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Finite mixture models are used in statistics and other disciplines, but inference for mixture models is challenging due, in part, to the multimodality of the likelihood function and the so-called label switching problem. We propose extensions of the Approximate Bayesian Computation-Population Monte Carlo (ABC-PMC) algorithm as an alternative framework for inference on finite mixture models. There are several decisions to make when implementing an ABC-PMC algorithm for finite mixture models, including the selection of the kernels used for moving the particles through the iterations, how to address the label switching problem, and the choice of informative summary statistics. Examples are presented to demonstrate the performance of the proposed ABC-PMC algorithm for mixture modeling. The performance of the proposed method is evaluated in a simulation study and for the popular recessional velocity galaxy data., 21 pages, 4 figures

The spatial distribution of galaxies at sufficiently small scales will encode information about the identity of the dark matter. We develop a novel description of the halo distribution using persistent homology summaries, in which collections of points are decomposed into clusters, loops and voids. We apply these methods, together with a set of hypothesis tests, to dark matter haloes in MW-analog environment regions of the cold dark matter (CDM) and warm dark matter (WDM) Copernicus Complexio $N$-body cosmological simulations. The results of the hypothesis tests find statistically significant differences (p-values $\leq$ 0.001) between the CDM and WDM structures, and the functional summaries of persistence diagrams detect differences at scales that are distinct from the comparison spatial point process functional summaries considered (including the two-point correlation function). The differences between the models are driven most strongly at filtration scales $\sim100$~kpc, where CDM generates larger numbers of unconnected halo clusters while WDM instead generates loops. This study was conducted on dark matter haloes generally; future work will involve applying the same methods to realistic galaxy catalogues., 17 pages, 11 figures

One of the primary areas of interest in applied algebraic topology is persistent homology, and, more specifically, the persistence diagram. Persistence diagrams have also become objects of interest in topological data analysis. However, persistence diagrams do not naturally lend themselves to statistical goals, such as inferring certain population characteristics, because their complicated structure makes common algebraic operations--such as addition, division, and multiplication-- challenging (e.g., the mean might not be unique). To bypass these issues, several functional summaries of persistence diagrams have been proposed in the literature (e.g. landscape and silhouette functions). The problem of analyzing a set of persistence diagrams then becomes the problem of analyzing a set of functions, which is a topic that has been studied for decades in statistics. First, we review the various functional summaries in the literature and propose a unified framework for the functional summaries. Then, we generalize the definition of persistence landscape functions, establish several theoretical properties of the persistence functional summaries, and demonstrate and discuss their performance in the context of classification using simulated prostate cancer histology data, and two-sample hypothesis tests comparing human and monkey fibrin images, after developing a simulation study using a new data generator we call the Pickup Sticks Simulator (STIX).

Trend filtering---first introduced into the astronomical literature in Paper I of this series---is a state-of-the-art statistical tool for denoising one-dimensional signals that possess varying degrees of smoothness. In this work, we demonstrate the broad utility of trend filtering to observational astronomy by discussing how it can contribute to a variety of spectroscopic and time-domain studies. The observations we discuss are (1) the Lyman-$\alpha$ forest of quasar spectra; (2) more general spectroscopy of quasars, galaxies, and stars; (3) stellar light curves with planetary transits; (4) eclipsing binary light curves; and (5) supernova light curves. We study the Lyman-$\alpha$ forest in the greatest detail---using trend filtering to map the large-scale structure of the intergalactic medium along quasar-observer lines of sight. The remaining studies share broad themes of: (1) estimating observable parameters of light curves and spectra; and (2) constructing observational spectral/light-curve templates. We also briefly discuss the utility of trend filtering as a tool for one-dimensional data reduction and compression., Comment: Part 2 of 2, Link to Part 1: arXiv:1908.07151; 15 pages, 7 figures

Persistent homology is a tool within topological data analysis to detect different dimensional holes in a dataset. The boundaries of the empty territories (i.e., holes) are not well-defined and each has multiple representations. The proposed method, Empty Territory (EmT), provides representations of different dimensional holes with a specified level of complexity of the territory boundary. EmT is designed for the setting where persistent homology uses a Vietoris-Rips complex filtration, and works as a post-analysis to refine the hole representation of the persistent homology algorithm. In particular, EmT uses alpha shapes to obtain a special class of representations that captures the empty territories with a complexity determined by the size of the alpha balls. With a fixed complexity, EmT returns the representation that contains the most points within the special class of representations. This method is limited to finding 1D holes in 2D data and 2D holes in 3D data, and is illustrated on simulation datasets of a homogeneous Poisson point process in 2D and a uniform sampling in 3D. Furthermore, the method is applied to a 2D cell tower location geography dataset and 3D Sloan Digital Sky Survey (SDSS) galaxy dataset, where it works well in capturing the empty territories.

