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Arfon M. Smith

Publications and source records attributed to Arfon M. Smith.

At least 19 recordsLinked to original sources
arXiv2024

Cycling on the Freeway: The Perilous State of Open Source Neuroscience Software

Most scientists need software to perform their research (Barker et al., 2020; Carver et al., 2022; Hettrick, 2014; Hettrick et al., 2014; Switters and Osimo, 2019), and neuroscientists are no exception. Whether we work with reaction times, electrophysiological signals, or magnetic resonance imaging data, we rely on software to acquire, analyze, and statistically evaluate the raw data we obtain - or to generate such data if we work with simulations. In recent years there has been a shift toward relying on free, open-source scientific software (FOSSS) for neuroscience data analysis (Poldrack et al., 2019), in line with the broader open science movement in academia (McKiernan et al., 2016) and wider industry trends (Eghbal, 2016). Importantly, FOSSS is typically developed by working scientists (not professional software developers) which sets up a precarious situation given the nature of the typical academic workplace (wherein academics, especially in their early careers, are on short and fixed term contracts). In this paper, we will argue that the existing ecosystem of neuroscientific open source software is brittle, and discuss why and how the neuroscience community needs to come together to ensure a healthy growth of our software landscape to the benefit of all.

cs.CY↗
arXiv2019

Petabytes to Science

A Kavli foundation sponsored workshop on the theme \emph{Petabytes to Science} was held 12$^{th}$ to 14$^{th}$ of February 2019 in Las Vegas. The aim of the this workshop was to discuss important trends and technologies which may support astronomy. We also tackled how to better shape the workforce for the new trends and how we should approach education and public outreach. This document was coauthored during the workshop and edited in the weeks after. It comprises the discussions and highlights many recommendations which came out of the workshop. We shall distill parts of this document and formulate potential white papers for the decadal survey.

astro-ph.IM↗
arXiv2019

Algorithms and Statistical Models for Scientific Discovery in the Petabyte Era

The field of astronomy has arrived at a turning point in terms of size and complexity of both datasets and scientific collaboration. Commensurately, algorithms and statistical models have begun to adapt --- e.g., via the onset of artificial intelligence --- which itself presents new challenges and opportunities for growth. This white paper aims to offer guidance and ideas for how we can evolve our technical and collaborative frameworks to promote efficient algorithmic development and take advantage of opportunities for scientific discovery in the petabyte era. We discuss challenges for discovery in large and complex data sets; challenges and requirements for the next stage of development of statistical methodologies and algorithmic tool sets; how we might change our paradigms of collaboration and education; and the ethical implications of scientists' contributions to widely applicable algorithms and computational modeling. We start with six distinct recommendations that are supported by the commentary following them. This white paper is related to a larger corpus of effort that has taken place within and around the Petabytes to Science Workshops (https://petabytestoscience.github.io/).

astro-ph.IM↗
arXiv2019

The demise of the filesystem and multi level service architecture

Many astronomy data centres still work on filesystems. Industry has moved on; current practice in computing infrastructure is to achieve Big Data scalability using object stores rather than POSIX file systems. This presents us with opportunities for portability and reuse of software underlying processing and archive systems but it also causes problems for legacy implementations in current data centers.

astro-ph.IM↗
arXiv2019

Astro2020 APC White Paper: Astronomy should be in the clouds

Commodity cloud computing, as provided by commercial vendors such as Amazon, Google, and Microsoft, has revolutionized computing in many sectors. With the advent of a new class of big data, public access astronomical facility such as LSST, DKIST, and WFIRST, there exists a real opportunity to combine these missions with cloud computing platforms and fundamentally change the way astronomical data is collected, processed, archived, and curated. Making these changes in a cross-mission, coordinated way can provide unprecedented economies of scale in personnel, data collection and management, archiving, algorithm and software development and, most importantly, science.

