Showing 1–48 of 48 results for author: Miller, J A

PyPeakRankR: Reproducible Peak-Level Feature Extraction for Regulatory Element Ranking

Authors: Saroja Somasundaram, Nelson J. Johansen, Trygve E. Bakken, Jeremy A. Miller

Abstract: High-throughput chromatin accessibility assays such as ATAC-seq generate thousands of candidate regulatory elements (peaks), yet no standardized tool exists for assembling the diverse quantitative features needed to prioritize peaks for functional validation. Here we present PyPeakRankR, an open-source Python package that extracts peak-level features, namely BigWig signal summaries, GC content, Ph… ▽ More High-throughput chromatin accessibility assays such as ATAC-seq generate thousands of candidate regulatory elements (peaks), yet no standardized tool exists for assembling the diverse quantitative features needed to prioritize peaks for functional validation. Here we present PyPeakRankR, an open-source Python package that extracts peak-level features, namely BigWig signal summaries, GC content, PhyloP conservation scores, distribution moments (kurtosis, skewness, bimodality), and cell-type specificity rankings, into a single reproducible peak by feature matrix stored as a tab-separated values (TSV) file. PyPeakRankR separates deterministic feature extraction from downstream ranking, enabling transparent benchmarking of prioritization strategies on the same upstream data. The package provides both a command-line interface and a matching Python API, supports cross-assembly scoring via liftOver, and runs in minutes on thousands of peaks. PyPeakRankR was validated in the Brain Initiative Cell Census Network (BICCN) community challenge, where its predecessor PeakRankR ranked among the top 3 of 16 methods for cell-type specific enhancer prediction. In a recent basal ganglia study, PyPeakRankR was used within the Cross-species Enhancer Ranking Pipeline (CERP) to identify enhancer-AAV tools achieving greater than 70% on-target specificity across cell types. PyPeakRankR is freely available under the MIT license at https://github.com/AllenInstitute/PeakRankR/tree/python-package. △ Less

Submitted 16 June, 2026; originally announced June 2026.

Comments: Software paper. Code: https://github.com/AllenInstitute/PeakRankR/tree/python-package. 6 pages, 1 figure

AGN STORM 2. XII. Ground-Based Optical Photometry and Lag Measurements of Mrk 817

Authors: John W. Montano, Aaron J. Barth, Keith Horne, Edward M. Cackett, Gisella De Rosa, Yasaman Homayouni, Erin A. Kara, Gerard A. Kriss, Hermine Landt, Gilvan G. Apolonio, Nahum Arav, Benjamin D. Boizelle, Elena Dalla Bonta, Doron Chelouche, Maryam Dehghanian, Rick Edelson, Gary J. Ferland, Carina Fian, CHen Hu, Dragana Ilic, Michael D. Joner, Shai Kaspi, Christopher S. Kochanek, Andjelka B. Kovacevic, Collin Lewin , et al. (18 additional authors not shown)

Abstract: We present the ground-based imaging campaign and light curves of Markarian 817 as part of the multiwavelength monitoring program AGN STORM\,2. Observations were carried out over 1.4 years in \emph{uBgVriz} filters, with a median cadence of 0.4 days in \emph{g}. Reverberation lags are measured using three methods (ICCF, JAVELIN, and PyROA) with the Swift UVW2 band (1928 Å) as the reference light cu… ▽ More We present the ground-based imaging campaign and light curves of Markarian 817 as part of the multiwavelength monitoring program AGN STORM\,2. Observations were carried out over 1.4 years in \emph{uBgVriz} filters, with a median cadence of 0.4 days in \emph{g}. Reverberation lags are measured using three methods (ICCF, JAVELIN, and PyROA) with the Swift UVW2 band (1928 Å) as the reference light curve. The ICCF centroid lags range from $3.0\pm0.8$ days for the $u$ band up to $7.9\pm1.5$ days for $z$, and are consistent with a $τ\propto λ^{4/3}$ dependence, the relation expected for lamp-post reprocessing by a Shakura-Sunyaev disk. Lags measured with the other methods are systematically shorter, and deviate from a $λ^{4/3}$ power-law spectrum at long wavelengths. The lags exceed thin-disk reprocessing predictions by factors of $\sim$3-6, similar to the ``disk size discrepancy'' seen in other Seyfert galaxies. We divide the campaign into three epochs with different levels of mean luminosity and X-ray obscuring column density and find that the lags vary by as much as a factor of 2 between epochs. The intrinsic spectral energy distribution is bluer and brighter during the first third of the campaign, and the longest continuum reverberation lags are obtained during that period. These results suggest that changes in ionizing luminosity can produce large variations in continuum lags on short timescales by altering the diffuse continuum luminosity emitted by the broad-line region and/or obscuring outflow, although changes in obscuration between the central engine and broad-line region may also contribute to the lag variations. △ Less

Submitted 4 May, 2026; originally announced May 2026.

Comments: 33 pages, 11 figures, 7 tables

Increased and Varied Radiation during the Sun's Encounters with Cold Clouds in the last 10 million years

Authors: Merav Opher, Joe Giacalone, Abraham Loeb, Evan P. Economo, Alan Cummings, Jennifer Middleton, Catherine Zucker, Jesse A. Miller, Anna Nica, Maria Hatzaki

Abstract: Recent research raises the possibility that 3 and 7 million years ago, the Sun encountered massive clouds that shrank the heliosphere--the solar cocoon protecting our solar system--exposing Earth to its interstellar environment, in agreement with geological evidence from 60Fe and 244Pu isotopes. Here we show that during such encounters Earth was exposed to increased radiation in the form of high-e… ▽ More Recent research raises the possibility that 3 and 7 million years ago, the Sun encountered massive clouds that shrank the heliosphere--the solar cocoon protecting our solar system--exposing Earth to its interstellar environment, in agreement with geological evidence from 60Fe and 244Pu isotopes. Here we show that during such encounters Earth was exposed to increased radiation in the form of high-energy particles. During periods of Earth's immersion in the heliosphere, it received particle radiation that we name Heliospheric Energetic Particles (HEPs). The intensity of < 10 MeV protons was at least an order of magnitude more intense than today's most extreme solar energetic particle (SEP) events. SEPs today last minutes to hours, but HEP exposure then lasted for extensive periods of several months, making it a prolonged external driver. During Earth's excursion outside the heliosphere, it was exposed to a galactic cosmic ray radiation with the intensity of < 1 GeV protons at least an order of magnitude more intense than today. Therefore, the space surrounding Earth was permeated by a variable high-energy radiation. We discuss the implications for Earth's climate and biodiversity. △ Less

Submitted 16 January, 2026; originally announced January 2026.

Comments: 34 pages, 4 figures

Cosmogenic 10Be as a Tracer for Recent Heliospheric Encounters with Interstellar Cold Clouds

Authors: Anna Nica, Merav Opher, Jesse A. Miller, Jennifer L. Middleton

Abstract: Recent works suggest there are periods when the Sun encountered massive interstellar cold clouds which compressed the heliosphere to within Earth's orbit. This would expose Earth to increased galactic cosmic rays (GCRs) and energetic particles of heliospheric origin (HEPs). We model 10Be production in Earth's atmosphere during possible interstellar cloud encounters and supernovae, and estimate the… ▽ More Recent works suggest there are periods when the Sun encountered massive interstellar cold clouds which compressed the heliosphere to within Earth's orbit. This would expose Earth to increased galactic cosmic rays (GCRs) and energetic particles of heliospheric origin (HEPs). We model 10Be production in Earth's atmosphere during possible interstellar cloud encounters and supernovae, and estimate their detectability in marine and ice records of variable temporal resolution. We find that encounters with sub-parsec-scale clouds cannot be detected via 10Be measurements in iron-manganese crusts. GCR signal is not detectable in ocean sediments; only parsec-scale clouds can be detected in iron-manganese crusts. Encounters with sub-parsec-scale clouds can be detected if Earth is exposed to HEPs, or by measuring ice cores with less than or equal to 10 kyr temporal resolution. We find that the peak observed by Koll et al. (2025) 10 Ma cannot be attributed to a supernova, but could be attributed to an interstellar cloud crossing. △ Less

Submitted 23 March, 2026; v1 submitted 12 January, 2026; originally announced January 2026.

Comments: 17 pages, 4 figures, submitted to GRL

Continuum Reverberation Mapping of 18 AGN Over Four Years

Authors: Jake A. Miller, Edward M. Cackett, Misty C. Bentz, Michael R. Goad, Kirk T. Korista, Ian M. McHardy

Abstract: Continuum reverberation mapping probes the size scale of the optical continuum-emitting region in active galactic nuclei (AGN). The source of this emission has long been thought to originate from the accretion disk, but recent studies suggest the broad line region (BLR) may significantly contribute to both the observed flux and continuum interband delays. We monitored 18 AGN over four years of obs… ▽ More Continuum reverberation mapping probes the size scale of the optical continuum-emitting region in active galactic nuclei (AGN). The source of this emission has long been thought to originate from the accretion disk, but recent studies suggest the broad line region (BLR) may significantly contribute to both the observed flux and continuum interband delays. We monitored 18 AGN over four years of observations to acquire high quality optical continuum light curves, measuring time lags between different photometric bands and determining continuum emission sizes for each AGN. We add this sample to existing lag measurements to test the correlation between continuum lags at $5100Å$ ($τ_{5100}$) and $5100Å$ luminosity ($L_{5100}$). We observe that $τ_{5100} \propto L_{5100}^{0.4}$, broadly consistent with the theoretical expectations of $τ\propto L^{1/2}$ expected for continuum reverberation from either the accretion disk or the BLR. △ Less

Submitted 7 November, 2025; originally announced November 2025.

Comments: 26 Pages, 7 Figures (5 In Main and 2 in Appendix), Accepted for publication in ApJ

Intensive X-ray/UVOIR continuum reverberation mapping of the Seyfert AGN MCG+08-11-11

Authors: D. Kynoch, I. M. McHardy, E. M. Cackett, J. Gelbord, J. V. Hernández Santisteban, K. Horne, J. A. Miller, H. Netzer, C. Done, R. Edelson, M. M. Fausnaugh, M. R. Goad, B. M. Peterson, F. M. Vincentelli

Abstract: We present results from intensive (x3 daily), three-month-long X-ray, UV and optical monitoring of the bright Seyfert active galactic nucleus (AGN) MCG+08-11-11 with Swift, supported by optical-infrared ground-based monitoring. The 12 resultant, well-sampled, lightcurves are highly correlated; in particular, the X-ray to UV correlation r_max = 0.85 is, as far as we know, the highest yet recorded i… ▽ More We present results from intensive (x3 daily), three-month-long X-ray, UV and optical monitoring of the bright Seyfert active galactic nucleus (AGN) MCG+08-11-11 with Swift, supported by optical-infrared ground-based monitoring. The 12 resultant, well-sampled, lightcurves are highly correlated; in particular, the X-ray to UV correlation r_max = 0.85 is, as far as we know, the highest yet recorded in a Seyfert galaxy. The lags increase with wavelength, as expected from reprocessing of central high-energy emission by surrounding material. Our lag spectrum is much shallower than that obtained from an optical monitoring campaign conducted a year earlier when MCG+08-11-11 was approximately 4 times brighter. After filtering out long-term trends in the earlier optical lightcurves we recover shorter lags consistent with our own - demonstrating concurrent reverberation signals from different spatial scales and the luminosity dependence of the measured lags. We use our lag spectrum to test several physical models, finding that disc reprocessing models cannot account for the observed 'excess' lags in the u and r-i-bands that are highly indicative of the Balmer and Paschen continua produced by reprocessing in the broad line region (BLR) gas. The structure seen in both the variable (rms) and lag spectra, and the large time delay between X-ray and UV variations (approximately 2 days) all suggest that the BLR is the dominant reprocessor. The hard X-ray spectrum (Gamma approximately 1.7) and faint, red, UV-optical spectrum both indicate that the Eddington accretion ratio is low: approximately 0.03. The bolometric luminosity then requires that the black hole mass is substantially greater than current reverberation mapping derived estimates. △ Less

Submitted 7 November, 2025; originally announced November 2025.

