intense intracavity optical standing wave fields, subwavelength localization of individual ions is achieved for one-, two-, and three-dimensional crystals. Based on these findings, we illustrate numerically how the application of such optical potentials can be used to tailor the normal mode spectra and patterns of multi-dimensional Coulomb crystals. The results represent, among others, important steps towards controlling the crystalline structure of Coulomb crystals, investigating heat transfer processes at the quantum limit and quantum simulations of many-body systems.Comment: 6+12 pages. arXiv admin note: substantial text overlap with arXiv:1703.0508

K2P2^2 −- A photometry pipeline for the K2 mission

With the loss of a second reaction wheel, resulting in the inability to point continuously and stably at the same field of view, the NASA Kepler satellite recently entered a new mode of observation known as the K2 mission. The data from this redesigned mission present a specific challenge; the targets systematically drift in position on a ~6 hour time scale, inducing a significant instrumental signal in the photometric time series --- this greatly impacts the ability to detect planetary signals and perform asteroseismic analysis. Here we detail our version of a reduction pipeline for K2 target pixel data, which automatically: defines masks for all targets in a given frame; extracts the target's flux- and position time series; corrects the time series based on the apparent movement on the CCD (either in 1D or 2D) combined with the correction of instrumental and/or planetary signals via the KASOC filter (Handberg & Lund 2014), thus rendering the time series ready for asteroseismic analysis; computes power spectra for all targets, and identifies potential contaminations between targets. From a test of our pipeline on a sample of targets from the K2 campaign 0, the recovery of data for multiple targets increases the amount of potential light curves by a factor ${\geq}10$. Our pipeline could be applied to the upcoming TESS (Ricker et al. 2014) and PLATO 2.0 (Rauer et al. 2013) missions.Comment: 14 pages, 20 figures, Accepted for publication in The Astrophysical Journal (Apj

Pinning an Ion with an Intracavity Optical Lattice

We report one-dimensional pinning of a single ion by an optical lattice. The lattice potential is produced by a standing-wave cavity along the rf-field-free axis of a linear Paul trap. The ion's localization is detected by measuring its fluorescence when excited by standing-wave fields with the same period, but different spatial phases. The experiments agree with an analytical model of the localization process, which we test against numerical simulations. For the best localization achieved, the ion's average coupling to the cavity field is enhanced from 50% to 81(3)% of its maximum possible value, and we infer that the ion is bound in a lattice well with over 97% probability.Comment: 5 pages, 4 figures; Text edited for clarity, results unchange

Ultra-low-noise supercontinuum generation with a flat near-zero normal dispersion fiber

A pure silica photonic crystal fiber with a group velocity dispersion ($\beta_2$) of 4 ps$^2$/km at 1.55 $\mu$m and less than 7 ps$^2$/km from 1.32 $\mu$m to the zero dispersion wavelength (ZDW) 1.80 $\mu$m was designed and fabricated. The dispersion of the fiber was measured experimentally and found to agree with the fiber design, which also provides low loss below 1.83 $\mu$m due to eight outer rings with increased hole diameter. The fiber was pumped with a 1.55 $\mu$m, 125 fs laser and, at the maximum in-coupled peak power (P$_0$) of 9 kW, a 1.34$-$1.82 $\mu$m low-noise spectrum with a relative intensity noise below 2.2\% was measured. The numerical modeling agreed very well with the experiments and showed that P$_0$ could be increased to 26 kW before noise from solitons above the ZDW started to influence the spectrum by pushing high-noise dispersive waves through the spectrum

Gaussian-Charge Polarizable Interaction Potential for Carbon Dioxide

A number of simple pair interaction potentials of the carbon dioxide molecule are investigated and found to underestimate the magnitude of the second virial coefficient in the temperature interval 220 K to 448 K by up to 20%. Also the third virial coefficient is underestimated by these models. A rigid, polarizable, three-site interaction potential reproduces the experimental second and third virial coefficients to within a few percent. It is based on the modified Buckingham exp-6 potential, an anisotropic Axilrod-Teller correction and Gaussian charge densities on the atomic sites with an inducible dipole at the center of mass. The electric quadrupole moment, polarizability and bond distances are set to equal experiment. Density of the fluid at 200 and 800 bars pressure is reproduced to within some percent of observation over the temperature range 250 K to 310 K. The dimer structure is in passable agreement with electronically resolved quantum-mechanical calculations in the literature, as are those of the monohydrated monomer and dimer complexes using the polarizable GCPM water potential. Qualitative agreement with experiment is also obtained, when quantum corrections are included, for the relative stability of the trimer conformations, which is not the case for the pair potentials.Comment: Error in the long-range correction fixed and three-body dispersion introduced. 32 pages (incl. title page), 7 figures, 9 tables, double-space