Model Criticism in Latent Space

Model criticism is usually carried out by assessing if replicated data generated under the fitted model looks similar to the observed data, see e.g. Gelman, Carlin, Stern, and Rubin [2004, p. 165]. This paper presents a method for latent variable models by pulling back the data into the space of latent variables, and carrying out model criticism in that space. Making use of a model's structure enables a more direct assessment of the assumptions made in the prior and likelihood. We demonstrate the method with examples of model criticism in latent space applied to factor analysis, linear dynamical systems and Gaussian processes

Estimating Bacterial and Cellular Load in FCFM Imaging

We address the task of estimating bacterial and cellular load in the human distal lung with fibered confocal fluorescence microscopy (FCFM). In pulmonary FCFM some cells can display autofluorescence, and they appear as disc like objects in the FCFM images, whereas bacteria, although not autofluorescent, appear as bright blinking dots when exposed to a targeted smartprobe. Estimating bacterial and cellular load becomes a challenging task due to the presence of background from autofluorescent human lung tissues, i.e., elastin, and imaging artifacts from motion etc. We create a database of annotated images for both these tasks where bacteria and cells were annotated, and use these databases for supervised learning. We extract image patches around each pixel as features, and train a classifier to predict if a bacterium or cell is present at that pixel. We apply our approach on two datasets for detecting bacteria and cells respectively. For the bacteria dataset, we show that the estimated bacterial load increases after introducing the targeted smartprobe in the presence of bacteria. For the cell dataset, we show that the estimated cellular load agrees with a clinician’s assessment

Voltage Biasing, Cyclic Voltammetry, & Electrical Impedance Spectroscopy for Neural Interfaces

Electrical impedance spectroscopy (EIS) and cyclic voltammetry (CV) measure properties of the electrode-tissue interface without additional invasive procedures, and can be used to monitor electrode performance over the long term. EIS measures electrical impedance at multiple frequencies, and increases in impedance indicate increased glial scar formation around the device, while cyclic voltammetry measures the charge carrying capacity of the electrode, and indicates how charge is transferred at different voltage levels. As implanted electrodes age, EIS and CV data change, and electrode sites that previously recorded spiking neurons often exhibit significantly lower efficacy for neural recording. The application of a brief voltage pulse to implanted electrode arrays, known as rejuvenation, can bring back spiking activity on otherwise silent electrode sites for a period of time. Rejuvenation alters EIS and CV, and can be monitored by these complementary methods. Typically, EIS is measured daily as an indication of the tissue response at the electrode site. If spikes are absent in a channel that previously had spikes, then CV is used to determine the charge carrying capacity of the electrode site, and rejuvenation can be applied to improve the interface efficacy. CV and EIS are then repeated to check the changes at the electrode-tissue interface, and neural recordings are collected. The overall goal of rejuvenation is to extend the functional lifetime of implanted arrays

The Panchromatic Hubble Andromeda Treasury XI: The Spatially-Resolved Recent Star Formation History of M31

We measure the recent star formation history (SFH) across M31 using optical images taken with the \texit{Hubble Space Telescope} as part of the Panchromatic Hubble Andromeda Treasury (PHAT). We fit the color-magnitude diagrams in ~9000 regions that are ~100 pc $\times$ 100 pc in projected size, covering a 0.5 square degree area (~380 kpc$^2$, deprojected) in the NE quadrant of M31. We show that the SFHs vary significantly on these small spatial scales but that there are also coherent galaxy-wide fluctuations in the SFH back to ~500 Myr, most notably in M31's 10-kpc star-forming ring. We find that the 10-kpc ring is at least 400 Myr old, showing ongoing star formation over the past ~500 Myr. This indicates the presence of molecular gas in the ring over at least 2 dynamical times at this radius. We also find that the ring's position is constant throughout this time, and is stationary at the level of 1 km/s, although there is evidence for broadening of the ring due to diffusion of stars into the disk. Based on existing models of M31's ring features, the lack of evolution in the ring's position makes a purely collisional ring origin highly unlikely. We find that the global SFR has been fairly constant over the last ~500 Myr, though it does show a small increase at 50 Myr that is 1.3 times the average SFR over the past 100 Myr. During the last ~500 Myr, ~60% of all SF occurs in the 10-kpc ring. Finally, we find that in the past 100 Myr, the average SFR over the PHAT survey area is $0.28\pm0.03$ M$_\odot$ yr$^{-1}$ with an average deprojected intensity of $7.3 \times 10^{-4}$ M$_\odot$ yr$^{-1}$ kpc$^{-2}$, which yields a total SFR of ~0.7 M$_\odot$ yr$^{-1}$ when extrapolated to the entire area of M31's disk. This SFR is consistent with measurements from broadband estimates. [abridged]Comment: 23 pages, 17 figures, 2 tables, accepted for publication in Ap

The Triangulum Extended (TREX) Survey: The Stellar Disk Dynamics of M33 as a Function of Stellar Age

Triangulum, M33, is a low mass, relatively undisturbed spiral galaxy that offers a new regime in which to test models of dynamical heating. In spite of its proximity, the dynamical heating history of M33 has not yet been well constrained. In this work, we present the TREX Survey, the largest stellar spectroscopic survey across the disk of M33. We present the stellar disk kinematics as a function of age to study the past and ongoing dynamical heating of M33. We measure line of sight velocities for ~4,500 disk stars. Using a subset, we divide the stars into broad age bins using Hubble Space Telescope and Canada-France-Hawaii-Telescope photometric catalogs: massive main sequence stars and helium burning stars (~80 Myr), intermediate mass asymptotic branch stars (~1 Gyr), and low mass red giant branch stars (~4 Gyr). We compare the stellar disk dynamics to that of the gas using existing HI, CO, and Halpha kinematics. We find that the disk of M33 has relatively low velocity dispersion (~16 km/s), and unlike in the Milky Way and Andromeda galaxies, there is no strong trend in velocity dispersion as a function of stellar age. The youngest disk stars are as dynamically hot as the oldest disk stars and are dynamically hotter than predicted by most M33 like low mass simulated analogs in Illustris. The velocity dispersion of the young stars is highly structured, with the large velocity dispersion fairly localized. The cause of this high velocity dispersion is not evident from the observations and simulated analogs presented here.Comment: 27 pages, 15 figures, 6 table