Comments: 24 pages, 13 figures (including appendices). Revised following referee's report

Journal ref: Mon Not R Astron Soc (2026)

A Survey Of Model Fits to Brown Dwarf Spectra Through the L-T Sequence

Authors: Savanah K. Turner, Denise C. Stephens, Conner B. Scoresby, Josh A. Miller

Abstract: We fit archival near-infrared spectra of 305 brown dwarfs with atmosphere models from the Sonora and Phoenix groups. Using the parameters of the best-fit models as estimates for the physical properties of the brown dwarfs in our sample, we have performed a survey of how brown dwarf atmospheres evolve with spectral type and temperature. We present the fit results and observed trends. We find that c… ▽ More We fit archival near-infrared spectra of 305 brown dwarfs with atmosphere models from the Sonora and Phoenix groups. Using the parameters of the best-fit models as estimates for the physical properties of the brown dwarfs in our sample, we have performed a survey of how brown dwarf atmospheres evolve with spectral type and temperature. We present the fit results and observed trends. We find that clouds have a more significant impact on near infrared spectra than disequilibrium chemistry, and that silicate clouds influence the near infrared spectrum through the late T types. We note where current atmosphere models are able to replicate the data and where the models and data conflict. We also categorize objects with similar spectral morphologies into families and discuss possible causes for their unique spectral traits. We identify two spectral families with morphologies that are likely indicative of binarity. △ Less

Submitted 1 May, 2025; originally announced May 2025.

Testing X-ray Reprocessing and Mapping the Soft Excess of NGC 7469 with NICER

Authors: Ethan R. Partington, Edward M. Cackett, Rick Edelson, Keith Horne, Jake A. Miller, Aaron J. Barth, Jonathan Gelbord, Juan V. Hernández Santisteban

Abstract: We present an X-ray/UV reverberation analysis of NGC 7469 across 210 days, using daily NICER observations with contemporaneous monitoring by Swift UVOT+XRT. We model the X-ray spectrum with a power law continuum and a soft excess during each NICER epoch. These emission sources demonstrate correlated flux variability with a lag consistent with zero days. We find that the power law emission is consi… ▽ More We present an X-ray/UV reverberation analysis of NGC 7469 across 210 days, using daily NICER observations with contemporaneous monitoring by Swift UVOT+XRT. We model the X-ray spectrum with a power law continuum and a soft excess during each NICER epoch. These emission sources demonstrate correlated flux variability with a lag consistent with zero days. We find that the power law emission is consistent with a compact X-ray corona, and that the soft excess can be explainedby reflected coronal emission from the inner accretion disk. We test the relationship between changes in the flux of the X-ray corona and the UVW2 continuum, finding strong correlation and a negative X-ray lag of less than one day. This is consistent with a scenario in which the X-ray corona drives the UVW2 light curve through thermal reprocessing △ Less

Submitted 28 April, 2025; originally announced April 2025.

Comments: 18 pages, 8 figures, Accepted to ApJ

Journal ref: ApJ 986 81 (2025)

Investigating the Variable Continuum Lags in PG 2130+099

Authors: Jake A. Miller, Edward M. Cackett, Mike Goad, Kirk T. Korista

Abstract: Broadband photometric reverberation mapping (RM) provides a measure of the size of the continuum-emitting region in active galactic nuclei (AGN). Previous monitoring campaigns of PG 2130+099 disagree as to whether the continuum emitting region size is consistent with that predicted for a standard optically thick geometrically thin accretion disk. We present $\sim$6 months of observations from seve… ▽ More Broadband photometric reverberation mapping (RM) provides a measure of the size of the continuum-emitting region in active galactic nuclei (AGN). Previous monitoring campaigns of PG 2130+099 disagree as to whether the continuum emitting region size is consistent with that predicted for a standard optically thick geometrically thin accretion disk. We present $\sim$6 months of observations from several robotic telescopes, providing the highest cadence and widest wavelength coverage photometric RM study of PG 2130+099 to date. Our results indicate that inferred size of the continuum-emitting region in PG 2130+099, like many recently observed AGN, is larger than the simplest predictions for an irradiated geometrically thin, optically thick accretion disk. We also perform a flux-flux analysis, finding a variable spectrum broadly consistent with a disk, and a constant component with enhanced $\textit{i}$-band emission, potentially due to H$α$. We find some evidence of increasing lag with luminosity, but previous lag measurements are too uncertain to be definitive. △ Less

Submitted 2 April, 2025; originally announced April 2025.

Comments: 16 Pages (14 Main + 2 Appendix), 8 Figures, 4 Tables. Accepted for publication in ApJ

The Rizzeta Stone: Adopting Gen-$α$ Colloquial Language to Improve Scientific Paper Rizz and Aura from a Skibidi Perspective

Authors: Anne E Blackwell, David L Moutard, Jake A Miller

Abstract: The field of astronomy evolves rapidly, and it is essential to keep up with these changes in order to effectively communicate with the broader community. However, communication itself also changes as new words, phrases, and slang terms enter the common vernacular. This is especially true for the current youngest generations, who are capable of efficiently communicating via the Internet. In order t… ▽ More The field of astronomy evolves rapidly, and it is essential to keep up with these changes in order to effectively communicate with the broader community. However, communication itself also changes as new words, phrases, and slang terms enter the common vernacular. This is especially true for the current youngest generations, who are capable of efficiently communicating via the Internet. In order to maintain effective communication, we explore the possibility of expanding the language used in scientific communication to include recently coined slang. This attempt at outreach, while potentially very difficult, could provide a means to expand the field and capture the attention of early-career scientists, improving retention within the field. However, our results indicate that, while possible, this method of communication is, like, probably not really worth it, no cap. △ Less

Submitted 31 March, 2025; originally announced April 2025.

Connecting the X-ray/UV variability of Fairall 9 with NICER: A Possible Warm Corona

Authors: Ethan R. Partington, Edward M. Cackett, Rick Edelson, Keith Horne, Jonathan Gelbord, Erin Kara, Christian Malacaria, Jake A. Miller, James F. Steiner, Andrea Sanna

Abstract: The Seyfert 1 AGN Fairall 9 was targeted by NICER, Swift, and ground-based observatories for a $\sim$1000-day long reverberation mapping campaign. The following analysis of NICER spectra taken at a two-day cadence provides new insights into the structure and heating mechanisms of the central black hole environment. Observations of Fairall 9 with NICER and Swift revealed a strong relationship betwe… ▽ More The Seyfert 1 AGN Fairall 9 was targeted by NICER, Swift, and ground-based observatories for a $\sim$1000-day long reverberation mapping campaign. The following analysis of NICER spectra taken at a two-day cadence provides new insights into the structure and heating mechanisms of the central black hole environment. Observations of Fairall 9 with NICER and Swift revealed a strong relationship between the flux of the UV continuum and the X-ray soft excess, indicating the presence of a "warm" Comptonized corona which likely lies in the upper layers of the innermost accretion flow, serving as a second reprocessor between the "hot" X-ray corona and the accretion disk. The X-ray emission from the hot corona lacks sufficient energy and variability to power slow changes in the UV light curve on timescales of 30 days or longer, suggesting an intrinsic disk-driven variability process in the UV and soft X-rays. Fast variability in the UV on timescales shorter than 30 days can be explained through X-ray reprocessing, and the observed weak X-ray/UV correlation suggests that the corona changes dynamically throughout the campaign. △ Less

Submitted 28 October, 2024; originally announced October 2024.

Comments: 23 pages, 14 figures, Accepted to ApJ

Journal ref: ApJ 977 77 (2024)

Nearby Supernova and Cloud Crossing Effects on the Orbits of Small Bodies in the Solar System

Authors: Leeanne Smith, Jesse A. Miller, Brian D. Fields

Abstract: Supernova blasts envelop many surrounding stellar systems, transferring kinetic energy to small bodies in the systems. Geologic evidence from $^{60}\rm Fe$ points to recent nearby supernova activity within the past several Myr. Here, we model the transfer of energy and resulting orbital changes from these supernova blasts to the Oort Cloud, the Kuiper belt, and Saturn's Phoebe ring. For the Oort C… ▽ More Supernova blasts envelop many surrounding stellar systems, transferring kinetic energy to small bodies in the systems. Geologic evidence from $^{60}\rm Fe$ points to recent nearby supernova activity within the past several Myr. Here, we model the transfer of energy and resulting orbital changes from these supernova blasts to the Oort Cloud, the Kuiper belt, and Saturn's Phoebe ring. For the Oort Cloud, an impulse approximation shows that a 50 pc supernova can eject approximately half of all objects less than 1 cm while altering the trajectories of larger ones, depending on their orbital parameters. For stars closest to supernovae, objects up to $\sim$100 m can be ejected. Turning to the explored solar system, we find that supernovae closer than 50 pc may affect Saturn's Phoebe ring and can sweep away Kuiper belt dust. It is also possible that the passage of the solar system through a dense interstellar cloud could have a similar effect; a numerical trajectory simulation shows that the location of the dust grains and the direction of the wind (from a supernova or interstellar cloud) has a significant impact on whether or not the grains will become unbound from their orbit in the Kuiper belt. Overall, nearby supernovae sweep micron-sized dust from the solar system, though whether the grains are ultimately cast towards the Sun or altogether ejected depends on various factors. Evidence of supernova-modified dust grain trajectories may be observed by New Horizons, though further modeling efforts are required. △ Less

Submitted 16 October, 2024; originally announced October 2024.

