arXiv subjects

Hugh Dickinson

Publications and source records attributed to Hugh Dickinson.

At least 37 records · Page 2Linked to original sources

arXiv2023

Rapid prediction of lab-grown tissue properties using deep learning

The interactions between cells and the extracellular matrix are vital for the self-organisation of tissues. In this paper we present proof-of-concept to use machine learning tools to predict the role of this mechanobiology in the self-organisation of cell-laden hydrogels grown in tethered moulds. We develop a process for the automated generation of mould designs with and without key symmetries. We create a large training set with $N=6500$ cases by running detailed biophysical simulations of cell-matrix interactions using the contractile network dipole orientation (CONDOR) model for the self-organisation of cellular hydrogels within these moulds. These are used to train an implementation of the \texttt{pix2pix} deep learning model, reserving $740$ cases that were unseen in the training of the neural network for training and validation. Comparison between the predictions of the machine learning technique and the reserved predictions from the biophysical algorithm show that the machine learning algorithm makes excellent predictions. The machine learning algorithm is significantly faster than the biophysical method, opening the possibility of very high throughput rational design of moulds for pharmaceutical testing, regenerative medicine and fundamental studies of biology. Future extensions for scaffolds and 3D bioprinting will open additional applications.

q-bio.TO↗

arXiv2022

Galaxy Zoo: Clump Scout -- Design and first application of a two-dimensional aggregation tool for citizen science

Galaxy Zoo: Clump Scout is a web-based citizen science project designed to identify and spatially locate giant star forming clumps in galaxies that were imaged by the Sloan Digital Sky Survey Legacy Survey. We present a statistically driven software framework that is designed to aggregate two-dimensional annotations of clump locations provided by multiple independent Galaxy Zoo: Clump Scout volunteers and generate a consensus label that identifies the locations of probable clumps within each galaxy. The statistical model our framework is based on allows us to assign false-positive probabilities to each of the clumps we identify, to estimate the skill levels of each of the volunteers who contribute to Galaxy Zoo: Clump Scout and also to quantitatively assess the reliability of the consensus labels that are derived for each subject. We apply our framework to a dataset containing 3,561,454 two-dimensional points, which constitute 1,739,259 annotations of 85,286 distinct subjects provided by 20,999 volunteers. Using this dataset, we identify 128,100 potential clumps distributed among 44,126 galaxies. This dataset can be used to study the prevalence and demographics of giant star forming clumps in low-redshift galaxies. The code for our aggregation software framework is publicly available at: https://github.com/ou-astrophysics/BoxAggregator

astro-ph.GA↗

arXiv2022

Practical Galaxy Morphology Tools from Deep Supervised Representation Learning

Astronomers have typically set out to solve supervised machine learning problems by creating their own representations from scratch. We show that deep learning models trained to answer every Galaxy Zoo DECaLS question learn meaningful semantic representations of galaxies that are useful for new tasks on which the models were never trained. We exploit these representations to outperform several recent approaches at practical tasks crucial for investigating large galaxy samples. The first task is identifying galaxies of similar morphology to a query galaxy. Given a single galaxy assigned a free text tag by humans (e.g. "#diffuse"), we can find galaxies matching that tag for most tags. The second task is identifying the most interesting anomalies to a particular researcher. Our approach is 100% accurate at identifying the most interesting 100 anomalies (as judged by Galaxy Zoo 2 volunteers). The third task is adapting a model to solve a new task using only a small number of newly-labelled galaxies. Models fine-tuned from our representation are better able to identify ring galaxies than models fine-tuned from terrestrial images (ImageNet) or trained from scratch. We solve each task with very few new labels; either one (for the similarity search) or several hundred (for anomaly detection or fine-tuning). This challenges the longstanding view that deep supervised methods require new large labelled datasets for practical use in astronomy. To help the community benefit from our pretrained models, we release our fine-tuning code Zoobot. Zoobot is accessible to researchers with no prior experience in deep learning.

astro-ph.GA↗

arXiv2022

Detecting gravitational lenses using machine learning: exploring interpretability and sensitivity to rare lensing configurations