In the search for planets orbiting distant stars the presence of stellar activity in the atmospheres of observed stars can obscure the radial velocity signal used to detect such planets. Furthermore, this stellar activity contamination is set by the star itself and cannot simply be avoided with better instrumentation. Various stellar activity indicators have been developed that may correlate with this contamination. We introduce a new stellar activity indicator called the Stellar Activity F-statistic for Exoplanet surveys (SAFE) that has higher statistical power (i.e., probability of detecting a true stellar activity signal) than many traditional stellar activity indicators in a simulation study of an active region on a Sun-like star with moderate to high signal-to-noise. Also through simulation, the SAFE is demonstrated to be associated with the projected area on the visible side of the star covered by active regions. We also demonstrate that the SAFE detects statistically significant stellar activity in most of the spectra for HD 22049, a star known to have high stellar variability. Additionally, the SAFE is calculated for recent observations of the three low-variability stars HD 34411, HD 10700, and HD 3651, the latter of which is known to have a planetary companion. As expected, the SAFE for these three only occasionally detects activity. Furthermore, initial exploration appears to indicate that the SAFE may be useful for disentangling stellar activity signals from planet-induced Doppler shifts., Comment: 20 pages, 12 figures, accepted for publication in The Astronomical Journal

The radial velocity method of exoplanet detection has led to some fantastic discoveries of planets outside our solar system. But the hunt for true Earth analogues is hampered by noisy data from stars. Jessi Cisewski outlines the challenge, and how statisticians and statistically savvy astronomers are trying to help

Accurate specification of a likelihood function is becoming increasingly difficult in many inference problems in astronomy. As sample sizes resulting from astronomical surveys continue to grow, deficiencies in the likelihood function lead to larger biases in key parameter estimates. These deficiencies result from the oversimplification of the physical processes that generated the data, and from the failure to account for observational limitations. Unfortunately, realistic models often do not yield an analytical form for the likelihood. The estimation of a stellar initial mass function (IMF) is an important example. The stellar IMF is the mass distribution of stars initially formed in a given cluster of stars, a population which is not directly observable due to stellar evolution and other disruptions and observational limitations of the cluster. There are several difficulties with specifying a likelihood in this setting since the physical processes and observational challenges result in measurable masses that cannot legitimately be considered independent draws from an IMF. This work improves inference of the IMF by using an approximate Bayesian computation approach that both accounts for observational and astrophysical effects and incorporates a physically-motivated model for star cluster formation. The methodology is illustrated via a simulation study, demonstrating that the proposed approach can recover the true posterior in realistic situations, and applied to observations from astrophysical simulation data.

Context.Stellar activity is one of the primary limitations to the detection of low-mass exoplanets using the radial-velocity (RV) technique. Stellar activity can be probed by measuring time-dependent variations in the shape of the cross-correlation function (CCF). It is therefore critical to measure with high-precision these shape variations to decorrelate the signal of an exoplanet from spurious RV signals caused by stellar activity.Aims.We propose to estimate the variations in shape of the CCF by fitting a Skew Normal (SN) density which, unlike the commonly employed Normal density, includes a Skewness parameter to capture the asymmetry of the CCF induced by stellar activity and the convective blueshift.Methods.We compared the performances of the proposed method to the commonly employed Normal density using both simulations and real observations with different levels of activity and signal-to-noise ratios.Results.When considering real observations, the correlation between the RV and the asymmetry of the CCF and between the RV and the width of the CCF are stronger when using the parameters estimated with the SN density rather than those obtained with the commonly employed Normal density. In particular, the strongest correlations have been obtained when using the mean of the SN as an estimate for the RV. This suggests that the CCF parameters estimated using a SN density are more sensitive to stellar activity, which can be helpful when estimating stellar rotational periods and when characterizing stellar activity signals. Using the proposed SN approach, the uncertainties estimated on the RV defined as the median of the SN are on average 10% smaller than the uncertainties calculated on the mean of the Normal. The uncertainties estimated on the asymmetry parameter of the SN are on average 15% smaller than the uncertainties measured on the Bisector Inverse Slope Span (BIS SPAN), which is the commonly used parameter to evaluate the asymmetry of the CCF. We also propose a new model to account for stellar activity when fitting a planetary signal to RV data. Based on simple simulations, we were able to demonstrate that this new model improves the planetary detection limits by 12% compared to the model commonly used to account for stellar activity.Conclusions.The SN density is a better model than the Normal density for characterizing the CCF since the correlations used to probe stellar activity are stronger and the uncertainties of the RV estimate and the asymmetry of the CCF are both smaller.