Comments: 7 pages, 4 figures. Published in Astrophysical Journal Letters (ApJL)

Journal ref: ApJL 974 L29 (2024)

AGN STORM 2. VII. A Frequency-resolved Map of the Accretion Disk in Mrk 817: Simultaneous X-ray Reverberation and UVOIR Disk Reprocessing Time Lags

Authors: Collin Lewin, Erin Kara, Aaron J. Barth, Edward M. Cackett, Gisella De Rosa, Yasaman Homayouni, Keith Horne, Gerard A. Kriss, Hermine Landt, Jonathan Gelbord, John Montano, Nahum Arav, Misty C. Bentz, Benjamin D. Boizelle, Elena Dalla Bontà, Michael S. Brotherton, Maryam Dehghanian, Gary J. Ferland, Carina Fian, Michael R. Goad, Juan V. Hernández Santisteban, Dragana Ilić, Jelle Kaastra, Shai Kaspi, Kirk T. Korista , et al. (13 additional authors not shown)

Abstract: X-ray reverberation mapping is a powerful technique for probing the innermost accretion disk, whereas continuum reverberation mapping in the UV, optical, and infrared (UVOIR) reveals reprocessing by the rest of the accretion disk and broad-line region (BLR). We present the time lags of Mrk 817 as a function of temporal frequency measured from 14 months of high-cadence monitoring from Swift and gro… ▽ More X-ray reverberation mapping is a powerful technique for probing the innermost accretion disk, whereas continuum reverberation mapping in the UV, optical, and infrared (UVOIR) reveals reprocessing by the rest of the accretion disk and broad-line region (BLR). We present the time lags of Mrk 817 as a function of temporal frequency measured from 14 months of high-cadence monitoring from Swift and ground-based telescopes, in addition to an XMM-Newton observation, as part of the AGN STORM 2 campaign. The XMM-Newton lags reveal the first detection of a soft lag in this source, consistent with reverberation from the innermost accretion flow. These results mark the first simultaneous measurement of X-ray reverberation and UVOIR disk reprocessing lags$\unicode{x2013}$effectively allowing us to map the entire accretion disk surrounding the black hole. Similar to previous continuum reverberation mapping campaigns, the UVOIR time lags arising at low temporal frequencies are longer than those expected from standard disk reprocessing by a factor of 2-3. The lags agree with the anticipated disk reverberation lags when isolating short-timescale variability, namely timescales shorter than the H$β$ lag. Modeling the lags requires additional reprocessing constrained at a radius consistent with the BLR size scale inferred from contemporaneous H$β$-lag measurements. When we divide the campaign light curves, the UVOIR lags show substantial variations, with longer lags measured when obscuration from an ionized outflow is greatest. We suggest that, when the obscurer is strongest, reprocessing by the BLR elongates the lags most significantly. As the wind weakens, the lags are dominated by shorter accretion disk lags. △ Less

Submitted 13 September, 2024; originally announced September 2024.

Comments: 28 pages, 11 figures, 3 tables. Accepted for publication in the Astrophysical Journal

Journal ref: ApJ 974 271 (2024)

Earth's Mesosphere During Possible Encounters With Massive Interstellar Clouds 2 and 7 Million Years Ago

Authors: Jesse A. Miller, Merav Opher, Maria Hatzaki, Kyriakoula Papachristopoulou, Brian C. Thomas

Abstract: Our solar system's path has recently been shown to potentially intersect dense interstellar clouds 2 and 7 million years ago: the Local Lynx of Cold Cloud and the edge of the Local Bubble. These clouds compressed the heliosphere, directly exposing Earth to the interstellar medium. Previous studies that examined climate effects of these encounters argued for an induced ice age due to the formation… ▽ More Our solar system's path has recently been shown to potentially intersect dense interstellar clouds 2 and 7 million years ago: the Local Lynx of Cold Cloud and the edge of the Local Bubble. These clouds compressed the heliosphere, directly exposing Earth to the interstellar medium. Previous studies that examined climate effects of these encounters argued for an induced ice age due to the formation of global noctilucent clouds (NLCs). Here, we revisit such studies with a modern 2D atmospheric chemistry model using parameters of global heliospheric magnetohydrodynamic models as input. We show that NLCs remain confined to polar latitudes and short seasonal lifetimes during these dense cloud crossings lasting $\sim10^5$ years. Polar mesospheric ozone becomes significantly depleted, but the total ozone column broadly increases. Furthermore, we show that the densest NLCs lessen the amount of sunlight reaching the surface instantaneously by up to 7% while halving outgoing longwave radiation. △ Less

Submitted 10 September, 2024; originally announced September 2024.

Comments: 12 pages, 4 figures

Journal ref: Geophysical Research Letters, volume 51, issue 17, id e2024GL110174 (7 September 2024)

Spaceport Facility Location Planning within the US National Airspace System

Authors: Haochen Wu, Kevin R. Sun, Jackson A. Miller, Oliver Jia-Richards, Max Z. Li

Abstract: The burgeoning commercial space transportation industry necessitates an expansion of launch infrastructure to meet rising demands. However, future operations from these large-scale infrastructures can result in new impacts, particularly to air traffic operations. To rigorously reason about where such future spaceports might be located and what their impacts might be, we introduce a facility locati… ▽ More The burgeoning commercial space transportation industry necessitates an expansion of launch infrastructure to meet rising demands. However, future operations from these large-scale infrastructures can result in new impacts, particularly to air traffic operations. To rigorously reason about where such future spaceports might be located and what their impacts might be, we introduce a facility location planning model for future US spaceports (SPFLP). Central considerations for the SPFLP include population density, space launch trajectories, and potential impacts to air traffic within the US National Airspace System (NAS). The SPFLP outputs a cost-optimal set of candidate locations for future spaceports while satisfying a range of operational constraints. By conducting sensitivity analyses on the SPFLP, we are able to examine differences in flight rerouting costs and optimal launch mission allocations. Our model and numerical experiments offer valuable insights for future spaceport site selection, contributing to the strategic development of commercial space transportation while keeping in mind the need to integrate these operations within the NAS. △ Less

Submitted 17 February, 2024; originally announced February 2024.

Comments: 10 pages, 5 figures

A Survey of Deep Learning and Foundation Models for Time Series Forecasting

Authors: John A. Miller, Mohammed Aldosari, Farah Saeed, Nasid Habib Barna, Subas Rana, I. Budak Arpinar, Ninghao Liu

Abstract: Deep Learning has been successfully applied to many application domains, yet its advantages have been slow to emerge for time series forecasting. For example, in the well-known Makridakis (M) Competitions, hybrids of traditional statistical or machine learning techniques have only recently become the top performers. With the recent architectural advances in deep learning being applied to time seri… ▽ More Deep Learning has been successfully applied to many application domains, yet its advantages have been slow to emerge for time series forecasting. For example, in the well-known Makridakis (M) Competitions, hybrids of traditional statistical or machine learning techniques have only recently become the top performers. With the recent architectural advances in deep learning being applied to time series forecasting (e.g., encoder-decoders with attention, transformers, and graph neural networks), deep learning has begun to show significant advantages. Still, in the area of pandemic prediction, there remain challenges for deep learning models: the time series is not long enough for effective training, unawareness of accumulated scientific knowledge, and interpretability of the model. To this end, the development of foundation models (large deep learning models with extensive pre-training) allows models to understand patterns and acquire knowledge that can be applied to new related problems before extensive training data becomes available. Furthermore, there is a vast amount of knowledge available that deep learning models can tap into, including Knowledge Graphs and Large Language Models fine-tuned with scientific domain knowledge. There is ongoing research examining how to utilize or inject such knowledge into deep learning models. In this survey, several state-of-the-art modeling techniques are reviewed, and suggestions for further work are provided. △ Less

Submitted 24 January, 2024; originally announced January 2024.

AGN STORM 2. VI. Mapping Temperature Fluctuations in the Accretion Disk of Mrk 817

Authors: Jack M. M. Neustadt, Christopher S. Kochanek, John Montano, Jonathan Gelbord, Aaron J. Barth, Gisella De Rosa, Gerard A. Kriss, Edward M. Cackett, Keith Horne, Erin A. Kara, Hermine Landt, Hagai Netzer, Nahum Arav, Misty C. Bentz, Elena Dalla Bonta, Maryam Dehghanian, Pu Du, Rick Edelson, Gary J. Ferland, Carina Fian, Travis Fischer, Michael R. Goad, Diego H. Gonzalez Buitrago, Varoujan Gorjian, Catherine J. Grier , et al. (27 additional authors not shown)

Abstract: We fit the UV/optical lightcurves of the Seyfert 1 galaxy Mrk 817 to produce maps of the accretion disk temperature fluctuations $δT$ resolved in time and radius. The $δT$ maps are dominated by coherent radial structures that move slowly ($v \ll c$) inwards and outwards, which conflicts with the idea that disk variability is driven only by reverberation. Instead, these slow-moving temperature fluc… ▽ More We fit the UV/optical lightcurves of the Seyfert 1 galaxy Mrk 817 to produce maps of the accretion disk temperature fluctuations $δT$ resolved in time and radius. The $δT$ maps are dominated by coherent radial structures that move slowly ($v \ll c$) inwards and outwards, which conflicts with the idea that disk variability is driven only by reverberation. Instead, these slow-moving temperature fluctuations are likely due to variability intrinsic to the disk. We test how modifying the input lightcurves by smoothing and subtracting them changes the resulting $δT$ maps and find that most of the temperature fluctuations exist over relatively long timescales ($\sim$100s of days). We show how detrending AGN lightcurves can be used to separate the flux variations driven by the slow-moving temperature fluctuations from those driven by reverberation. We also simulate contamination of the continuum emission from the disk by continuum emission from the broad line region (BLR), which is expected to have spectral features localized in wavelength, such as the Balmer break contaminating the $U$ band. We find that a disk with a smooth temperature profile cannot produce a signal localized in wavelength and that any BLR contamination should appear as residuals in our model lightcurves. Given the observed residuals, we estimate that only $\sim$20% of the variable flux in the $U$ and $u$ lightcurves can be due to BLR contamination. Finally, we discus how these maps not only describe the data, but can make predictions about other aspects of AGN variability. △ Less

Submitted 2 October, 2023; originally announced October 2023.

Comments: 23 pages, 18 figures, submitting to ApJ, comments welcome

Decoding the Alphabet Soup of Degrees in the United States Postsecondary Education System Through Hybrid Method: Database and Text Mining

Authors: Sahar Voghoei, James Byars, John A Miller, Khaled Rasheed, Hamid A Arabnia

Abstract: This paper proposes a model to predict the levels (e.g., Bachelor, Master, etc.) of postsecondary degree awards that have been ambiguously expressed in the student tracking reports of the National Student Clearinghouse (NSC). The model will be the hybrid of two modules. The first module interprets the relevant abbreviatory elements embedded in NSC reports by referring to a comprehensive database t… ▽ More This paper proposes a model to predict the levels (e.g., Bachelor, Master, etc.) of postsecondary degree awards that have been ambiguously expressed in the student tracking reports of the National Student Clearinghouse (NSC). The model will be the hybrid of two modules. The first module interprets the relevant abbreviatory elements embedded in NSC reports by referring to a comprehensive database that we have made of nearly 950 abbreviations for degree titles used by American postsecondary educators. The second module is a combination of feature classification and text mining modeled with CNN-BiLSTM, which is preceded by several steps of heavy pre-processing. The model proposed in this paper was trained with four multi-label datasets of different grades of resolution and returned 97.83\% accuracy with the most sophisticated dataset. Such a thorough classification of degree levels will provide insights into the modeling patterns of student success and mobility. To date, such a classification strategy has not been attempted except using manual methods and simple text parsing logic. △ Less

Submitted 6 September, 2023; originally announced September 2023.