Microstructure and kinematics of H2O masers in the massive star forming region IRAS 06061+2151

We have made multi-epoch VLBI observations of H2O maser emission in the massive star forming region IRAS 06061+2151 with the Japanese VLBI network (JVN) from 2005 May to 2007 October. The detected maser features are distributed within an 1\arcsec$\times$1\arcsec (2000 au$\times$2000 au at the source position) around the ultra-compact H {\small\bf II} region seen in radio continuum emission. Their bipolar morphology and expanding motion traced through their relative proper motions indicate that they are excited by an energetic bipolar outflow. Our three-dimensional model fitting has shown that the maser kinematical structure in IRAS 06061+2151 is able to be explained by a biconical outflow with a large opening angle ($>$ 50\degr). The position angle of the flow major axis coincides very well with that of the large scale jet seen in 2.1\:\mu\rmn{m} hydrogen emission. This maser geometry indicates the existence of dual structures composed of a collimated jet and a less collimated massive molecular flow. We have also detected a large velocity gradient in the southern maser group. This can be explained by a very small (on a scale of several tens of au) and clumpy (the density contrast by an order of magnitude or more) structure of the parental cloud. Such a structure may be formed by strong instability of shock front or splitting of high density core.Comment: 14 pages, 6 figures accepted for publication in MNRA

The Panchromatic Hubble Andromeda Treasury

The Panchromatic Hubble Andromeda Treasury (PHAT) is an on-going HST Multicycle Treasury program to image ~1/3 of M31's star forming disk in 6 filters, from the UV to the NIR. The full survey will resolve the galaxy into more than 100 million stars with projected radii from 0-20 kpc over a contiguous 0.5 square degree area in 828 orbits, producing imaging in the F275W and F336W filters with WFC3/UVIS, F475W and F814W with ACS/WFC, and F110W and F160W with WFC3/IR. The resulting wavelength coverage gives excellent constraints on stellar temperature, bolometric luminosity, and extinction for most spectral types. The photometry reaches SNR=4 at F275W=25.1, F336W=24.9, F475W=27.9, F814W=27.1, F110W=25.5, and F160W=24.6 for single pointings in the uncrowded outer disk; however, the optical and NIR data are crowding limited, and the deepest reliable magnitudes are up to 5 magnitudes brighter in the inner bulge. All pointings are dithered and produce Nyquist-sampled images in F475W, F814W, and F160W. We describe the observing strategy, photometry, astrometry, and data products, along with extensive tests of photometric stability, crowding errors, spatially-dependent photometric biases, and telescope pointing control. We report on initial fits to the structure of M31's disk, derived from the density of RGB stars, in a way that is independent of the assumed M/L and is robust to variations in dust extinction. These fits also show that the 10 kpc ring is not just a region of enhanced recent star formation, but is instead a dynamical structure containing a significant overdensity of stars with ages >1 Gyr. (Abridged)Comment: 48 pages including 22 pages of figures. Accepted to the Astrophysical Journal Supplements. Some figures slightly degraded to reduce submission siz

Stellar SEDs from 0.3-2.5 Microns: Tracing the Stellar Locus and Searching for Color Outliers in SDSS and 2MASS

The Sloan Digital Sky Survey (SDSS) and Two Micron All Sky Survey (2MASS) are rich resources for studying stellar astrophysics and the structure and formation history of the Galaxy. As new surveys and instruments adopt similar filter sets, it is increasingly important to understand the properties of the ugrizJHKs stellar locus, both to inform studies of `normal' main sequence stars as well as for robust searches for point sources with unusual colors. Using a sample of ~600,000 point sources detected by SDSS and 2MASS, we tabulate the position and width of the ugrizJHKs stellar locus as a function of g-i color, and provide accurate polynomial fits. We map the Morgan-Keenan spectral type sequence to the median stellar locus by using synthetic photometry of spectral standards and by analyzing 3000 SDSS stellar spectra with a custom spectral typing pipeline. We develop an algorithm to calculate a point source's minimum separation from the stellar locus in a seven-dimensional color space, and use it to robustly identify objects with unusual colors, as well as spurious SDSS/2MASS matches. Analysis of a final catalog of 2117 color outliers identifies 370 white-dwarf/M dwarf (WDMD) pairs, 93 QSOs, and 90 M giant/carbon star candidates, and demonstrates that WDMD pairs and QSOs can be distinguished on the basis of their J-Ks and r-z colors. We also identify a group of objects with correlated offsets in the u-g vs. g-r and g-r vs. r-i color-color spaces, but subsequent follow-up is required to reveal the nature of these objects. Future applications of this algorithm to a matched SDSS-UKIDSS catalog may well identify additional classes of objects with unusual colors by probing new areas of color-magnitude space.Comment: 23 pages in emulateapj format, 17 figures, 7 tables. Accepted for publication in the Astronomical Journal. To access a high-resolution version of this paper, as well as machine readable tables and an archive of 'The Hammer' spectral typing suite, see http://www.cfa.harvard.edu/~kcovey v2 -- fixed typos in Table 7 (mainly affecting lines for M8-M10 III stars