Continuum normalization of echelle spectra is an important data analysis step that is difficult to automate. Polynomial fitting requires a reasonably high order model to follow the steep slope of the blaze function. However, in the presence of deep spectral lines, a high order polynomial fit can result in ripples in the normalized continuum that increase errors in spectral analysis. Here, we present two algorithms for flattening the spectrum continuum. The Alpha-shape Fitting to Spectrum algorithm (AFS) is completely data-driven, using an alpha shape to obtain an initial estimate of the blaze function. The Alpha-shape and Lab Source Fitting to Spectrum algorithm (ALSFS) incorporates a continuum constraint from a lab source reference spectrum for the blaze function estimation. These algorithms are tested on a simulated spectrum, where we demonstrate improved normalization compared to polynomial regression for continuum fitting. We show an additional application, using the algorithms for mitigation of spatially correlated quantum efficiency variations and fringing in the CCD detector of the EXtreme PREcision Spectrometer (EXPRES).

The problem of denoising a one-dimensional signal possessing varying degrees of smoothness is ubiquitous in time-domain astronomy and astronomical spectroscopy. For example, in the time domain, an astronomical object may exhibit a smoothly varying intensity that is occasionally interrupted by abrupt dips or spikes. Likewise, in the spectroscopic setting, a noiseless spectrum typically contains intervals of relative smoothness mixed with localized higher frequency components such as emission peaks and absorption lines. In this work, we present trend filtering, a modern nonparametric statistical tool that yields significant improvements in this broad problem space of denoising $spatially$ $heterogeneous$ signals. When the underlying signal is spatially heterogeneous, trend filtering is superior to any statistical estimator that is a linear combination of the observed data---including kernel smoothers, LOESS, smoothing splines, Gaussian process regression, and many other popular methods. Furthermore, the trend filtering estimate can be computed with practical and scalable efficiency via a specialized convex optimization algorithm, e.g. handling sample sizes of $n\gtrsim10^7$ within a few minutes. In a companion paper, we explicitly demonstrate the broad utility of trend filtering to observational astronomy by carrying out a diverse set of spectroscopic and time-domain analyses., Comment: Part 1 of 2; 15 pages, 3 figures

Like most areas of science, astronomy has benefited from a tremendous increase in the amount of available data gathered in recent decades, from both ground- and space-based instruments. For example...

The disciplines of astronomy and statistics are coming together to answer some of the biggest questions in modern science. By Joseph M. Hilbe Impacts from space rocks have set off mass extinctions at least twice in Earth's history. Should we be worried that another strike is imminent? Joseph M. Hilbe and Jamie Riggs assess the risks An overview of meteorite strikes observed through the ages, designed by Carlo Zapponi If you want to know why the universe is the way it is, you have to understand its initial state. Benjamin Wandelt takes us back billions of years to show how statistics is helping cosmologists understand the origins of everything – including life itself Astronomy data sets are astronomically big – that is why statistical approaches are needed to analyse, organise and unravel the mysteries of the universe. By Rafael de Souza and Emille Ishida There's more to the universe than meets the eye – over 80% is made up of stuff we cannot see. Jessi Cisewski explores the nature of dark matter, and how statistics is helping locate it 30 billion? 225 billion? 400 billion? Vladimir Surdin finds no exact answer, but plenty of estimates There isn't a set of scales big enough to measure the most massive objects in the universe. Madhura Killedar considers alternative methods, and the associated statistical challenges Our universe is fine-tuned for life to such a degree that it would seem improbable were it the only universe in existence – which means there is a good chance that we live in a multiverse. Roberto Trotta explains the idea, and the discoveries that gave rise to it It began with a bang, but current models suggest the universe will go out with a whimper. Chris Impey explores the long, dark fate that awaits