Comments: 18 Pages, 8 figures

Synergies between interstellar dust and heliospheric science with an Interstellar Probe

Authors: Veerle J. Sterken, Silvan Hunziker, Kostas Dialynas, Jan Leitner, Maximilian Sommer, Ralf Srama, Lennart R. Baalmann, Aigen Li, Konstantin Herbst, André Galli, Pontus Brandt, My Riebe, Jack Baggaley, Michel Blanc, Andrej Czechowski, Frederic Effenberger, Brian Fields, Priscilla Frisch, Mihaly Horanyi, Hsiang-Wen Hsu, Nozair Khawaja, Harald Krüger, Bill S. Kurth, Niels F. W. Ligterink, Jeffrey L. Linsky , et al. (18 additional authors not shown)

Abstract: We discuss the synergies between heliospheric and dust science, the open science questions, the technological endeavors and programmatic aspects that are important to maintain or develop in the decade to come. In particular, we illustrate how we can use interstellar dust in the solar system as a tracer for the (dynamic) heliosphere properties, and emphasize the fairly unexplored, but potentially i… ▽ More We discuss the synergies between heliospheric and dust science, the open science questions, the technological endeavors and programmatic aspects that are important to maintain or develop in the decade to come. In particular, we illustrate how we can use interstellar dust in the solar system as a tracer for the (dynamic) heliosphere properties, and emphasize the fairly unexplored, but potentially important science question of the role of cosmic dust in heliospheric and astrospheric physics. We show that an Interstellar Probe mission with a dedicated dust suite would bring unprecedented advances to interstellar dust research, and can also contribute-through measuring dust - to heliospheric science. This can, in particular, be done well if we work in synergy with other missions inside the solar system, thereby using multiple vantage points in space to measure the dust as it `rolls' into the heliosphere. Such synergies between missions inside the solar system and far out are crucial for disentangling the spatially and temporally varying dust flow. Finally, we highlight the relevant instrumentation and its suitability for contributing to finding answers to the research questions. △ Less

Submitted 21 August, 2023; originally announced August 2023.

Comments: 18 pages, 7 Figures, 5 Tables. Originally submitted as white paper for the National Academies Decadal Survey for Solar and Space Physics 2024-2033

Journal ref: RAS Techniques and Instruments, rzad034 (2023)

AGN STORM 2: V. Anomalous Behavior of the CIV Light Curve in Mrk 817

Authors: Y. Homayouni, Gerard A. Kriss, Gisella De Rosa, Rachel Plesha, Edward M. Cackett, Michael R. Goad, Kirk T. Korista, Keith Horne, Travis Fischer, Tim Waters, Aaron J. Barth, Erin A. Kara, Hermine Landt, Nahum Arav, Benjamin D. Boizelle, Misty C. Bentz, Michael S. Brotherton, Doron Chelouche, Elena Dalla Bonta, Maryam Dehghanian, Pu Du, Gary J. Ferland, Carina Fian, Jonathan Gelbord, Catherine J. Grier , et al. (27 additional authors not shown)

Abstract: An intensive reverberation mapping campaign on the Seyfert 1 galaxy Mrk817 using the Cosmic Origins Spectrograph (COS) on the Hubble Space Telescope (HST) revealed significant variations in the response of the broad UV emission lines to fluctuations in the continuum emission. The response of the prominent UV emission lines changes over a $\sim$60-day duration, resulting in distinctly different tim… ▽ More An intensive reverberation mapping campaign on the Seyfert 1 galaxy Mrk817 using the Cosmic Origins Spectrograph (COS) on the Hubble Space Telescope (HST) revealed significant variations in the response of the broad UV emission lines to fluctuations in the continuum emission. The response of the prominent UV emission lines changes over a $\sim$60-day duration, resulting in distinctly different time lags in the various segments of the light curve over the 14 months observing campaign. One-dimensional echo-mapping models fit these variations if a slowly varying background is included for each emission line. These variations are more evident in the CIV light curve, which is the line least affected by intrinsic absorption in Mrk817 and least blended with neighboring emission lines. We identify five temporal windows with distinct emission line response, and measure their corresponding time delays, which range from 2 to 13 days. These temporal windows are plausibly linked to changes in the UV and X-ray obscuration occurring during these same intervals. The shortest time lags occur during periods with diminishing obscuration, whereas the longest lags occur during periods with rising obscuration. We propose that the obscuring outflow shields the ultraviolet broad lines from the ionizing continuum. The resulting change in the spectral energy distribution of the ionizing continuum, as seen by clouds at a range of distances from the nucleus, is responsible for the changes in the line response. △ Less

Submitted 5 January, 2024; v1 submitted 1 August, 2023; originally announced August 2023.

Comments: 20 pages, 8 figures, Accepted for publication in ApJ

Continuum Reverberation Mapping of Mrk 876 Over Three Years With Remote Robotic Observatories

Authors: Jake A. Miller, Edward M. Cackett, Michael R. Goad, Keith Horne, Aaron J. Barth, Encarni Romero-Colmenero, Michael Fausnaugh, Jonathan Gelbord, Kirk T. Korista, Hermine Landt, Tommaso Treu, Hartmut Winkler

Abstract: Continuum reverberation mapping probes the sizescale of the optical continuum-emitting region in active galactic nuclei (AGN). Through 3 years of multiwavelength photometric monitoring in the optical with robotic observatories, we perform continuum reverberation mapping on Mrk~876. All wavebands show large amplitude variability and are well correlated. Slow variations in the light curves broaden t… ▽ More Continuum reverberation mapping probes the sizescale of the optical continuum-emitting region in active galactic nuclei (AGN). Through 3 years of multiwavelength photometric monitoring in the optical with robotic observatories, we perform continuum reverberation mapping on Mrk~876. All wavebands show large amplitude variability and are well correlated. Slow variations in the light curves broaden the cross-correlation function (CCF) significantly, requiring detrending in order to robustly recover interband lags. We measure consistent interband lags using three techniques (CCF, JAVELIN, PyROA), with a lag of around 13~days from $u$ to $z$. These lags are longer than the expected radius of 12~days for the self-gravitating radius of the disk. The lags increase with wavelength roughly following $λ^{4/3}$, as would be expected from thin disk theory, but the lag normalization is approximately a factor of 3 longer than expected, as has also been observed in other AGN. The lag in the $i$ band shows an excess which we attribute to variable H$α$ broad-line emission. A flux-flux analysis shows a variable spectrum that follows $f_ν\propto λ^{-1/3}$ as expected for a disk, and an excess in the $i$ band that also points to strong variable H$α$ emission in that band. △ Less

Submitted 26 July, 2023; v1 submitted 5 July, 2023; originally announced July 2023.

Comments: 14 pages, 6 figures, 6 tables, accepted for publication in ApJ

AGN STORM 2. IV. Swift X-ray and ultraviolet/optical monitoring of Mrk 817

Authors: Edward M. Cackett, Jonathan Gelbord, Aaron J. Barth, Gisella De Rosa, Rick Edelson, Michael R. Goad, Yasaman Homayouni, Keith Horne, Erin A. Kara, Gerard A. Kriss, Kirk T. Korista, Hermine Landt, Rachel Plesha, Nahum Arav, Misty C. Bentz, Benjamin D. Boizelle, Elena Dalla Bonta, Maryam Dehghanian, Fergus Donnan, Pu Du, Gary J. Ferland, Carina Fian, Alexei V. Filippenko, Diego H. Gonzalez Buitrago, Catherine J. Grier , et al. (26 additional authors not shown)

Abstract: The AGN STORM 2 campaign is a large, multiwavelength reverberation mapping project designed to trace out the structure of Mrk 817 from the inner accretion disk to the broad emission line region and out to the dusty torus. As part of this campaign, Swift performed daily monitoring of Mrk 817 for approximately 15 months, obtaining observations in X-rays and six UV/optical filters. The X-ray monitori… ▽ More The AGN STORM 2 campaign is a large, multiwavelength reverberation mapping project designed to trace out the structure of Mrk 817 from the inner accretion disk to the broad emission line region and out to the dusty torus. As part of this campaign, Swift performed daily monitoring of Mrk 817 for approximately 15 months, obtaining observations in X-rays and six UV/optical filters. The X-ray monitoring shows that Mrk 817 was in a significantly fainter state than in previous observations, with only a brief flare where it reached prior flux levels. The X-ray spectrum is heavily obscured. The UV/optical light curves show significant variability throughout the campaign and are well correlated with one another, but uncorrelated with the X-rays. Combining the Swift UV/optical light curves with Hubble UV continuum light curves, we measure interband continuum lags, $τ(λ)$, that increase with increasing wavelength roughly following $τ(λ) \propto λ^{4/3}$, the dependence expected for a geometrically thin, optically thick, centrally illuminated disk. Modeling of the light curves reveals a period at the beginning of the campaign where the response of the continuum is suppressed compared to later in the light curve - the light curves are not simple shifted and scaled versions of each other. The interval of suppressed response corresponds to a period of high UV line and X-ray absorption, and reduced emission line variability amplitudes. We suggest that this indicates a significant contribution to the continuum from the broad line region gas that sees an absorbed ionizing continuum. △ Less

Submitted 26 September, 2023; v1 submitted 30 June, 2023; originally announced June 2023.

Comments: 20 pages, 13 figures, 3 tables, accepted for publication in ApJ

AGN STORM 2: II. Ultraviolet Observations of Mrk817 with the Cosmic Origins Spectrograph on the Hubble Space Telescope

Authors: Y. Homayouni, Gisella De Rosa, Rachel Plesha, Gerard A. Kriss, Aaron J. Barth, Edward M. Cackett, Keith Horne, Erin A. Kara, Hermine Landt, Nahum Arav, Benjamin D. Boizelle, Misty C. Bentz, Thomas G. Brink, Michael S. Brotherton, Doron Chelouche, Elena Dalla Bonta, Maryam Dehghanian, Pu Du, Gary J. Ferland, Laura Ferrarese, Carina Fian, Alexei V. Filippenko, Travis Fischer, Ryan J. Foley, Jonathan Gelbord , et al. (40 additional authors not shown)

Abstract: We present reverberation mapping measurements for the prominent ultraviolet broad emission lines of the active galactic nucleus Mrk817 using 165 spectra obtained with the Cosmic Origins Spectrograph on the Hubble Space Telescope. Our ultraviolet observations are accompanied by X-ray, optical, and near-infrared observations as part of the AGN Space Telescope and Optical Reverberation Mapping Progra… ▽ More We present reverberation mapping measurements for the prominent ultraviolet broad emission lines of the active galactic nucleus Mrk817 using 165 spectra obtained with the Cosmic Origins Spectrograph on the Hubble Space Telescope. Our ultraviolet observations are accompanied by X-ray, optical, and near-infrared observations as part of the AGN Space Telescope and Optical Reverberation Mapping Program 2 (AGN STORM 2). Using the cross-correlation lag analysis method, we find significant correlated variations in the continuum and emission-line light curves. We measure rest-frame delayed responses between the far-ultraviolet continuum at 1180 A and Ly$α$ $\lambda1215$ A ($10.4_{-1.4}^{+1.6}$ days), N V $\lambda1240$ A ($15.5_{-4.8}^{+1.0}$days), SiIV + OIV] $\lambda1397$ A ($8.2_{-1.4}^{+1.4}$ days), CIV $\lambda1549$ A ($11.8_{-2.8}^{+3.0}$ days), and HeII $\lambda1640$ A ($9.0_{-1.9}^{+4.5}$ days) using segments of the emission-line profile that are unaffected by absorption and blending, which results in sampling different velocity ranges for each line. However, we find that the emission-line responses to continuum variations are more complex than a simple smoothed, shifted, and scaled version of the continuum light curve. We also measure velocity-resolved lags for the Ly$α$, and CIV emission lines. The lag profile in the blue wing of Ly$α$ is consistent with virial motion, with longer lags dominating at lower velocities, and shorter lags at higher velocities. The CIV lag profile shows the signature of a thick rotating disk, with the shortest lags in the wings, local peaks at $\pm$ 1500 $\rm km\,s^{-1}$, and a local minimum at line center. The other emission lines are dominated by broad absorption lines and blending with adjacent emission lines. These require detailed models, and will be presented in future work. △ Less

Submitted 22 February, 2023; originally announced February 2023.

