29 research outputs found
TensorFlow Enabled Genetic Programming
Genetic Programming, a kind of evolutionary computation and machine learning
algorithm, is shown to benefit significantly from the application of vectorized
data and the TensorFlow numerical computation library on both CPU and GPU
architectures. The open source, Python Karoo GP is employed for a series of 190
tests across 6 platforms, with real-world datasets ranging from 18 to 5.5M data
points. This body of tests demonstrates that datasets measured in tens and
hundreds of data points see 2-15x improvement when moving from the scalar/SymPy
configuration to the vector/TensorFlow configuration, with a single core
performing on par or better than multiple CPU cores and GPUs. A dataset
composed of 90,000 data points demonstrates a single vector/TensorFlow CPU core
performing 875x better than 40 scalar/Sympy CPU cores. And a dataset containing
5.5M data points sees GPU configurations out-performing CPU configurations on
average by 1.3x.Comment: 8 pages, 5 figures; presented at GECCO 2017, Berlin, German
Phenotyping of Drosophila Melanogaster-A Nutritional Perspective
The model organism Drosophila melanogaster was increasingly applied in nutrition research in recent years. A range of methods are available for the phenotyping of D. melanogaster, which are outlined in the first part of this review. The methods include determinations of body weight, body composition, food intake, lifespan, locomotor activity, reproductive capacity and stress tolerance. In the second part, the practical application of the phenotyping of flies is demonstrated via a discussion of obese phenotypes in response to high-sugar diet (HSD) and high-fat diet (HFD) feeding. HSD feeding and HFD feeding are dietary interventions that lead to an increase in fat storage and affect carbohydrate-insulin homeostasis, lifespan, locomotor activity, reproductive capacity and stress tolerance. Furthermore, studies regarding the impacts of HSD and HFD on the transcriptome and metabolome of D. melanogaster are important for relating phenotypic changes to underlying molecular mechanisms. Overall, D. melanogaster was demonstrated to be a valuable model organism with which to examine the pathogeneses and underlying molecular mechanisms of common chronic metabolic diseases in a nutritional context
The ABC130 barrel module prototyping programme for the ATLAS strip tracker
For the Phase-II Upgrade of the ATLAS Detector, its Inner Detector,
consisting of silicon pixel, silicon strip and transition radiation
sub-detectors, will be replaced with an all new 100 % silicon tracker, composed
of a pixel tracker at inner radii and a strip tracker at outer radii. The
future ATLAS strip tracker will include 11,000 silicon sensor modules in the
central region (barrel) and 7,000 modules in the forward region (end-caps),
which are foreseen to be constructed over a period of 3.5 years. The
construction of each module consists of a series of assembly and quality
control steps, which were engineered to be identical for all production sites.
In order to develop the tooling and procedures for assembly and testing of
these modules, two series of major prototyping programs were conducted: an
early program using readout chips designed using a 250 nm fabrication process
(ABCN-25) and a subsequent program using a follow-up chip set made using 130 nm
processing (ABC130 and HCC130 chips). This second generation of readout chips
was used for an extensive prototyping program that produced around 100
barrel-type modules and contributed significantly to the development of the
final module layout. This paper gives an overview of the components used in
ABC130 barrel modules, their assembly procedure and findings resulting from
their tests.Comment: 82 pages, 66 figure
GROWTH on GW190425: Searching thousands of square degrees to identify an optical or infrared counterpart to a binary neutron star merger with the Zwicky Transient Facility and Palomar Gattini IR
The beginning of the third observing run by the network of gravitational-wave
detectors has brought the discovery of many compact binary coalescences.