astro-ph.IM↗
arXiv2019

Astro2020 APC White Paper: Elevating the Role of Software as a Product of the Research Enterprise

Software is a critical part of modern research, and yet there are insufficient mechanisms in the scholarly ecosystem to acknowledge, cite, and measure the impact of research software. The majority of academic fields rely on a one-dimensional credit model whereby academic articles (and their associated citations) are the dominant factor in the success of a researcher's career. In the petabyte era of astronomical science, citing software and measuring its impact enables academia to retain and reward researchers that make significant software contributions. These highly skilled researchers must be retained to maximize the scientific return from petabyte-scale datasets. Evolving beyond the one-dimensional credit model requires overcoming several key challenges, including the current scholarly ecosystem and scientific culture issues. This white paper will present these challenges and suggest practical solutions for elevating the role of software as a product of the research enterprise.

astro-ph.IM↗
arXiv2018

Planet Four: Probing Springtime Winds on Mars by Mapping the Southern Polar CO$_2$ Jet Deposits

The springtime sublimation process of Mars' southern seasonal polar CO$_2$ ice cap features dark fan-shaped deposits appearing on the top of the thawing ice sheet. The fan material likely originates from the surface below the ice sheet, brought up via CO$_2$ jets breaking through the seasonal ice cap. Once the dust and dirt is released into the atmosphere, the material may be blown by the surface winds into the dark streaks visible from orbit. The location, size and direction of these fans record a number of parameters important to quantifying seasonal winds and sublimation activity, the most important agent of geological change extant on Mars. We present results of a systematic mapping of these south polar seasonal fans with the Planet Four online citizen science project. Planet Four enlists the general public to map the shapes, directions, and sizes of the seasonal fans visible in orbital images. Over 80,000 volunteers have contributed to the Planet Four project, reviewing 221 images, from Mars Reconnaissance Orbiter's HiRISE (High Resolution Imaging Science Experiment) camera, taken in southern spring during Mars Years 29 and 30. We provide an overview of Planet Four and detail the processes of combining multiple volunteer assessments together to generate a high fidelity catalog of $\sim$ 400,000 south polar seasonal fans. We present the results from analyzing the wind directions at several locations monitored by HiRISE over two Mars years, providing new insights into polar surface winds.

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arXiv2016

Galaxy Zoo: Morphological Classifications for 120,000 Galaxies in HST Legacy Imaging

We present the data release paper for the Galaxy Zoo: Hubble (GZH) project. This is the third phase in a large effort to measure reliable, detailed morphologies of galaxies by using crowdsourced visual classifications of colour composite images. Images in GZH were selected from various publicly-released Hubble Space Telescope Legacy programs conducted with the Advanced Camera for Surveys, with filters that probe the rest-frame optical emission from galaxies out to $z \sim 1$. The bulk of the sample is selected to have $m_{I814W} < 23.5$,but goes as faint as $m_{I814W} < 26.8$ for deep images combined over 5 epochs. The median redshift of the combined samples is $z = 0.9 \pm 0.6$, with a tail extending out to $z \sim 4$. The GZH morphological data include measurements of both bulge- and disk-dominated galaxies, details on spiral disk structure that relate to the Hubble type, bar identification, and numerous measurements of clump identification and geometry. This paper also describes a new method for calibrating morphologies for galaxies of different luminosities and at different redshifts by using artificially-redshifted galaxy images as a baseline. The GZH catalogue contains both raw and calibrated morphological vote fractions for 119,849 galaxies, providing the largest dataset to date suitable for large-scale studies of galaxy evolution out to $z \sim 1$.