Comments: Submitted to ApJ. 25 pages, 8 figures, and 6 tables

Near-Earth Supernovae in the Past 10 Myr: Implications for the Heliosphere

Authors: Jesse A. Miller, Brian D. Fields, Thomas Y. Chen, John Ellis, Adrienne F. Ertel, Jerry W. Manweiler, Merav Opher, Elena Provornikova, Jonathan D. Slavin, Justyna Sokół, Veerle Sterken, Rebecca Surman, Xilu Wang

Abstract: We summarize evidence that multiple supernovae exploded within 100 pc of Earth in the past few Myr. These events had dramatic effects on the heliosphere, compressing it to within ~20 au. We advocate for cross-disciplinary research of nearby supernovae, including on interstellar dust and cosmic rays. We urge for support of theory work, direct exploration, and study of extrasolar astrospheres. We summarize evidence that multiple supernovae exploded within 100 pc of Earth in the past few Myr. These events had dramatic effects on the heliosphere, compressing it to within ~20 au. We advocate for cross-disciplinary research of nearby supernovae, including on interstellar dust and cosmic rays. We urge for support of theory work, direct exploration, and study of extrasolar astrospheres. △ Less

Submitted 7 September, 2022; originally announced September 2022.

Comments: White paper submitted to the Solar and Space Physics 2024 Decadal Survey

EXPANSE: A Deep Continual / Progressive Learning System for Deep Transfer Learning

Authors: Mohammadreza Iman, John A. Miller, Khaled Rasheed, Robert M. Branch, Hamid R. Arabnia

Abstract: Deep transfer learning techniques try to tackle the limitations of deep learning, the dependency on extensive training data and the training costs, by reusing obtained knowledge. However, the current DTL techniques suffer from either catastrophic forgetting dilemma (losing the previously obtained knowledge) or overly biased pre-trained models (harder to adapt to target data) in finetuning pre-trai… ▽ More Deep transfer learning techniques try to tackle the limitations of deep learning, the dependency on extensive training data and the training costs, by reusing obtained knowledge. However, the current DTL techniques suffer from either catastrophic forgetting dilemma (losing the previously obtained knowledge) or overly biased pre-trained models (harder to adapt to target data) in finetuning pre-trained models or freezing a part of the pre-trained model, respectively. Progressive learning, a sub-category of DTL, reduces the effect of the overly biased model in the case of freezing earlier layers by adding a new layer to the end of a frozen pre-trained model. Even though it has been successful in many cases, it cannot yet handle distant source and target data. We propose a new continual/progressive learning approach for deep transfer learning to tackle these limitations. To avoid both catastrophic forgetting and overly biased-model problems, we expand the pre-trained model by expanding pre-trained layers (adding new nodes to each layer) in the model instead of only adding new layers. Hence the method is named EXPANSE. Our experimental results confirm that we can tackle distant source and target data using this technique. At the same time, the final model is still valid on the source data, achieving a promising deep continual learning approach. Moreover, we offer a new way of training deep learning models inspired by the human education system. We termed this two-step training: learning basics first, then adding complexities and uncertainties. The evaluation implies that the two-step training extracts more meaningful features and a finer basin on the error surface since it can achieve better accuracy in comparison to regular training. EXPANSE (model expansion and two-step training) is a systematic continual learning approach applicable to different problems and DL models. △ Less

Submitted 23 May, 2022; v1 submitted 18 May, 2022; originally announced May 2022.

Comments: 12 Pages, 2 figures, 4 tables, submitting to NIPS 2022

Journal ref: Technologies, 2023

Heliospheric Compression due to Recent Nearby Supernova Explosions

Authors: Jesse A. Miller, Brian D. Fields

Abstract: The widespread detection of 60Fe in geological and lunar archives provides compelling evidence for recent nearby supernova explosions within $\sim 100$ pc around 3 Myr and 7 Myr ago. The blasts from these explosions had a profound effect on the heliosphere. We perform new calculations to study the compression of the heliosphere due to a supernova blast. Assuming a steady but non-isotropic solar wi… ▽ More The widespread detection of 60Fe in geological and lunar archives provides compelling evidence for recent nearby supernova explosions within $\sim 100$ pc around 3 Myr and 7 Myr ago. The blasts from these explosions had a profound effect on the heliosphere. We perform new calculations to study the compression of the heliosphere due to a supernova blast. Assuming a steady but non-isotropic solar wind, we explore a range of properties appropriate for supernova distances inspired by recent 60Fe data, and for a 20 pc supernova proposed to account for mass extinctions at the end-Devonian period. We examine the locations of the termination shock decelerating the solar wind and the heliopause that marks the boundary between the solar wind and supernova material. Pressure balance scaling holds, consistent with studies of other astrospheres. Solar wind anisotropy does not have an appreciable effect on shock geometry. We find that supernova explosions at 50 pc (95 pc) lead to heliopause locations at 16 au (23 au) when the forward shock arrives. Thus, the outer solar system was directly exposed to the blast, but the inner planets -- including the Earth -- were not. This finding reaffirms that the delivery of supernova material to the Earth is not from the blast plasma itself, but likely is from supernova dust grains. After the arrival of the forward shock, the weakening supernova blast will lead to a gradual rebound of the heliosphere, taking $\sim100$s of kyr to expand beyond 100 au. Prospects for future work are discussed. △ Less

Submitted 3 May, 2022; originally announced May 2022.

Comments: 18 pages, 11 figures. Comments welcome

Updated QCD global analysis of single transverse-spin asymmetries I: Extracting $\tilde{H}$, and the role of the Soffer bound and lattice QCD

Authors: Leonard Gamberg, Michel Malda, Joshua A. Miller, Daniel Pitonyak, Alexei Prokudin, Nobuo Sato

Abstract: We present an update to the QCD global analysis of single transverse-spin asymmetries presented in Cammarota, et al., PRD 102, 054002 (2020) (JAM3D-20). JAM3D-20 simultaneously included transverse momentum dependent and collinear twist-3 observables, both of which are sensitive to quark-gluon-quark correlations in hadrons. In this study we extract for the first time the twist-3 chiral odd fragment… ▽ More We present an update to the QCD global analysis of single transverse-spin asymmetries presented in Cammarota, et al., PRD 102, 054002 (2020) (JAM3D-20). JAM3D-20 simultaneously included transverse momentum dependent and collinear twist-3 observables, both of which are sensitive to quark-gluon-quark correlations in hadrons. In this study we extract for the first time the twist-3 chiral odd fragmentation function $\tilde{H}$ by incorporating the $\sinφ_s$ modulation data from SIDIS along with its contribution to the single transverse-spin asymmetry in pion production from proton-proton collisions. We also explore the impact of lattice QCD tensor charge calculations and the Soffer bound on our global analysis. We find that both constraints can be accommodated within our results, with $\tilde{H}$ playing a key role in maintaining agreement with the data from proton-proton collisions. △ Less

Submitted 8 August, 2022; v1 submitted 2 May, 2022; originally announced May 2022.

Comments: 27 pages, 19 figures, 1 table; content added on uncertainties of non-perturbative functions, new section on the role of antiquarks, version to appear in PRD

Report number: JLAB-THY-22-3604

The luminosity-dependent contribution from the broad line region to the wavelength-dependent lags in Mrk 110

Authors: F. M. Vincentelli, I. McHardy, V. Hernández Santisteban, E. M. Cackett, J. Gelbord, Keith Horne, J. A. Miller, A. Lobban

Abstract: We have measured the wavelength-dependent lags between the X-ray, UV and optical bands in the high accretion rate ($L/L_{\rm Edd}\approx40\%$) Active Galactic Nucleus Mrk 110 during two intensive monitoring campaigns in February and September 2019. We divide the observations into three intervals with different X-ray luminosities. The first interval, already published in Vincentelli et al. (2021),… ▽ More We have measured the wavelength-dependent lags between the X-ray, UV and optical bands in the high accretion rate ($L/L_{\rm Edd}\approx40\%$) Active Galactic Nucleus Mrk 110 during two intensive monitoring campaigns in February and September 2019. We divide the observations into three intervals with different X-ray luminosities. The first interval, already published in Vincentelli et al. (2021), has the lowest X-ray luminosity and did not exhibit the U-band excess positive lag, or the X-ray excess negative lag that is seen in most AGN. However, these excess lags are seen in the two subsequent intervals of higher X-ray luminosity. Although the data are limited, the excess lags appear to scale with X-ray luminosity. Our modelling shows that lags expected from reprocessing of X-rays by the accretion disc vary hardly at all with increasing luminosity. Therefore, as the U-band excess almost certainly arises from Balmer continuum emission from the broad line region (BLR), we attribute these lag changes to changes in the contribution from the BLR. The change is easily explained by the usual increase in the inner radius of the BLR with increasing ionising luminosity. △ Less

Submitted 24 January, 2022; originally announced January 2022.

Comments: 6 pages, 4 figures. Accepted for publication in MNRAS Letters

Proposed Lunar Measurements of $r$-Process Radioisotopes to Distinguish Origin of Deep-sea 244Pu

Authors: Xilu Wang, Adam M. Clark, John Ellis, Adrienne F. Ertel, Brian D. Fields, Brian J. Fry, Zhenghai Liu, Jesse A. Miller, Rebecca Surman

Abstract: 244Pu has recently been discovered in deep-sea deposits spanning the past 10 Myr, a period that includes two 60Fe pulses from nearby supernovae. 244Pu is among the heaviest $r$-process products, and we consider whether it was created in the supernovae, which is disfavored by nucleosynthesis simulations, or in an earlier kilonova event that seeded 244Pu in the nearby interstellar medium that was su… ▽ More 244Pu has recently been discovered in deep-sea deposits spanning the past 10 Myr, a period that includes two 60Fe pulses from nearby supernovae. 244Pu is among the heaviest $r$-process products, and we consider whether it was created in the supernovae, which is disfavored by nucleosynthesis simulations, or in an earlier kilonova event that seeded 244Pu in the nearby interstellar medium that was subsequently swept up by the supernova debris. We discuss how these possibilities can be probed by measuring 244Pu and other $r$-process radioisotopes such as 129I and 182Hf, both in lunar regolith samples returned to Earth by missions such as Chang'e and Artemis, and in deep-sea deposits. △ Less

Submitted 29 March, 2023; v1 submitted 17 December, 2021; originally announced December 2021.