Forthcoming large imaging surveys such as Euclid and the Vera Rubin Observatory Legacy Survey of Space and Time are expected to find more than $10^5$ strong gravitational lens systems, including many rare and exotic populations such as compound lenses, but these $10^5$ systems will be interspersed among much larger catalogues of $\sim10^9$ galaxies. This volume of data is too much for visual inspection by volunteers alone to be feasible and gravitational lenses will only appear in a small fraction of these data which could cause a large amount of false positives. Machine learning is the obvious alternative but the algorithms' internal workings are not obviously interpretable, so their selection functions are opaque and it is not clear whether they would select against important rare populations. We design, build, and train several Convolutional Neural Networks (CNNs) to identify strong gravitational lenses using VIS, Y, J, and H bands of simulated data, with F1 scores between 0.83 and 0.91 on 100,000 test set images. We demonstrate for the first time that such CNNs do not select against compound lenses, obtaining recall scores as high as 76\% for compound arcs and 52\% for double rings. We verify this performance using Hubble Space Telescope (HST) and Hyper Suprime-Cam (HSC) data of all known compound lens systems. Finally, we explore for the first time the interpretability of these CNNs using Deep Dream, Guided Grad-CAM, and by exploring the kernels of the convolutional layers, to illuminate why CNNs succeed in compound lens selection.

astro-ph.GA↗

arXiv2022

Galaxy Zoo: Clump Scout: Surveying the Local Universe for Giant Star-forming Clumps

Massive, star-forming clumps are a common feature of high-redshift star-forming galaxies. How they formed, and why they are so rare at low redshift, remains unclear. In this paper we identify the largest yet sample of clumpy galaxies (7,052) at low redshift using data from the citizen science project \textit{Galaxy Zoo: Clump Scout}, in which volunteers classified over 58,000 Sloan Digital Sky Survey (SDSS) galaxies spanning redshift $0.02 < z < 0.15$. We apply a robust completeness correction by comparing with simulated clumps identified by the same method. Requiring that the ratio of clump-to-galaxy flux in the SDSS $u$ band be greater than 8\% (similar to clump definitions used by other works), we estimate the fraction of local galaxies hosting at least one clump ($f_{clumpy}$) to be $2.68_{-0.30}^{+0.33}\%$. We also compute the same fraction with a less stringent cut of 3\% ($11.33_{-1.16}^{+0.89}\%$), as the higher number count and lower statistical noise of this fraction permits sharper comparison with future low-redshift clumpy galaxy studies. Our results reveal a sharp decline in $f_{clumpy}$ over $0 < z < 0.5$. The minor merger rate remains roughly constant over the same span, so we suggest that minor mergers are unlikely to be the primary driver of clump formation. Instead, the rate of galaxy turbulence is a better tracer for $f_{clumpy}$ over $0 < z < 1.5$ for galaxies of all masses, which supports the idea that clump formation is primarily driven by violent disk instability for all galaxy populations during this period.

astro-ph.GA↗

arXiv2021

Super-resolving Herschel imaging: a proof of concept using Deep Neural Networks

Wide-field sub-millimetre surveys have driven many major advances in galaxy evolution in the past decade, but without extensive follow-up observations the coarse angular resolution of these surveys limits the science exploitation. This has driven the development of various analytical deconvolution methods. In the last half a decade Generative Adversarial Networks have been used to attempt deconvolutions on optical data. Here we present an autoencoder with a novel loss function to overcome this problem in the sub-millimeter wavelength range. This approach is successfully demonstrated on Herschel SPIRE 500$μ$m COSMOS data, with the super-resolving target being the JCMT SCUBA-2 450$μ$m observations of the same field. We reproduce the JCMT SCUBA-2 images with high fidelity using this autoencoder. This is quantified through the point source fluxes and positions, the completeness and the purity.

astro-ph.GA↗

arXiv2021

Identifying muon rings in VERITAS data using convolutional neural networks trained on images classified with Muon Hunters 2

Muons from extensive air showers appear as rings in images taken with imaging atmospheric Cherenkov telescopes, such as VERITAS. These muon-ring images are used for the calibration of the VERITAS telescopes, however the calibration accuracy can be improved with a more efficient muon-identification algorithm. Convolutional neural networks (CNNs) are used in many state-of-the-art image-recognition systems and are ideal for muon image identification, once trained on a suitable dataset with labels for muon images. However, by training a CNN on a dataset labelled by existing algorithms, the performance of the CNN would be limited by the suboptimal muon-identification efficiency of the original algorithms. Muon Hunters 2 is a citizen science project that asks users to label grids of VERITAS telescope images, stating which images contain muon rings. Each image is labelled 10 times by independent volunteers, and the votes are aggregated and used to assign a `muon' or `non-muon' label to the corresponding image. An analysis was performed using an expert-labelled dataset in order to determine the optimal vote percentage cut-offs for assigning labels to each image for CNN training. This was optimised so as to identify as many muon images as possible while avoiding false positives. The performance of this model greatly improves on existing muon identification algorithms, identifying approximately 30 times the number of muon images identified by the current algorithm implemented in VEGAS (VERITAS Gamma-ray Analysis Suite), and roughly 2.5 times the number identified by the Hough transform method, along with significantly outperforming a CNN trained on VEGAS-labelled data.