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arXiv2016

Galaxy Zoo: Mergers - Dynamical Models of Interacting Galaxies

The dynamical history of most merging galaxies is not well understood. Correlations between galaxy interaction and star formation have been found in previous studies, but require the context of the physical history of merging systems for full insight into the processes that lead to enhanced star formation. We present the results of simulations that reconstruct the orbit trajectories and disturbed morphologies of pairs of interacting galaxies. With the use of a restricted three-body simulation code and the help of Citizen Scientists, we sample 10^5 points in parameter space for each system. We demonstrate a successful recreation of the morphologies of 62 pairs of interacting galaxies through the review of more than 3 million simulations. We examine the level of convergence and uniqueness of the dynamical properties of each system. These simulations represent the largest collection of models of interacting galaxies to date, providing a valuable resource for the investigation of mergers. This paper presents the simulation parameters generated by the project. They are now publicly available in electronic format at http://data.galaxyzoo.org/mergers.html. Though our best-fit model parameters are not an exact match to previously published models, our method for determining uncertainty measurements will aid future comparisons between models. The dynamical clocks from our models agree with previous results of the time since the onset of star formation from star burst models in interacting systems and suggests that tidally induced star formation is triggered very soon after closest approach.

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arXiv2015

Space Warps II. New Gravitational Lens Candidates from the CFHTLS Discovered through Citizen Science

We report the discovery of 29 promising (and 59 total) new lens candidates from the CFHT Legacy Survey (CFHTLS) based on about 11 million classifications performed by citizen scientists as part of the first Space Warps lens search. The goal of the blind lens search was to identify lens candidates missed by robots (the RingFinder on galaxy scales and ArcFinder on group/cluster scales) which had been previously used to mine the CFHTLS for lenses. We compare some properties of the samples detected by these algorithms to the Space Warps sample and find them to be broadly similar. The image separation distribution calculated from the Space Warps sample shows that previous constraints on the average density profile of lens galaxies are robust. SpaceWarps recovers about 65% of known lenses, while the new candidates show a richer variety compared to those found by the two robots. This detection rate could be increased to 80% by only using classifications performed by expert volunteers (albeit at the cost of a lower purity), indicating that the training and performance calibration of the citizen scientists is very important for the success of Space Warps. In this work we present the SIMCT pipeline, used for generating in situ a sample of realistic simulated lensed images. This training sample, along with the false positives identified during the search, has a legacy value for testing future lens finding algorithms. We make the pipeline and the training set publicly available.

astro-ph.CO↗
arXiv2015

Space Warps: I. Crowd-sourcing the Discovery of Gravitational Lenses

We describe Space Warps, a novel gravitational lens discovery service that yields samples of high purity and completeness through crowd-sourced visual inspection. Carefully produced colour composite images are displayed to volunteers via a web- based classification interface, which records their estimates of the positions of candidate lensed features. Images of simulated lenses, as well as real images which lack lenses, are inserted into the image stream at random intervals; this training set is used to give the volunteers instantaneous feedback on their performance, as well as to calibrate a model of the system that provides dynamical updates to the probability that a classified image contains a lens. Low probability systems are retired from the site periodically, concentrating the sample towards a set of lens candidates. Having divided 160 square degrees of Canada-France-Hawaii Telescope Legacy Survey (CFHTLS) imaging into some 430,000 overlapping 82 by 82 arcsecond tiles and displaying them on the site, we were joined by around 37,000 volunteers who contributed 11 million image classifications over the course of 8 months. This Stage 1 search reduced the sample to 3381 images containing candidates; these were then refined in Stage 2 to yield a sample that we expect to be over 90% complete and 30% pure, based on our analysis of the volunteers performance on training images. We comment on the scalability of the SpaceWarps system to the wide field survey era, based on our projection that searches of 10$^5$ images could be performed by a crowd of 10$^5$ volunteers in 6 days.