Comments: 19 pages, 4 figures, 2 tables, v3 matches version to appear in ApJ

Report number: KCL-PH-TH/2021-91, CERN-TH-2021-208, N3AS-21-017

Journal ref: The Astrophysical Journal, 2023, Volume 948, Issue 2, id.113, 13 pp

AGN STORM 2: I. First results: A Change in the Weather of Mrk 817

Authors: Erin Kara, Missagh Mehdipour, Gerard A. Kriss, Edward M. Cackett, Nahum Arav, Aaron J. Barth, Doyee Byun, Michael S. Brotherton, Gisella De Rosa, Jonathan Gelbord, Juan V. Hernandez Santisteban, Chen Hu, Jelle Kaastra, Hermine Landt, Yan-Rong Li, Jake A. Miller, John Montano, Ethan Partington, Jesus Aceituno, Jin-Ming Bai, Dongwei Bao, Misty C. Bentz, Thomas G. Brink, Doron Chelouche, Yong-Jie Chen , et al. (47 additional authors not shown)

Abstract: We present the first results from the ongoing, intensive, multi-wavelength monitoring program of the luminous Seyfert 1 galaxy Mrk 817. While this AGN was, in part, selected for its historically unobscured nature, we discovered that the X-ray spectrum is highly absorbed, and there are new blueshifted, broad and narrow UV absorption lines, which suggest that a dust-free, ionized obscurer located at… ▽ More We present the first results from the ongoing, intensive, multi-wavelength monitoring program of the luminous Seyfert 1 galaxy Mrk 817. While this AGN was, in part, selected for its historically unobscured nature, we discovered that the X-ray spectrum is highly absorbed, and there are new blueshifted, broad and narrow UV absorption lines, which suggest that a dust-free, ionized obscurer located at the inner broad line region partially covers the central source. Despite the obscuration, we measure UV and optical continuum reverberation lags consistent with a centrally illuminated Shakura-Sunyaev thin accretion disk, and measure reverberation lags associated with the optical broad line region, as expected. However, in the first 55 days of the campaign, when the obscuration was becoming most extreme, we observe a de-coupling of the UV continuum and the UV broad emission line variability. The correlation recovers in the next 42 days of the campaign, as Mrk 817 enters a less obscured state. The short CIV and Ly alpha lags suggest that the accretion disk extends beyond the UV broad line region. △ Less

Submitted 12 May, 2021; originally announced May 2021.

Comments: 28 pages, 14 figures, submitted to ApJ. Comments welcome

r-Process Radioisotopes from Near-Earth Supernovae and Kilonovae

Authors: Xilu Wang, Adam M. Clark, John Ellis, Adrienne F. Ertel, Brian D. Fields, Zhenghai Liu, Jesse A. Miller, Rebecca Surman

Abstract: The astrophysical sites where r-process elements are synthesized remain mysterious: it is clear that neutron star mergers (kilonovae (KNe)) contribute, and some classes of core-collapse supernovae (SNe) are also likely sources of at least the lighter r-process species. The discovery of 60Fe on the Earth and Moon implies that one or more astrophysical explosions have occurred near the Earth within… ▽ More The astrophysical sites where r-process elements are synthesized remain mysterious: it is clear that neutron star mergers (kilonovae (KNe)) contribute, and some classes of core-collapse supernovae (SNe) are also likely sources of at least the lighter r-process species. The discovery of 60Fe on the Earth and Moon implies that one or more astrophysical explosions have occurred near the Earth within the last few million years, probably SNe. Intriguingly, 244Pu has now been detected, mostly overlapping with 60Fe pulse. However, the 244Pu flux may extend to before 12 Myr ago, pointing to a different origin. Motivated by these observations and difficulties for r-process nucleosynthesis in SN models, we propose that ejecta from a KN enriched the giant molecular cloud that gave rise to the Local Bubble, where the Sun resides. Accelerator mass spectrometry (AMS) measurements of 244Pu and searches for other live isotopes could probe the origins of the r-process and the history of the solar neighborhood, including triggers for mass extinctions, e.g., that at the end of the Devonian epoch, motivating the calculations of the abundances of live r-process radioisotopes produced in SNe and KNe that we present here. Given the presence of 244Pu, other r-process species such as 93Zr, 107Pd, 129I, 135Cs, 182Hf, 236U, 237Np and 247Cm should be present. Their abundances and well-resolved time histories could distinguish between the SN and KN scenarios, and we discuss prospects for their detection in deep-ocean deposits and the lunar regolith. We show that AMS 129I measurements in Fe-Mn crusts already constrain a possible nearby KN scenario. △ Less

Submitted 24 December, 2021; v1 submitted 11 May, 2021; originally announced May 2021.

Comments: 45 pages, 14 figures, 11 tables, v2 matches version to appear in ApJ

Report number: KCL-PH-TH/2021-03, CERN-TH-2021-014, N3AS-21-007

Journal ref: The Astrophysical Journal, 2021, Volume 923, Number 2

Revisiting Citizen Science Through the Lens of Hybrid Intelligence

Authors: Janet Rafner, Miroslav Gajdacz, Gitte Kragh, Arthur Hjorth, Anna Gander, Blanka Palfi, Aleks Berditchevskaia, François Grey, Kobi Gal, Avi Segal, Mike Walmsley, Josh Aaron Miller, Dominik Dellerman, Muki Haklay, Pietro Michelucci, Jacob Sherson

Abstract: Artificial Intelligence (AI) can augment and sometimes even replace human cognition. Inspired by efforts to value human agency alongside productivity, we discuss the benefits of solving Citizen Science (CS) tasks with Hybrid Intelligence (HI), a synergetic mixture of human and artificial intelligence. Currently there is no clear framework or methodology on how to create such an effective mixture.… ▽ More Artificial Intelligence (AI) can augment and sometimes even replace human cognition. Inspired by efforts to value human agency alongside productivity, we discuss the benefits of solving Citizen Science (CS) tasks with Hybrid Intelligence (HI), a synergetic mixture of human and artificial intelligence. Currently there is no clear framework or methodology on how to create such an effective mixture. Due to the unique participant-centered set of values and the abundance of tasks drawing upon both human common sense and complex 21st century skills, we believe that the field of CS offers an invaluable testbed for the development of HI and human-centered AI of the 21st century, while benefiting CS as well. In order to investigate this potential, we first relate CS to adjacent computational disciplines. Then, we demonstrate that CS projects can be grouped according to their potential for HI-enhancement by examining two key dimensions: the level of digitization and the amount of knowledge or experience required for participation. Finally, we propose a framework for types of human-AI interaction in CS based on established criteria of HI. This "HI lens" provides the CS community with an overview of several ways to utilize the combination of AI and human intelligence in their projects. It also allows the AI community to gain ideas on how developing AI in CS projects can further their own field. △ Less

Submitted 30 April, 2021; originally announced April 2021.

On the multi-wavelength variability of Mrk 110: Two components acting at different timescales

Authors: F. M. Vincentelli, I. McHardy, E. M. Cackett, A. J. Barth, K. Horne, M. Goad, K. Korista, J. Gelbord, W. Brandt, R. Edelson, J. A. Miller, M. Pahari, B. M. Peterson, T. Schmidt, R. D. Baldi, E. Breedt, J. V. Hernandez Santisteban, E. Romero-Colmenero, M. Ward, D. R. A. Williams

Abstract: We present the first intensive continuum reverberation mapping study of the high accretion rate Seyfert galaxy Mrk 110. The source was monitored almost daily for more than 200 days with the Swift X-ray and UV/optical telescopes, supported by ground-based observations from Las Cumbres Observatory, the Liverpool Telescope, and the Zowada Observatory, thus extending the wavelength coverage to 9100 Å.… ▽ More We present the first intensive continuum reverberation mapping study of the high accretion rate Seyfert galaxy Mrk 110. The source was monitored almost daily for more than 200 days with the Swift X-ray and UV/optical telescopes, supported by ground-based observations from Las Cumbres Observatory, the Liverpool Telescope, and the Zowada Observatory, thus extending the wavelength coverage to 9100 Å. Mrk 110 was found to be significantly variable at all wavebands. Analysis of the intraband lags reveals two different behaviours, depending on the timescale. On timescales shorter than 10 days the lags, relative to the shortest UV waveband ($\sim1928$ Å), increase with increasing wavelength up to a maximum of $\sim2$days lag for the longest waveband ($\sim9100$ Å), consistent with the expectation from disc reverberation. On longer timescales, however, the g-band lags the Swift BAT hard X-rays by $\sim10$ days, with the z-band lagging the g-band by a similar amount, which cannot be explained in terms of simple reprocessing from the accretion disc. We interpret this result as an interplay between the emission from the accretion disc and diffuse continuum radiation from the broad line region. △ Less

Submitted 9 April, 2021; originally announced April 2021.

Comments: 19 pages, 11 figures. Accepted for publication in MNRAS

Improving Neural Networks for Time Series Forecasting using Data Augmentation and AutoML

Authors: Indrajeet Y. Javeri, Mohammadhossein Toutiaee, Ismailcem B. Arpinar, Tom W. Miller, John A. Miller

Abstract: Statistical methods such as the Box-Jenkins method for time-series forecasting have been prominent since their development in 1970. Many researchers rely on such models as they can be efficiently estimated and also provide interpretability. However, advances in machine learning research indicate that neural networks can be powerful data modeling techniques, as they can give higher accuracy for a p… ▽ More Statistical methods such as the Box-Jenkins method for time-series forecasting have been prominent since their development in 1970. Many researchers rely on such models as they can be efficiently estimated and also provide interpretability. However, advances in machine learning research indicate that neural networks can be powerful data modeling techniques, as they can give higher accuracy for a plethora of learning problems and datasets. In the past, they have been tried on time-series forecasting as well, but their overall results have not been significantly better than the statistical models especially for intermediate length times series data. Their modeling capacities are limited in cases where enough data may not be available to estimate the large number of parameters that these non-linear models require. This paper presents an easy to implement data augmentation method to significantly improve the performance of such networks. Our method, Augmented-Neural-Network, which involves using forecasts from statistical models, can help unlock the power of neural networks on intermediate length time-series and produces competitive results. It shows that data augmentation, when paired with Automated Machine Learning techniques such as Neural Architecture Search, can help to find the best neural architecture for a given time-series. Using the combination of these, demonstrates significant enhancement in the forecasting accuracy of three neural network-based models for a COVID-19 dataset, with a maximum improvement in forecasting accuracy by 21.41%, 24.29%, and 16.42%, respectively, over the neural networks that do not use augmented data. △ Less

Submitted 7 May, 2021; v1 submitted 2 March, 2021; originally announced March 2021.