Visualizing the high-redshift Universe is difficult due to the dearth of available data; however, the Lyman-alpha forest provides a means to map the intergalactic medium at redshifts not accessible to large galaxy surveys. Large-scale structure surveys, such as the Baryon Oscillation Spectroscopic Survey (BOSS), have collected quasar (QSO) spectra that enable the reconstruction of H I density fluctuations. The data fall on a collection of lines defined by the lines of sight (LOS) of the QSO, and a major issue with producing a 3D reconstruction is determining how to model the regions between the LOS. We present a method that produces a 3D map of this relatively uncharted portion of the Universe by employing local polynomial smoothing, a non-parametric methodology. The performance of the method is analysed on simulated data that mimics the varying number of LOS expected in real data, and then is applied to a sample region selected from BOSS. Evaluation of the reconstruction is assessed by considering various features of the predicted 3D maps including visual comparison of slices, probability density functions (PDFs), counts of local minima and maxima, and standardized correlation functions. This 3D reconstruction allows for an initial investigation of the topology of this portion of the Universe using persistent homology.

Approximate Bayesian Computation (ABC) enables parameter inference for complex physical systems in cases where the true likelihood function is unknown, unavailable, or computationally too expensive. It relies on the forward simulation of mock data and comparison between observed and synthetic catalogues. Here we present cosmoabc, a Python ABC sampler featuring a Population Monte Carlo (PMC) variation of the original ABC algorithm, which uses an adaptive importance sampling scheme. The code is very flexible and can be easily coupled to an external simulator, while allowing to incorporate arbitrary distance and prior functions. As an example of practical application, we coupled cosmoabc with the numcosmo library and demonstrate how it can be used to estimate posterior probability distributions over cosmological parameters based on measurements of galaxy clusters number counts without computing the likelihood function. cosmoabc is published under the GPLv3 license on PyPI and GitHub and documentation is available at http://goo.gl/SmB8EX, Add missing variable to algorithm 1 description. To see all frames in figure 4 download the pdf and open with Adobe Reader (or equivalent) and use the controls bellow the plot

Photospheric velocities and stellar activity features such as spots and faculae produce measurable radial velocity signals that currently obscure the detection of sub-meter-per-second planetary signals. However, photospheric velocities are imprinted differently in a high-resolution spectrum than Keplerian Doppler shifts. Photospheric activity produces subtle differences in the shapes of absorption lines due to differences in how temperature or pressure affects the atomic transitions. In contrast, Keplerian Doppler shifts affect every spectral line in the same way. With high enough S/N and high enough resolution, statistical techniques can exploit differences in spectra to disentangle the photospheric velocities and detect lower-amplitude exoplanet signals. We use simulated disk-integrated time-series spectra and principal component analysis (PCA) to show that photospheric signals introduce spectral line variability that is distinct from Doppler shifts. We quantify the impact of instrumental resolution and S/N for this work., Comment: 12 pages, 7 figures, accepted to ApJ

We present a new approach for quantifying the abundance of galaxy clusters and constraining cosmological parameters using dynamical measurements. In the standard method, galaxy line-of-sight (LOS) velocities, $v$, or velocity dispersions are used to infer cluster masses, $M$, in order to quantify the halo mass function (HMF), $dn(M)/d\log(M)$, which is strongly affected by mass measurement errors. In our new method, the probability distribution of velocities for each cluster in the sample are summed to create a new statistic called the velocity distribution function (VDF), $dn(v)/dv$. The VDF can be measured more directly and precisely than the HMF and it can also be robustly predicted with cosmological simulations which capture the dynamics of subhalos or galaxies. We apply these two methods to mock cluster catalogs and forecast the bias and constraints on the matter density parameter $\Omega_m$ and the amplitude of matter fluctuations $\sigma_8$ in flat $\Lambda$CDM cosmologies. For an example observation of 200 massive clusters, the VDF with (without) velocity errors constrains the parameter combination $\sigma_8\Omega_m^{0.29\ (0.29)} = 0.587 \pm 0.011\ (0.583 \pm 0.011)$ and shows only minor bias. However, the HMF with dynamical mass errors is biased to low $\Omega_m$ and high $\sigma_8$ and the fiducial model lies well outside of the forecast constraints, prior to accounting for Eddington bias. When the VDF is combined with constraints from the cosmic microwave background (CMB), the degeneracy between cosmological parameters can be significantly reduced. Upcoming spectroscopic surveys that probe larger volumes and fainter magnitudes will provide a larger number of clusters for applying the VDF as a cosmological probe., Comment: 10 pages, 4 figures, accepted for publication at ApJ