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arXiv2014

Planet Hunters VII. Discovery of a New Low-Mass, Low-Density Planet (PH3 c) Orbiting Kepler-289 with Mass Measurements of Two Additional Planets (PH3 b and d)

We report the discovery of one newly confirmed planet ($P=66.06$ days, $R_{\rm{P}}=2.68\pm0.17R_\oplus$) and mass determinations of two previously validated Kepler planets, Kepler-289 b ($P=34.55$ days, $R_{\rm{P}}=2.15\pm0.10R_\oplus$) and Kepler-289-c ($P=125.85$ days, $R_{\rm{P}}=11.59\pm0.10R_\oplus$), through their transit timing variations (TTVs). We also exclude the possibility that these three planets reside in a $1:2:4$ Laplace resonance. The outer planet has very deep ($\sim1.3%$), high signal-to-noise transits, which puts extremely tight constraints on its host star's stellar properties via Kepler's Third Law. The star PH3 is a young ($\sim1$ Gyr as determined by isochrones and gyrochronology), Sun-like star with $M_*=1.08\pm0.02M_\odot$, $R_*=1.00\pm0.02R_\odot$, and $T_{\rm{eff}}=5990\pm38$ K. The middle planet's large TTV amplitude ($\sim5$ hours) resulted either in non-detections or inaccurate detections in previous searches. A strong chopping signal, a shorter period sinusoid in the TTVs, allows us to break the mass-eccentricity degeneracy and uniquely determine the masses of the inner, middle, and outer planets to be $M=7.3\pm6.8M_\oplus$, $4.0\pm0.9M_\oplus$, and $M=132\pm17M_\oplus$, which we designate PH3 b, c, and d, respectively. Furthermore, the middle planet, PH3 c, has a relatively low density, $ρ=1.2\pm0.3$ g/cm$^3$ for a planet of its mass, requiring a substantial H/He atmosphere of $2.1^{+0.8}_{-0.3}%$ by mass, and joins a growing population of low-mass, low-density planets.

astro-ph.EP↗
arXiv2014

Implementing Transitive Credit with JSON-LD

Science and engineering research increasingly relies on activities that facilitate research but are not currently rewarded or recognized, such as: data sharing; developing common data resources, software and methodologies; and annotating data and publications. To promote and advance these activities, we must develop mechanisms for assigning credit, facilitate the appropriate attribution of research outcomes, devise incentives for activities that facilitate research, and allocate funds to maximize return on investment. In this article, we focus on addressing the issue of assigning credit for both direct and indirect contributions, specifically by using JSON-LD to implement a prototype transitive credit system.

cs.CY↗
arXiv2014

Planet Hunters. VI: An Independent Characterization of KOI-351 and Several Long Period Planet Candidates from the Kepler Archival Data

We report the discovery of 14 new transiting planet candidates in the Kepler field from the Planet Hunters citizen science program. None of these candidates overlapped with Kepler Objects of Interest (KOIs) at the time of submission. We report the discovery of one more addition to the six planet candidate system around KOI-351, making it the only seven planet candidate system from Kepler. Additionally, KOI-351 bears some resemblance to our own solar system, with the inner five planets ranging from Earth to mini-Neptune radii and the outer planets being gas giants; however, this system is very compact, with all seven planet candidates orbiting $\lesssim 1$ AU from their host star. A Hill stability test and an orbital integration of the system shows that the system is stable. Furthermore, we significantly add to the population of long period transiting planets; periods range from 124-904 days, eight of them more than one Earth year long. Seven of these 14 candidates reside in their host star's habitable zone.

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arXiv2014

Galaxy Zoo: An independent look at the evolution of the bar fraction over the last eight billion years from HST-COSMOS