Supernova Triggers for End-Devonian Extinctions

Authors: Brian D. Fields, Adrian L. Melott, John Ellis, Adrienne F. Ertel, Brian J. Fry, Bruce S. Lieberman, Zhenghai Liu, Jesse A. Miller, Brian C. Thomas

Abstract: The Late Devonian was a protracted period of low speciation resulting in biodiversity decline, culminating in extinction events near the Devonian-Carboniferous boundary. Recent evidence indicates that the final extinction event may have coincided with a dramatic drop in stratospheric ozone, possibly due to a global temperature rise. Here we study an alternative possible cause for the postulated oz… ▽ More The Late Devonian was a protracted period of low speciation resulting in biodiversity decline, culminating in extinction events near the Devonian-Carboniferous boundary. Recent evidence indicates that the final extinction event may have coincided with a dramatic drop in stratospheric ozone, possibly due to a global temperature rise. Here we study an alternative possible cause for the postulated ozone drop: a nearby supernova explosion that could inflict damage by accelerating cosmic rays that can deliver ionizing radiation for up to $\sim 100$ kyr. We therefore propose that the end-Devonian extinctions were triggered by supernova explosions at $\sim 20$ pc, somewhat beyond the "kill distance" that would have precipitated a full mass extinction. Such nearby supernovae are likely due to core-collapses of massive stars; these are concentrated in the thin Galactic disk where the Sun resides. Detecting either of the long-lived radioisotopes Sm-146 or Pu-244 in one or more end-Devonian extinction strata would confirm a supernova origin, point to the core-collapse explosion of a massive star, and probe supernova nucleosythesis. Other possible tests of the supernova hypothesis are discussed. △ Less

Submitted 25 August, 2020; v1 submitted 3 July, 2020; originally announced July 2020.

Comments: 3 pages, no figures. Matches published version. Creative Commons CC BY-NC-ND license

Journal ref: PNAS 117, 35, 21008-21010 (2020)

Common Cell type Nomenclature for the mammalian brain: A systematic, extensible convention

Authors: Jeremy A. Miller, Nathan W. Gouwens, Bosiljka Tasic, Forrest Collman, Cindy T. J. van Velthoven, Trygve E. Bakken, Michael J. Hawrylycz, Hongkui Zeng, Ed S. Lein, Amy Bernard

Abstract: The advancement of single cell RNA-sequencing technologies has led to an explosion of cell type definitions across multiple organs and organisms. While standards for data and metadata intake are arising, organization of cell types has largely been left to individual investigators, resulting in widely varying nomenclature and limited alignment between taxonomies. To facilitate cross-dataset compari… ▽ More The advancement of single cell RNA-sequencing technologies has led to an explosion of cell type definitions across multiple organs and organisms. While standards for data and metadata intake are arising, organization of cell types has largely been left to individual investigators, resulting in widely varying nomenclature and limited alignment between taxonomies. To facilitate cross-dataset comparison, the Allen Institute created the Common Cell type Nomenclature (CCN) for matching and tracking cell types across studies that is qualitatively similar to gene transcript management across different genome builds. The CCN can be readily applied to new or established taxonomies and was applied herein to diverse cell type datasets derived from multiple quantifiable modalities. The CCN facilitates assigning accurate yet flexible cell type names in the mammalian cortex as a step towards community-wide efforts to organize multi-source, data-driven information related to cell type taxonomies from any organism. △ Less

Submitted 13 November, 2020; v1 submitted 9 June, 2020; originally announced June 2020.

Comments: 29 pages, 5 figures, 4 tables, 1 supplementary table

Stereotype-Free Classification of Fictitious Faces

Authors: Mohammadhossein Toutiaee, Soheyla Amirian, John A. Miller, Sheng Li

Abstract: Equal Opportunity and Fairness are receiving increasing attention in artificial intelligence. Stereotyping is another source of discrimination, which yet has been unstudied in literature. GAN-made faces would be exposed to such discrimination, if they are classified by human perception. It is possible to eliminate the human impact on fictitious faces classification task by the use of statistical a… ▽ More Equal Opportunity and Fairness are receiving increasing attention in artificial intelligence. Stereotyping is another source of discrimination, which yet has been unstudied in literature. GAN-made faces would be exposed to such discrimination, if they are classified by human perception. It is possible to eliminate the human impact on fictitious faces classification task by the use of statistical approaches. We present a novel approach through penalized regression to label stereotype-free GAN-generated synthetic unlabeled images. The proposed approach aids labeling new data (fictitious output images) by minimizing a penalized version of the least squares cost function between realistic pictures and target pictures. △ Less

Submitted 29 April, 2020; originally announced May 2020.

Video Contents Understanding using Deep Neural Networks

Authors: Mohammadhossein Toutiaee, Abbas Keshavarzi, Abolfazl Farahani, John A. Miller

Abstract: We propose a novel application of Transfer Learning to classify video-frame sequences over multiple classes. This is a pre-weighted model that does not require to train a fresh CNN. This representation is achieved with the advent of "deep neural network" (DNN), which is being studied these days by many researchers. We utilize the classical approaches for video classification task using object dete… ▽ More We propose a novel application of Transfer Learning to classify video-frame sequences over multiple classes. This is a pre-weighted model that does not require to train a fresh CNN. This representation is achieved with the advent of "deep neural network" (DNN), which is being studied these days by many researchers. We utilize the classical approaches for video classification task using object detection techniques for comparison, such as "Google Video Intelligence API" and this study will run experiments as to how those architectures would perform in foggy or rainy weather conditions. Experimental evaluation on video collections shows that the new proposed classifier achieves superior performance over existing solutions. △ Less

Submitted 29 April, 2020; originally announced April 2020.

A Digital Ecosystem for Animal Movement Science: Making animal movement datasets, data-linkage techniques, methods, and environmental layers easier to find, interpret, and analyze

Authors: Brendan Hoover, Gil Bohrer, Jerod Merkle, Jennifer A. Miller

Abstract: Movement is a fundamental aspect of animal life and plays a crucial role in determining the structure of population dynamics, communities, ecosystems, and diversity. In recent years, the recording of animal movements via GPS collars, camera traps, acoustic sensors, and citizen science, along with the abundance of environmental and other ancillary data used by researchers to contextualize those mov… ▽ More Movement is a fundamental aspect of animal life and plays a crucial role in determining the structure of population dynamics, communities, ecosystems, and diversity. In recent years, the recording of animal movements via GPS collars, camera traps, acoustic sensors, and citizen science, along with the abundance of environmental and other ancillary data used by researchers to contextualize those movements, has reached a level of volume, velocity, and variety that puts movement ecology research in the realm of big data science. That data growth has spawned increasingly complex methods for movement analysis. Consequently, animal ecologists need a greater understanding of technical skills such as statistics, geographic information systems (GIS), remote sensing, and coding. Therefore, collaboration has become increasingly crucial, as research requires both domain knowledge and technical expertise. Datasets of animal movement and environmental data are typically available in repositories run by government agencies, universities, and non-governmental organizations (NGOs) with methods described in scientific journals. However, there is little connectivity between these entities. The construction of a digital ecosystem for animal movement science is critically important right now. The digital ecosystem represents a setting where movement data, environmental layers, and analysis methods are discoverable and available for efficient storage, manipulation, and analysis. We argue that such a system which will help mature the field of movement ecology by engendering collaboration, facilitating replication, expanding the spatiotemporal range of potential analyses, and limiting redundancy in method development. We describe the key components of the digital ecosystem, the critical challenges that would need addressing, as well as potential solutions to those challenges. △ Less

Submitted 27 May, 2020; v1 submitted 13 April, 2020; originally announced April 2020.

Comments: Permission was not granted by the authors

Origin of single transverse-spin asymmetries in high-energy collisions

Authors: Justin Cammarota, Leonard Gamberg, Zhong-Bo Kang, Joshua A. Miller, Daniel Pitonyak, Alexei Prokudin, Ted C. Rogers, Nobuo Sato

Abstract: In this paper we perform the first simultaneous QCD global analysis of data from semi-inclusive deep inelastic scattering, Drell-Yan, $e^+e^-$ annihilation into hadron pairs, and proton-proton collisions. Consequently, we are able to extract a universal set of non-perturbative functions that describes the observed asymmetries in these reactions. The outcome of our analysis indicates single transve… ▽ More In this paper we perform the first simultaneous QCD global analysis of data from semi-inclusive deep inelastic scattering, Drell-Yan, $e^+e^-$ annihilation into hadron pairs, and proton-proton collisions. Consequently, we are able to extract a universal set of non-perturbative functions that describes the observed asymmetries in these reactions. The outcome of our analysis indicates single transverse-spin asymmetries in high-energy collisions have a common origin. Furthermore, we achieve the first phenomenological agreement with lattice QCD on the up and down quark tensor charges. △ Less

Submitted 2 September, 2020; v1 submitted 19 February, 2020; originally announced February 2020.

Comments: 8 pages, 6 figures, matches published version

Report number: JLAB-THY-20-3151

Journal ref: Phys. Rev. D 102, 054002 (2020)

Stack-Sorting, Set Partitions, and Lassalle's Sequence

Authors: Colin Defant, Michael Engen, Jordan A. Miller

Abstract: We exhibit a bijection between recently-introduced combinatorial objects known as valid hook configurations and certain weighted set partitions. When restricting our attention to set partitions that are matchings, we obtain three new combinatorial interpretations of Lassalle's sequence. One of these interpretations involves permutations that have exactly one preimage under the (West) stack-sorting… ▽ More We exhibit a bijection between recently-introduced combinatorial objects known as valid hook configurations and certain weighted set partitions. When restricting our attention to set partitions that are matchings, we obtain three new combinatorial interpretations of Lassalle's sequence. One of these interpretations involves permutations that have exactly one preimage under the (West) stack-sorting map. We prove that the sequences obtained by counting these permutations according to their first entries are symmetric, and we conjecture that they are log-concave. We also obtain new recurrence relations involving Lassalle's sequence and the sequence that enumerates valid hook configurations. We end with several suggestions for future work. △ Less

Submitted 30 May, 2020; v1 submitted 5 September, 2018; originally announced September 2018.

Comments: 20 pages, 11 figures

MSC Class: 05A05; 05A19; 05A18; 46L53

Journal ref: Journal of Combinatorial Theory Series A, 175 (2020)

The Foundation Supernova Survey: Motivation, Design, Implementation, and First Data Release

Authors: Ryan J. Foley, Daniel Scolnic, Armin Rest, S. W. Jha, Y. -C. Pan, A. G. Riess, P. Challis, K. C. Chambers, D. A. Coulter, K. G. Dettman, M. M. Foley, O. D. Fox, M. E. Huber, D. O. Jones, C. D. Kilpatrick, R. P. Kirshner, A. S. B. Schultz, M. R. Siebert, H. A. Flewelling, B. Gibson, E. A. Magnier, J. A. Miller, N. Primak, S. J. Smartt, K. W. Smith , et al. (3 additional authors not shown)

Abstract: The Foundation Supernova Survey aims to provide a large, high-fidelity, homogeneous, and precisely-calibrated low-redshift Type Ia supernova (SN Ia) sample for cosmology. The calibration of the current low-redshift SN sample is the largest component of systematic uncertainties for SN cosmology, and new data are necessary to make progress. We present the motivation, survey design, observation strat… ▽ More The Foundation Supernova Survey aims to provide a large, high-fidelity, homogeneous, and precisely-calibrated low-redshift Type Ia supernova (SN Ia) sample for cosmology. The calibration of the current low-redshift SN sample is the largest component of systematic uncertainties for SN cosmology, and new data are necessary to make progress. We present the motivation, survey design, observation strategy, implementation, and first results for the Foundation Supernova Survey. We are using the Pan-STARRS telescope to obtain photometry for up to 800 SNe Ia at z < 0.1. This strategy has several unique advantages: (1) the Pan-STARRS system is a superbly calibrated telescopic system, (2) Pan-STARRS has observed 3/4 of the sky in grizy making future template observations unnecessary, (3) we have a well-tested data-reduction pipeline, and (4) we have observed ~3000 high-redshift SNe Ia on this system. Here we present our initial sample of 225 SN Ia griz light curves, of which 180 pass all criteria for inclusion in a cosmological sample. The Foundation Supernova Survey already contains more cosmologically useful SNe Ia than all other published low-redshift SN Ia samples combined. We expect that the systematic uncertainties for the Foundation Supernova Sample will be 2-3 times smaller than other low-redshift samples. We find that our cosmologically useful sample has an intrinsic scatter of 0.111 mag, smaller than other low-redshift samples. We perform detailed simulations showing that simply replacing the current low-redshift SN Ia sample with an equally sized Foundation sample will improve the precision on the dark energy equation-of-state parameter by 35%, and the dark energy figure-of-merit by 72%. △ Less

Submitted 6 November, 2017; originally announced November 2017.