astro-ph.IM↗

arXiv2021

Predicting the self-lensing population in optical surveys

The vast majority of binaries containing a compact object and a regular star spend most of their time in a quiescent state where no strong interactions occur between components. Detection of these binaries is extremely challenging and only few candidates have been detected through optical spectroscopy. Self-lensing represents a new means of detecting compact objects in binaries, where gravitational lensing of the light from the visible component by the compact object produces periodic optical flares. Here we show that current and planned large-area optical surveys can detect a significant number ($\sim 100$-$10,000$s) of these self-lensing binaries and provide insights into the properties of the compact lenses. We show that many of the predicted population of observable self-lensing binaries will be observed with multiple self-lensing flares; this both improves the chances of detection and also immediately distinguishes them from chance-alignment micro-lensing events. Through self-lensing we can investigate long - but previously hidden - stages of binary evolution and consequently provide new constraints on evolutionary models which impact on the number and nature of double compact object mergers.

astro-ph.HE↗

arXiv2021

Investigating Clumpy Galaxies in the Sloan Digital Sky Survey Stripe 82 using the Galaxy Zoo

Giant, star-forming clumps are a common feature prevalent amongst high-redshift star-forming galaxies and play a critical role in shaping their chaotic morphologies and yet, their nature and role in galaxy evolution remains to be fully understood. A majority of the effort to study clumps has been focused at high redshifts, and local clump studies have often suffered from small sample sizes. In this work, we present an analysis of clump properties in the local universe, and for the first time, performed with a statistically significant sample. With the help of the citizen science-powered Galaxy Zoo: Hubble project, we select a sample of 92 $z<0.06$ clumpy galaxies in Sloan Digital Sky Survey Stripe 82 galaxies. Within this sample, we identify 543 clumps using a contrast-based image analysis algorithm and perform photometry as well as estimate their stellar population properties. The overall properties of our $z<0.06$ clump sample are comparable to the high-redshift clumps. However, contrary to the high-redshift studies, we find no evidence of a gradient in clump ages or masses as a function of their galactocentric distances. Our results challenge the inward migration scenario for clump evolution for the local universe, potentially suggesting a larger contribution of ex-situ clumps and/or longer clump migration timescales.

astro-ph.GA↗

arXiv2020

An old stellar population or diffuse nebular continuum emission discovered in green pea galaxies

We use new HST images of nine Green Pea Galaxies (GPGs) to study their resolved structure and color. The choice of filters, F555W and F850LP, together with the redshift of the galaxies ($z\sim 0.25$), minimizes the contribution of the nebular [O\thinspace{\sc iii}] and H$α$ emission lines to the broad-band images. While these galaxies are typically very blue in color, our analysis reveals that it is only the dominant stellar clusters that are blue. Each GPG does clearly show the presence of at least one bright and compact star-forming region, but these are invariably superimposed on a more extended and lower surface brightness emission. Moreover, the colors of the star forming regions are on average bluer than those of the diffuse emission, reaching up to 0.6 magnitudes bluer. Assuming that the diffuse and compact components have constant and single burst Star Formation Histories, respectively, the observed colors imply that the diffuse components (possibly the host galaxy of the star-formation episode) have, on average, old stellar ages ($>1$Gyr), while the star-clusters are younger than 500Myrs. We also discuss the possibility that the diffuse red emission is due to a varying relative contribution of nebular continuum, rather than a different stellar population. With the available data, however, it is not possible to distinguish between these two interpretations. A substantial presence of old stars would indicate that the mechanisms that allow large escape fractions in these local galaxies may be different from those at play during the reionization epoch.

astro-ph.GA↗

arXiv2019

Galaxy Zoo: Probabilistic Morphology through Bayesian CNNs and Active Learning

We use Bayesian convolutional neural networks and a novel generative model of Galaxy Zoo volunteer responses to infer posteriors for the visual morphology of galaxies. Bayesian CNN can learn from galaxy images with uncertain labels and then, for previously unlabelled galaxies, predict the probability of each possible label. Our posteriors are well-calibrated (e.g. for predicting bars, we achieve coverage errors of 11.8% within a vote fraction deviation of 0.2) and hence are reliable for practical use. Further, using our posteriors, we apply the active learning strategy BALD to request volunteer responses for the subset of galaxies which, if labelled, would be most informative for training our network. We show that training our Bayesian CNNs using active learning requires up to 35-60% fewer labelled galaxies, depending on the morphological feature being classified. By combining human and machine intelligence, Galaxy Zoo will be able to classify surveys of any conceivable scale on a timescale of weeks, providing massive and detailed morphology catalogues to support research into galaxy evolution.

