152 research outputs found
Fast and scalable Gaussian process modeling with applications to astronomical time series
The growing field of large-scale time domain astronomy requires methods for
probabilistic data analysis that are computationally tractable, even with large
datasets. Gaussian Processes are a popular class of models used for this
purpose but, since the computational cost scales, in general, as the cube of
the number of data points, their application has been limited to small
datasets. In this paper, we present a novel method for Gaussian Process
modeling in one-dimension where the computational requirements scale linearly
with the size of the dataset. We demonstrate the method by applying it to
simulated and real astronomical time series datasets. These demonstrations are
examples of probabilistic inference of stellar rotation periods, asteroseismic
oscillation spectra, and transiting planet parameters. The method exploits
structure in the problem when the covariance function is expressed as a mixture
of complex exponentials, without requiring evenly spaced observations or
uniform noise. This form of covariance arises naturally when the process is a
mixture of stochastically-driven damped harmonic oscillators -- providing a
physical motivation for and interpretation of this choice -- but we also
demonstrate that it can be a useful effective model in some other cases. We
present a mathematical description of the method and compare it to existing
scalable Gaussian Process methods. The method is fast and interpretable, with a
range of potential applications within astronomical data analysis and beyond.
We provide well-tested and documented open-source implementations of this
method in C++, Python, and Julia.Comment: Updated in response to referee. Submitted to the AAS Journals.
Comments (still) welcome. Code available: https://github.com/dfm/celerit
Inferring probabilistic stellar rotation periods using Gaussian processes
Variability in the light curves of spotted, rotating stars is often
non-sinusoidal and quasi-periodic --- spots move on the stellar surface and
have finite lifetimes, causing stellar flux variations to slowly shift in
phase. A strictly periodic sinusoid therefore cannot accurately model a
rotationally modulated stellar light curve. Physical models of stellar surfaces
have many drawbacks preventing effective inference, such as highly degenerate
or high-dimensional parameter spaces. In this work, we test an appropriate
effective model: a Gaussian Process with a quasi-periodic covariance kernel
function. This highly flexible model allows sampling of the posterior
probability density function of the periodic parameter, marginalising over the
other kernel hyperparameters using a Markov Chain Monte Carlo approach. To test
the effectiveness of this method, we infer rotation periods from 333 simulated
stellar light curves, demonstrating that the Gaussian process method produces
periods that are more accurate than both a sine-fitting periodogram and an
autocorrelation function method. We also demonstrate that it works well on real
data, by inferring rotation periods for 275 Kepler stars with previously
measured periods. We provide a table of rotation periods for these 1132 Kepler
objects of interest and their posterior probability density function samples.
Because this method delivers posterior probability density functions, it will
enable hierarchical studies involving stellar rotation, particularly those
involving population modelling, such as inferring stellar ages, obliquities in
exoplanet systems, or characterising star-planet interactions. The code used to
implement this method is available online.Comment: Submitted to MNRAS. Replaced 27/06/2017: corrections made to
koi_periods.cs
Reprogramming cellular fate using defined factors
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2009.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections."March 2009."Includes bibliographical references.Embryonic stem (ES) cells have a vast therapeutic potential given their pluripotency, or the ability to differentiate into tissues from all three germ layers. One of the ultimate goals of regenerative medicine is to isolate pluripotent stem cells from patients. Nuclear reprogramming offers the possibility of creating patient-specific cell lines, thus abrogating the need for immunosuppressants following cell transplantation therapy. It was recently reported that the forced expression of four transcription factors, Oct4, Sox2, c-Myc and Klf4 can induce a pluripotent state in somatic cells, without the need for embryo destruction. The work presented here aims to characterize reprogramming using defined factors and provide insight into the mechanisms governing this process. It also seeks to identify transient cues to induce reprogramming in somatic cells, alleviating the need for virally transduced transcription factors that hinder its eventual clinical use.by Ruth K. Foreman.Ph.D
An Evaluation of the Developmental Reading Program at South Dakota State College