Prompted by the detection of the first binary neutron star merger in this run
(GW190425 / LIGO/Virgo S190425z), we performed a dedicated follow-up campaign
with the Zwicky Transient Facility (ZTF) and Palomar Gattini-IR telescopes. As
it was a single gravitational-wave detector discovery, the initial skymap
spanned most of the sky observable from Palomar Observatory, the site of both
instruments. Covering 8000 deg of the inner 99\% of the initial skymap over
the next two nights, corresponding to an integrated probability of 46\%, the
ZTF system achieved a depth of \,21 in - and
-bands. Palomar Gattini-IR covered a total of 2200 square degrees in
-band to a depth of 15.5\,mag, including 32\% of the integrated probability
based on the initial sky map. However, the revised skymap issued the following
day reduced these numbers to 21\% for the Zwicky Transient Facility and 19\%
for Palomar Gattini-IR. Out of the 338,646 ZTF transient "alerts" over the
first two nights of observations, we narrowed this list to 15 candidate
counterparts. Two candidates, ZTF19aarykkb and ZTF19aarzaod were particularly
compelling given that their location, distance, and age were consistent with
the gravitational-wave event, and their early optical lightcurves were
photometrically consistent with that of kilonovae. These two candidates were
spectroscopically classified as young core-collapse supernovae. The remaining
candidates were photometrically or spectroscopically ruled-out as supernovae.
Palomar Gattini-IR identified one fast evolving infrared transient after the
merger, PGIR19bn, which was later spectroscopically classified as an M-dwarf
flare. [abridged
GROWTH on S190425z: Searching Thousands of Square Degrees to Identify an Optical or Infrared Counterpart to a Binary Neutron Star Merger with the Zwicky Transient Facility and Palomar Gattini-IR
The third observing run by LVC has brought the discovery of many compact binary coalescences. Following the detection of the first binary neutron star merger in this run (LIGO/Virgo S190425z), we performed a dedicated follow-up campaign with the Zwicky Transient Facility (ZTF) and Palomar Gattini-IR telescopes. The initial skymap of this single-detector gravitational wave (GW) trigger spanned most of the sky observable from Palomar Observatory. Covering 8000 deg2 of the initial skymap over the next two nights, corresponding to 46% integrated probability, ZTF system achieved a depth of ≈21 m AB in g- and r-bands. Palomar Gattini-IR covered 2200 square degrees in J-band to a depth of 15.5 mag, including 32% integrated probability based on the initial skymap. The revised skymap issued the following day reduced these numbers to 21% for the ZTF and 19% for Palomar Gattini-IR. We narrowed 338,646 ZTF transient "alerts" over the first two nights of observations to 15 candidate counterparts. Two candidates, ZTF19aarykkb and ZTF19aarzaod, were particularly compelling given that their location, distance, and age were consistent with the GW event, and their early optical light curves were photometrically consistent with that of kilonovae. These two candidates were spectroscopically classified as young core-collapse supernovae. The remaining candidates were ruled out as supernovae. Palomar Gattini-IR did not identify any viable candidates with multiple detections only after merger time. We demonstrate that even with single-detector GW events localized to thousands of square degrees, systematic kilonova discovery is feasible
Genetic programming applied to RFI mitigation in radio astronomy
Genetic Programming is a type of machine learning that employs a stochastic search of a solutions space, genetic operators, a fitness function, and multiple generations of evolved programs to resolve a user-defined task, such as the classification of data. At the time of this research, the application of machine learning to radio astronomy was relatively new, with a limited number of publications on the subject. Genetic Programming had never been applied, and as such, was a novel approach to this challenging arena. Foundational to this body of research, the application Karoo GP was developed in the programming language Python following the fundamentals of tree-based Genetic Programming described in "A Field Guide to Genetic Programming" by Poli, et al. Karoo GP was tasked with the classification of data points as signal or radio frequency interference (RFI) generated by instruments and machinery which makes challenging astronomers' ability to discern the desired targets. The training data was derived from the output of an observation run of the KAT-7 radio telescope array built by the South African Square Kilometre Array (SKA-SA). Karoo GP, kNN, and SVM were comparatively employed, the outcome of which provided noteworthy correlations between input parameters, the complexity of the evolved hypotheses, and performance of raw data versus engineered features. This dissertation includes description of novel approaches to GP, such as upper and lower limits to the size of syntax trees, an auto-scaling multiclass classifier, and a Numpy array element manager. In addition to the research conducted at the SKA-SA, it is described how Karoo GP was applied to fine-tuning parameters of a weather prediction model at the South African Astronomical Observatory (SAAO), to glitch classification at the Laser Interferometer Gravitational-wave Observatory (LIGO), and to astro-particle physics at The Ohio State University