astro-ph.GA↗

arXiv2019

Modeling with the Crowd: Optimizing the Human-Machine Partnership with Zooniverse

LSST and Euclid must address the daunting challenge of analyzing the unprecedented volumes of imaging and spectroscopic data that these next-generation instruments will generate. A promising approach to overcoming this challenge involves rapid, automatic image processing using appropriately trained Deep Learning (DL) algorithms. However, reliable application of DL requires large, accurately labeled samples of training data. Galaxy Zoo Express (GZX) is a recent experiment that simulated using Bayesian inference to dynamically aggregate binary responses provided by citizen scientists via the Zooniverse crowd-sourcing platform in real time. The GZX approach enables collaboration between human and machine classifiers and provides rapidly generated, reliably labeled datasets, thereby enabling online training of accurate machine classifiers. We present selected results from GZX and show how the Bayesian aggregation engine it uses can be extended to efficiently provide object-localization and bounding-box annotations of two-dimensional data with quantified reliability. DL algorithms that are trained using these annotations will facilitate numerous panchromatic data modeling tasks including morphological classification and substructure detection in direct imaging, as well as decontamination and emission line identification for slitless spectroscopy. Effectively combining the speed of modern computational analyses with the human capacity to extrapolate from few examples will be critical if the potential of forthcoming large-scale surveys is to be realized.

astro-ph.IM↗

arXiv2018

Galaxy Nurseries: Crowdsourced analysis of slitless spectroscopic data

We present the results of Galaxy Nurseries project, which was designed to enable crowdsourced analysis of slitless spectroscopic data by volunteer citizen scientists using the Zooniverse online interface. The dataset was obtained by the WFC3 Infrared Spectroscopic Parallel (WISP) Survey collaboration and comprises NIR grism (G102 and G141) and direct imaging. Volunteers were instructed to evaluate indicated spectral features and decide whether it was a genuine emission line or more likely an artifact. Galaxy Nurseries was completed in only 40 days, gathering 414,360 classifications from 3003 volunteers for 27,333 putative emission lines. The results of Galaxy Nurseries demonstrate the feasibility of identifying genuine emission lines in slitless spectra by citizen scientists. Volunteer responses for each subject were aggregated to compute $f_{\mathrm{Real}}$, the fraction of volunteers who classified the corresponding emission line as "Real". To evaluate the accuracy of volunteer classifications, their aggregated responses were compared with independent assessments provided by members of the WISP Survey Science Team (WSST). Overall, there is a broad agreement between the WSST and volunteers' classifications, although we recognize that robust scientific analyses typically require samples with higher purity and completeness than raw volunteer classifications provide. Nonetheless, choosing optimal threshold values for $f_{\mathrm{Real}}$ allows a large fraction of spurious lines to be vetoed, substantially reducing the timescale for subsequent professional analysis of the remaining potential lines.

astro-ph.GA↗

arXiv2018

Integrating human and machine intelligence in galaxy morphology classification tasks

Quantifying galaxy morphology is a challenging yet scientifically rewarding task. As the scale of data continues to increase with upcoming surveys, traditional classification methods will struggle to handle the load. We present a solution through an integration of visual and automated classifications, preserving the best features of both human and machine. We demonstrate the effectiveness of such a system through a re-analysis of visual galaxy morphology classifications collected during the Galaxy Zoo 2 (GZ2) project. We reprocess the top level question of the GZ2 decision tree with a Bayesian classification aggregation algorithm dubbed SWAP, originally developed for the Space Warps gravitational lens project. Through a simple binary classification scheme we increase the classification rate nearly 5-fold, classifying 226,124 galaxies in 92 days of GZ2 project time while reproducing labels derived from GZ2 classification data with 95.7% accuracy. We next combine this with a Random Forest machine learning algorithm that learns on a suite of nonparametric morphology indicators widely used for automated morphologies. We develop a decision engine that delegates tasks between human and machine, and demonstrate that the combined system provides at least a factor of 8 increase in the classification rate, classifying 210,803 galaxies in just 32 days of GZ2 project time with 93.1% accuracy. As the Random Forest algorithm requires a minimal amount of computation cost, this result has important implications for galaxy morphology identification tasks in the era of Euclid and other large scale surveys.