We measure the redshift evolution of the bar fraction in a sample of 2380 visually selected disc galaxies found in Cosmic Evolution Survey (COSMOS) Hubble Space Telescope (HST) images. The visual classifications used to identify both the disc sample and to indicate the presence of stellar bars were provided by citizen scientists via the Galaxy Zoo: Hubble (GZH) project. We find that the overall bar fraction decreases by a factor of two, from 22+/-5% at z=0.4 (tlb = 4.2 Gyr) to 11+/-2% at z=1.0 (tlb = 7.8 Gyr), consistent with previous analysis. We show that this decrease, of the strong bar fraction in a volume limited sample of massive disc galaxies [stellar mass limit of log(Mstar/Msun) > 10.0], cannot be due to redshift dependent biases hiding either bars or disc galaxies at higher redshifts. Splitting our sample into three bins of mass we find that the decrease in bar fraction is most prominent in the highest mass bin, while the lower mass discs in our sample show a more modest evolution. We also include a sample of 98 red disc galaxies. These galaxies have a high bar fraction (45+/-5%), and are missing from other COSMOS samples which used SED fitting or colours to identify high redshift discs. Our results are consistent with a picture in which the evolution of massive disc galaxies begins to be affected by slow (secular) internal process at z~1. We discuss possible connections of the decrease in bar fraction to the redshift, including the growth of stable disc galaxies, mass evolution of the gas content in disc galaxies, as well as the mass dependent effects of tidal interactions.

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arXiv2013

Planet Hunters. V. A Confirmed Jupiter-Size Planet in the Habitable Zone and 42 Planet Candidates from the Kepler Archive Data

We report the latest Planet Hunter results, including PH2 b, a Jupiter-size (R_PL = 10.12 \pm 0.56 R_E) planet orbiting in the habitable zone of a solar-type star. PH2 b was elevated from candidate status when a series of false positive tests yielded a 99.9% confidence level that transit events detected around the star KIC 12735740 had a planetary origin. Planet Hunter volunteers have also discovered 42 new planet candidates in the Kepler public archive data, of which 33 have at least three transits recorded. Most of these transit candidates have orbital periods longer than 100 days and 20 are potentially located in the habitable zones of their host stars. Nine candidates were detected with only two transit events and the prospective periods are longer than 400 days. The photometric models suggest that these objects have radii that range between Neptune to Jupiter. These detections nearly double the number of gas giant planet candidates orbiting at habitable zone distances. We conducted spectroscopic observations for nine of the brighter targets to improve the stellar parameters and we obtained adaptive optics imaging for four of the stars to search for blended background or foreground stars that could confuse our photometric modeling. We present an iterative analysis method to derive the stellar and planet properties and uncertainties by combining the available spectroscopic parameters, stellar evolution models, and transiting light curve parameters, weighted by the measurement errors. Planet Hunters is a citizen science project that crowd-sources the assessment of NASA Kepler light curves. The discovery of these 43 planet candidates demonstrates the success of citizen scientists at identifying planet candidates, even in longer period orbits with only two or three transit events.

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arXiv2013

Galaxy Zoo 2: detailed morphological classifications for 304,122 galaxies from the Sloan Digital Sky Survey

We present the data release for Galaxy Zoo 2 (GZ2), a citizen science project with more than 16 million morphological classifications of 304,122 galaxies drawn from the Sloan Digital Sky Survey. Morphology is a powerful probe for quantifying a galaxy's dynamical history; however, automatic classifications of morphology (either by computer analysis of images or by using other physical parameters as proxies) still have drawbacks when compared to visual inspection. The large number of images available in current surveys makes visual inspection of each galaxy impractical for individual astronomers. GZ2 uses classifications from volunteer citizen scientists to measure morphologies for all galaxies in the DR7 Legacy survey with m_r>17, in addition to deeper images from SDSS Stripe 82. While the original Galaxy Zoo project identified galaxies as early-types, late-types, or mergers, GZ2 measures finer morphological features. These include bars, bulges, and the shapes of edge-on disks, as well as quantifying the relative strengths of galactic bulges and spiral arms. This paper presents the full public data release for the project, including measures of accuracy and bias. The majority (>90%) of GZ2 classifications agree with those made by professional astronomers, especially for morphological T-types, strong bars, and arm curvature. Both the raw and reduced data products can be obtained in electronic format at http://data.galaxyzoo.org .

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