Comments: MNRAS, accepted; 157 pages, but 139 pages are tables; 9 figures

Mining Massive Hierarchical Data Using a Scalable Probabilistic Graphical Model

Authors: Khalifeh AlJadda, Mohammed Korayem, Camilo Ortiz, Trey Grainger, John A. Miller, Khaled Rasheed, Krys J. Kochut, William S. York, Rene Ranzinger, Melody Porterfield

Abstract: Probabilistic Graphical Models (PGM) are very useful in the fields of machine learning and data mining. The crucial limitation of those models,however, is the scalability. The Bayesian Network, which is one of the most common PGMs used in machine learning and data mining, demonstrates this limitation when the training data consists of random variables, each of them has a large set of possible valu… ▽ More Probabilistic Graphical Models (PGM) are very useful in the fields of machine learning and data mining. The crucial limitation of those models,however, is the scalability. The Bayesian Network, which is one of the most common PGMs used in machine learning and data mining, demonstrates this limitation when the training data consists of random variables, each of them has a large set of possible values. In the big data era, one would expect new extensions to the existing PGMs to handle the massive amount of data produced these days by computers, sensors and other electronic devices. With hierarchical data - data that is arranged in a treelike structure with several levels - one would expect to see hundreds of thousands or millions of values distributed over even just a small number of levels. When modeling this kind of hierarchical data across large data sets, Bayesian Networks become infeasible for representing the probability distributions. In this paper we introduce an extension to Bayesian Networks to handle massive sets of hierarchical data in a reasonable amount of time and space. The proposed model achieves perfect precision of 1.0 and high recall of 0.93 when it is used as multi-label classifier for the annotation of mass spectrometry data. On another data set of 1.5 billion search logs provided by CareerBuilder.com the model was able to predict latent semantic relationships between search keywords with accuracy up to 0.80. △ Less

Submitted 28 December, 2015; originally announced December 2015.

Comments: To be submitted to Big Data Journal. arXiv admin note: substantial text overlap with arXiv:1407.5656

GELATO and SAGE: An Integrated Framework for MS Annotation

Authors: Khalifeh AlJadda, Rene Ranzinger, Melody Porterfield, Brent Weatherly, Mohammed Korayem, John A. Miller, Khaled Rasheed, Krys J. Kochut, William S. York

Abstract: Several algorithms and tools have been developed to (semi) automate the process of glycan identification by interpreting Mass Spectrometric data. However, each has limitations when annotating MSn data with thousands of MS spectra using uncurated public databases. Moreover, the existing tools are not designed to manage MSn data where n > 2. We propose a novel software package to automate the annota… ▽ More Several algorithms and tools have been developed to (semi) automate the process of glycan identification by interpreting Mass Spectrometric data. However, each has limitations when annotating MSn data with thousands of MS spectra using uncurated public databases. Moreover, the existing tools are not designed to manage MSn data where n > 2. We propose a novel software package to automate the annotation of tandem MS data. This software consists of two major components. The first, is a free, semi-automated MSn data interpreter called the Glycomic Elucidation and Annotation Tool (GELATO). This tool extends and automates the functionality of existing open source projects, namely, GlycoWorkbench (GWB) and GlycomeDB. The second is a machine learning model called Smart Anotation Enhancement Graph (SAGE), which learns the behavior of glycoanalysts to select annotations generated by GELATO that emulate human interpretation of the spectra. △ Less

Submitted 8 January, 2016; v1 submitted 28 December, 2015; originally announced December 2015.

Comments: To be submitted to Bioinformatics journal, Oxford press

PGMHD: A Scalable Probabilistic Graphical Model for Massive Hierarchical Data Problems

Authors: Khalifeh AlJadda, Mohammed Korayem, Camilo Ortiz, Trey Grainger, John A. Miller, William S. York

Abstract: In the big data era, scalability has become a crucial requirement for any useful computational model. Probabilistic graphical models are very useful for mining and discovering data insights, but they are not scalable enough to be suitable for big data problems. Bayesian Networks particularly demonstrate this limitation when their data is represented using few random variables while each random var… ▽ More In the big data era, scalability has become a crucial requirement for any useful computational model. Probabilistic graphical models are very useful for mining and discovering data insights, but they are not scalable enough to be suitable for big data problems. Bayesian Networks particularly demonstrate this limitation when their data is represented using few random variables while each random variable has a massive set of values. With hierarchical data - data that is arranged in a treelike structure with several levels - one would expect to see hundreds of thousands or millions of values distributed over even just a small number of levels. When modeling this kind of hierarchical data across large data sets, Bayesian networks become infeasible for representing the probability distributions for the following reasons: i) Each level represents a single random variable with hundreds of thousands of values, ii) The number of levels is usually small, so there are also few random variables, and iii) The structure of the network is predefined since the dependency is modeled top-down from each parent to each of its child nodes, so the network would contain a single linear path for the random variables from each parent to each child node. In this paper we present a scalable probabilistic graphical model to overcome these limitations for massive hierarchical data. We believe the proposed model will lead to an easily-scalable, more readable, and expressive implementation for problems that require probabilistic-based solutions for massive amounts of hierarchical data. We successfully applied this model to solve two different challenging probabilistic-based problems on massive hierarchical data sets for different domains, namely, bioinformatics and latent semantic discovery over search logs. △ Less

Submitted 19 August, 2014; v1 submitted 21 July, 2014; originally announced July 2014.

Unicode in Domain-Specific Programming Languages for Modeling & Simulation: ScalaTion as a Case Study

Authors: Michael E. Cotterell, John A. Miller, Tom Horton

Abstract: As recent programming languages provide improved conciseness and flexibility of syntax, the development of embedded or internal Domain-Specific Languages has increased. The field of Modeling and Simulation has had a long history of innovation in programming languages (e.g. Simula-67, GPSS). Much effort has gone into the development of Simulation Programming Languages. The ScalaTion project is wo… ▽ More As recent programming languages provide improved conciseness and flexibility of syntax, the development of embedded or internal Domain-Specific Languages has increased. The field of Modeling and Simulation has had a long history of innovation in programming languages (e.g. Simula-67, GPSS). Much effort has gone into the development of Simulation Programming Languages. The ScalaTion project is working to develop an embedded or internal Domain-Specific Language for Modeling and Simulation which could streamline language innovation in this domain. One of its goals is to make the code concise, readable, and in a form familiar to experts in the domain. In some cases the code looks very similar to textbook formulas. To enhance readability by domain experts, a version of ScalaTion is provided that heavily utilizes Unicode. This paper discusses the development of the ScalaTion DSL and the underlying features of Scala that make this possible. It then provides an overview of ScalaTion highlighting some uses of Unicode. Statistical analysis capabilities needed for Modeling and Simulation are presented in some detail. The notation developed is clear and concise which should lead to improved usability and extendibility. △ Less

Submitted 7 December, 2011; originally announced December 2011.

Report number: Technical Report #UGA-CS-LSDIS-TR-11-011, Department of Computer Science, University of Georgia, Athens, Georgia (May 2011)

Electron Acceleration and the Production of Nonthermal Electron Distributions in Accretion Disk Coronae

Authors: Hui Li, James A. Miller

Abstract: We consider electron acceleration by obliquely propagating fast mode waves in magnetically dominated accretion disk coronae. For low coronal plasma densities, acceleration can exceed Coulomb drag at lower energies and energize electrons out of the thermal background, resulting in a nonthermal tail. The extent of this tail is determined by the balance between acceleration and radiative cooling vi… ▽ More We consider electron acceleration by obliquely propagating fast mode waves in magnetically dominated accretion disk coronae. For low coronal plasma densities, acceleration can exceed Coulomb drag at lower energies and energize electrons out of the thermal background, resulting in a nonthermal tail. The extent of this tail is determined by the balance between acceleration and radiative cooling via inverse Compton scattering and synchrotron emission, and usually goes out to tens of MeV. This will have direct applications for explaining the gamma-rays from several galactic black hole candidates, such as Cyg X-1 and GRO J0422, which show 0.5--5 MeV emissions in excess over what most thermal models predict. Detailed time evolutions of the particle distributions and wave spectra are also presented. △ Less

Submitted 15 January, 1997; originally announced January 1997.

Comments: AASLaTeX, two figures, accepted for ApJL

Stochastic Particle Acceleration near Accreting Black Holes

Authors: Charles D. Dermer, James A. Miller, Hui Li

Abstract: We consider the stochastic acceleration of particles which results from resonant interactions with plasma waves in black hole magnetospheres. We calculate acceleration rates and escape time scales for protons and electrons resonating with Alfvén waves, and for electrons resonating with whistlers. Assuming either a Kolmogorov or Kraichnan wave spectrum, accretion at the Eddington limit, magnetic… ▽ More We consider the stochastic acceleration of particles which results from resonant interactions with plasma waves in black hole magnetospheres. We calculate acceleration rates and escape time scales for protons and electrons resonating with Alfvén waves, and for electrons resonating with whistlers. Assuming either a Kolmogorov or Kraichnan wave spectrum, accretion at the Eddington limit, magnetic field strengths near equipartition, and turbulence energy densities $\sim 10\%$ of the total magnetic field energy density, we find that Alfvén waves accelerate protons to Lorentz factors $\lte 10^4$--$10^6$ before they escape from the system. Acceleration of electrons by fast mode and whistler waves can produce a nonthermal population of relativistic electons whose maximum energy is determined by a competition with radiation losses. Particle energization and outflow is not possible at lower accretion rates, magnetic field strengths, or turbulence levels due to dominant Coulomb losses. Increases in the accretion luminosity relative to the Eddington luminosity can trigger particle acceleration out of the thermal background, and this mechanism could account for the differences between radio-quiet and radio-loud active galactic nuclei. Observations of outflowing radio-emitting components following transient X-ray events in galactic X-ray novae and gamma-ray flares in blazars are in accord with this scenario. △ Less

Submitted 16 August, 1995; originally announced August 1995.

Comments: 31 pages, 8 figures, uuencoded compressed postscript file. Accepted for publication in The Astrophysical Journal (1 January 1996)

Report number: NRL 7653-15

Journal ref: Astrophys.J. 456 (1996) 106