astro-ph.IM↗

arXiv2018

An image-based array trigger for Imaging Atmospheric Cherenkov Telescope Arrays

It is anticipated that forthcoming, next generation, atmospheric Cherenkov telescope arrays will include a number of medium-sized telescopes that are constructed using a dual-mirror Schwarzschild-Couder configuration. These telescopes will sample a wide ($8^{\circ}$) field of view using a densely pixelated camera comprising over $10^{4}$ individual readout channels. A readout frequency congruent with the expected single-telescope trigger rates would result in substantial data rates. To ameliorate these data rates, a novel, hardware-level Distributed Intelligent Array Trigger (DIAT) is envisioned. A copy of the DIAT operates autonomously at each telescope and uses reduced resolution imaging data from a limited subset of nearby telescopes to veto events prior to camera readout {and any subsequent network transmission of camera data that is required for centralized storage or aggregation}. We present the results of Monte-Carlo simulations that evaluate the efficacy of a "Parallax width" discriminator that can be used by the DIAT to efficiently distinguish between genuine gamma-ray initiated events and unwanted background events that are initiated by hadronic cosmic rays.

astro-ph.IM↗

arXiv2018

Galaxy Zoo: Morphological classification of galaxy images from the Illustris simulation

Modern cosmological simulations model the universe with increasing sophistication and at higher spatial and temporal resolutions. These enhancements permit detailed comparisons between the simulation outputs and real observational data. Recent projects such as Illustris are capable of producing simulated images that are comparable to those obtained from local surveys. This paper tests how well Illustris achieves this goal across a diverse population of galaxies using visual morphologies derived from Galaxy Zoo citizen scientists. Morphological classifications provided by volunteers for simulated galaxies are compared with similar data for a compatible sample of images drawn from the SDSS Legacy Survey. This paper investigates how simple morphological characterization by human volunteers asked to distinguish smooth from featured systems differs between simulated and real galaxy images. Differences are identified, which are likely due to the limited resolution of the simulation, but which could be revealing real differences in the dynamical evolution of populations of galaxies in the real and model universes. Specifically, for stellar masses $M_{\star}\lesssim10^{11}M_{\odot}$, a larger proportion of Illustris galaxies that exhibit disk-like morphology or visible substructure, relative to their SDSS counterparts. Toward higher masses, simulated and observed galaxies converge and exhibit similar morphology distributions. The stellar mass threshold indicated by this divergent behavior confirms recent works using parametric measures of morphology from Illustris simulated images. When $M_{\star}\gtrsim10^{11}M_{\odot}$, the Illustris dataset contains fewer galaxies that classifiers regard as unambiguously featured. These results suggest that comparison between the detailed properties of observed and simulated galaxies, even when limited to reasonably massive systems, may be misleading.

astro-ph.GA↗

arXiv2017

GAMBIT: The Global and Modular Beyond-the-Standard-Model Inference Tool

We describe the open-source global fitting package GAMBIT: the Global And Modular Beyond-the-Standard-Model Inference Tool. GAMBIT combines extensive calculations of observables and likelihoods in particle and astroparticle physics with a hierarchical model database, advanced tools for automatically building analyses of essentially any model, a flexible and powerful system for interfacing to external codes, a suite of different statistical methods and parameter scanning algorithms, and a host of other utilities designed to make scans faster, safer and more easily-extendible than in the past. Here we give a detailed description of the framework, its design and motivation, and the current models and other specific components presently implemented in GAMBIT. Accompanying papers deal with individual modules and present first GAMBIT results. GAMBIT can be downloaded from gambit.hepforge.org.

hep-ph↗

arXiv2016

Sensitivity of the Cherenkov Telescope Array to the Detection of Intergalactic Magnetic Fields

Very high energy (VHE; energy $E \gtrsim 100\,$GeV) $γ$-rays originating from extragalactic sources undergo pair production with low-energy photons of background radiation fields. These pairs can inverse-Compton-scatter background photons, initiating an electromagnetic cascade. The spatial and temporal structure of this secondary $γ$-ray signal is altered as the $e^+e^-$ pairs are deflected in an intergalactic magnetic field (IGMF). We investigate how VHE observations with the future Cherenkov Telescope Array with its high angular resolution and broad energy range, can potentially probe the IGMF. We identify promising sources and simulate $γ$-ray spectra over a wide range of values of the IGMF strength and coherence length using the publicly available ELMAG Monte Carlo code. Combining simulated observations in a joint likelihood approach, we find that current limits on the IGMF can be significantly improved. The projected sensitivity depends strongly on the time a source has been $γ$-ray active and on the emitted maximum $γ$-ray energy.

astro-ph.HE↗