In the past twenty years, much interest has been shown in the student who is handicapped in learning because of reading problems, whether of speed or comprehension or both. Attempts are being made in many colleges throughout the nation to set up reading laboratories for remedial training of these students. Since most educators assume a close correlation between reading comprehension and success in college, there is hope that by improvement of reading, more students may be able to continue and complete their college careers. The primary objective of the study is to evaluate the help given by the developmental reading course to students low in reading comprehension. The problem of evaluating a reading program is a complex one. In the first place, the program deals with two groups of students – those required to take the course and those elect the course. In the second place, the benefits derived from a developmental reading course are difficult to measure. In the third place, many variables which concern the success or lack of success of a college student cannot be controlled, such as motivation, emotional disturbances, economic and financial problem, difficulty of other course work, and health problems. A basic procedure was set up to involve a four-step investigation, each step revealing information about the Developmental Reading Program and lending its information to the next step until the fourth, final, and conclusive step. The results were then studied and final observations and conclusions made about the value of the developmental reading program to students at South Dakota State College, and also what expansions or revisions could be employed to make the course more meaningful and more valuable
In this Day and Age: An Empirical Gyrochronology Relation for Partially and Fully Convective Single Field Stars
Gyrochronology, the field of age-dating stars using mainly their rotation
periods and masses, is ideal for inferring the ages of individual main-sequence
stars. However, due to the lack of physical understanding of the complex
magnetic fields in stars, gyrochronology relies heavily on empirical
calibrations that require consistent and reliable stellar age measurements
across a wide range of periods and masses. In this paper, we obtain a sample of
consistent ages using the gyro-kinematic age-dating method, a technique to
calculate the kinematics ages of stars. Using a Gaussian Process model
conditioned on ages from this sample (~ 1 - 14 Gyr) and known clusters (0.67 -
3.8 Gyr), we calibrate the first empirical gyrochronology relation that is
capable of inferring ages for single, main-sequence stars between 0.67 Gyr to
14 Gyr. Cross-validating and testing results suggest our model can infer
cluster and asteroseismic ages with an average uncertainty of just over 1 Gyr.
With this model, we obtain gyrochronology ages for ~ 100,000 stars within 1.5
kpc of the Sun with period measurements from Kepler and ZTF, and 384 unique
planet host stars.Comment: Submitted to AJ. Missing citations welcom
Detecting Solar System Analogs through Joint Radial Velocity/Astrometric Surveys
Earth-mass exoplanets on year-long orbits and cool gas giants (CGG) on
decade-long orbits lie at the edge of current detection limits. The Terra
Hunting Experiment (THE) will take nightly radial velocity (RV) observations on
HARPS3 of at least 40 bright nearby G and K dwarfs for 10 years, with a target
1 measurement error of 0.3 m/s, in search of exoplanets that are
Earth-like in mass and temperature. However, RV observations can only provide
minimum mass estimates, due to the mass-inclination degeneracy. Astrometric
observations of these same stars, with sufficient precision, could break this
degeneracy. Gaia will soon release 100-200 astrometric observations of
the THE stars with a 10 year baseline and 34.2 as 1
along-scan measurement error. The Nancy Grace Roman Space Telescope will be
capable of precision astrometry using its wide field imager (target 5-20
as 1 measurement error for bright stars) and could extend the
astrometric observational baseline to 25 years. We simulate and model an
observing program that combines data from these three telescopes. We find that
(1) THE RVs and Gaia astrometry can detect Earth-like and CGG-like exoplanets
around bright Sun-like stars at 10 parsecs and that (2) adding Roman astrometry
improves the detection precision for CGG masses and periods by a factor up to
10 and 4, respectively. Such a survey could provide insight into
the prevalence of Solar System analogs, exoplanet architectures reminiscent of
the mass and orbital separation hierarchy of our Solar System, for the nearest
Sun-like stars.Comment: 21 pages, 10 figures. Revised based on comments from anonymous
reviewer at AAS Journals. Code available at
https://github.com/dyahalomi/rv_and_astrometr
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Small lymphocytic lymphoma presenting as chronic diffuse lip swelling
Although rare, small lymphocytic lymphoma can present as chronic lip swelling and papules, thus mimicking the features of orofacial granulomatosis, a chronic inflammatory disorder characterized by subepithelial noncaseating granulomas, or papular mucinosis, characterized by localized dermal mucin deposition of mucin. When assessing lip swelling, one must carefully consider the clinical clues and have a low threshold to perform a diagnostic tissue biopsy, preventing delays in treatment or progression of the lymphoma
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