While linear mixed modeling methods are foundational concepts introduced in any statistical education, adequate general methods for interval estimation involving models with more than a few variance components are lacking, especially in the unbalanced setting. Generalized fiducial inference provides a possible framework that accommodates this absence of methodology. Under the fabric of generalized fiducial inference along with sequential Monte Carlo methods, we present an approach for interval estimation for both balanced and unbalanced Gaussian linear mixed models. We compare the proposed method to classical and Bayesian results in the literature in a simulation study of two-fold nested models and two-factor crossed designs with an interaction term. The proposed method is found to be competitive or better when evaluated based on frequentist criteria of empirical coverage and average length of confidence intervals for small sample sizes. A MATLAB implementation of the proposed algorithm is available from the authors., Published in at http://dx.doi.org/10.1214/12-AOS1030 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org)

We characterize the eccentricity distribution of a sample of ~50 short-period planet candidates using transit and occultation measurements from NASA's Kepler Mission. First, we evaluate the sensitivity of our hierarchical Bayesian modeling and test its robustness to model misspecification using simulated data. When analyzing actual data assuming a Rayleigh distribution for eccentricity, we find that the posterior mode for the dispersion parameter is $\sigma=0.081 \pm^{0.014}_{0.003}$. We find that a two-component Gaussian mixture model for $e \cos \omega$ and $e \sin \omega$ provides a better model than either a Rayleigh or Beta distribution. Based on our favored model, we find that $\sim90\%$ of planet candidates in our sample come from a population with an eccentricity distribution characterized by a small dispersion ($\sim0.01$), and $\sim10\%$ come from a population with a larger dispersion ($\sim0.22$). Finally, we investigate how the eccentricity distribution correlates with selected planet and host star parameters. We find evidence that suggests systems around higher metallicity stars and planet candidates with smaller radii come from a more complex eccentricity distribution., Comment: Accepted for publication in ApJ

Background: It is not well understood how sedentary women who wish to engage in regular exercise adhere to interventions during pregnancy and what factors may influence adherence over time. Objective: The aim of this study was to examine longitudinal patterns of pregnant women's adherence to exercise. Methods: Exploratory secondary data analyses were carried out with 124 previously sedentary pregnant women (ages 31 ± 5 years; 85% non-Hispanic White) from a randomized controlled trial. Daily exercise logs (n = 92) from 18 through 35 weeks of gestation were explored using linear regression, functional data, and principal component analyses. Results: Adherence decreased as gestation week increased (p < .001). The top adherers maintained levels of adherence, and the bottom adherers decreased levels of adherence. And adherence pattern was influenced by types of exercise throughout the study period. Discussion: Exercise behavior patterns were explored in a randomized controlled trial study, using chronometric data on exercise attendance. A new analytic approach revealed that sedentary pregnant women may adopt exercise habits differently from other populations.

(abridged) We present the Significant Cosmic Holes in Universe (SCHU) method for identifying cosmic voids and loops of filaments in cosmological datasets and assigning their statistical significance using techniques from topological data analysis. Persistent homology is used to find different dimensional holes. For dark matter halo catalogs and galaxy surveys, the 0-, 1-, and 2-dimensional holes can be identified with clusters, loops of filaments, and voids. The procedure overlays halos/galaxies on a 3D grid, and a distance-to-measure (DTM) function is calculated at each point of the grid. A filtration is generated over the lower-level sets of the DTM across increasing threshold values. The filtered simplicial complex can be used to summarize the birth/death times of the different dimension homology group generators (i.e., the holes). Persistence diagrams are produced from the dimension and birth/death times of each homology group generator. Using the persistence diagrams and bootstrap sampling, we explain how $p$-values can be assigned to each homology group generator. The homology group generators on a persistence diagram are not, in general, uniquely located back in the original dataset volume so we propose a method for finding a representation of the homology group generators. This method provides a novel, statistically rigorous approach for locating informative generators in cosmological datasets, which may be useful for providing complementary cosmological constraints on the effects of, for example, the sum of the neutrino masses. The method is tested on a Voronoi foam simulation, and then applied to a subset of the SDSS galaxy survey and a cosmological simulation. Lastly, we calculate Betti functions for two of the MassiveNuS simulations and discuss implications for using the persistent homology of the density field to help break degeneracy in the cosmological parameters., 23 pages, 17 figures