arXiv subjects

Brian Thomas

Publications and source records attributed to Brian Thomas.

At least 19 recordsLinked to original sources

arXiv2026

HDRL Staff Strategy Meeting Report

HDRL held its first HDRL wide strategy meeting in January 2026, pulling in a majority of HDRL member staff and selected HDRL grantees. Just over 40 people attended with a few more online to listen to over 30 lightning talks presented by their colleagues and leaders, participate in several breakout and group discussions, and cast 324 votes on over 50 strategic topic ideas contributed by the attendees. The many ideas generated by attendees can be grouped into seven themes which describe the overall breadth of discussion at the meeting. These themes included: Metadata, Standards, and Semantics Discovery, Search, and Recommendation Modernizing HDRL User experience Modernizing HDRL Staff experience Modernized, Scalable, and Dependable Infrastructure for Compute and Storage Metrics and Impact Assessment Community Engagement and Sustainability Considering the gathered information and the interconnections between the prioritized ideas we concluded that several strategic areas for action exist. This document provides an overview of contributed materials and post meeting strategic analysis.

astro-ph.IM↗

arXiv2024

Determining Research Priorities Using Machine Learning

We summarize our exploratory investigation into whether Machine Learning (ML) techniques applied to publicly available professional text can substantially augment strategic planning for astronomy. We find that an approach based on Latent Dirichlet Allocation (LDA) using content drawn from astronomy journal papers can be used to infer high-priority research areas. While the LDA models are challenging to interpret, we find that they may be strongly associated with meaningful keywords and scientific papers which allow for human interpretation of the topic models. Significant correlation is found between the results of applying these models to the previous decade of astronomical research ("1998-2010" corpus) and the contents of the science frontier panel report which contains high-priority research areas identified by the 2010 National Academies' Astronomy and Astrophysics Decadal Survey ("DS2010" corpus). Significant correlations also exist between model results of the 1998-2010 corpus and the submitted whitepapers to the Decadal Survey ("whitepapers" corpus). Importantly, we derive predictive metrics based on these results which can provide leading indicators of which content modeled by the topic models will become highly cited in the future. Using these identified metrics and the associations between papers and topic models it is possible to identify important papers for planners to consider. A preliminary version of our work was presented by Thronson etal. 2021 and Thomas etal. 2022.

cs.DL↗

arXiv2022

Determining Research Priorities for Astronomy Using Machine Learning

We summarize the first exploratory investigation into whether Machine Learning techniques can augment science strategic planning. We find that an approach based on Latent Dirichlet Allocation using abstracts drawn from high impact astronomy journals may provide a leading indicator of future interest in a research topic. We show two topic metrics that correlate well with the high-priority research areas identified by the 2010 National Academies' Astronomy and Astrophysics Decadal Survey science frontier panels. One metric is based on a sum of the fractional contribution to each topic by all scientific papers ("counts") while the other is the Compound Annual Growth Rate of these counts. These same metrics also show the same degree of correlation with the whitepapers submitted to the same Decadal Survey. Our results suggest that the Decadal Survey may under-emphasize fast growing research. A preliminary version of our work was presented by Thronson et al. 2021.

astro-ph.IM↗

arXiv2019

Using Artificial Intelligence to Augment Science Prioritization for Astro2020

Science funding agencies (NASA, DOE, and NSF), the science community, and the US taxpayer have all benefited enormously from the several-decade series of National Academies Decadal Surveys. These Surveys are one of the primary means whereby these agencies may align multi-year strategic priorities and funding to guide the scientific community. They comprise highly regarded subject matter experts whose goal is to develop a set of science and program priorities that are recommended for major investments in the subsequent 10+ years. They do this using both their own professional knowledge and by synthesizing details from many thousands of existing and solicited documents. Congress, the relevant funding agencies, and the scientific community have placed great respect and value on these recommendations. Consequently, any significant changes to the process of determining these recommendations should be scrutinized carefully. That said, we believe that there is currently sufficient justification for the National Academies to consider some changes. We advocate that they supplement the established survey process with predictions of promising science priorities identified by application of current Artificial Intelligence (AI) techniques These techniques are being applied elsewhere in long-range planning and prioritization. We present a proposal to apply AI to aid the Decadal Survey panel in prioritizing science objectives. We emphasize that while AI can assist a mass review of papers, the decision-making remains with humans. In our paper below we summarize the case for using AI in this manner and suggest small inexpensive demonstration trials, including an AI/ML assessment of the white papers submitted to Astro2020 and backcasting to evaluate AI in making predictions for the 2010 Decadal Survey.

astro-ph.IM↗

arXiv2018

The $P_2^1$ Margolis homology of connective topological modular forms

The element $P_2^1$ of the mod 2 Steenrod algebra has the property $(P_2^1)^2=0$. This property allows one to view $P_2^1$ as a differential on $H_*(X, \mathbb{F}_2)$ for any spectrum $X$. Homology with respect to this differential, $\mathcal{M}(X, P_2^1)$, is called the $P_2^1$ Margolis homology of $X$. In this paper we give a complete calculation of the $P_2^1$ Margolis homology of the 2-local spectrum of topological modular forms $tmf$ and identify its $\mathbb{F}_2$ basis via an iterated algorithm. We apply the same techniques to calculate $P_2^1$ Margolis homology for any smash power of $tmf$.

math.AT↗

arXiv2017

Hadwiger's conjecture for graphs with forbidden holes

Given a graph $G$, the Hadwiger number of $G$, denoted by $h(G)$, is the largest integer $k$ such that $G$ contains the complete graph $K_k$ as a minor. A hole in $G$ is an induced cycle of length at least four. Hadwiger's Conjecture from 1943 states that for every graph $G$, $h(G)\ge χ(G)$, where $χ(G)$ denotes the chromatic number of $G$. In this paper we establish more evidence for Hadwiger's conjecture by showing that if a graph $G$ with independence number $α(G)\ge3$ has no hole of length between $4$ and $2α(G)-1$, then $h(G)\geχ(G)$. We also prove that if a graph $G$ with independence number $α(G)\ge2$ has no hole of length between $4$ and $2α(G)$, then $G$ contains an odd clique minor of size $χ(G)$, that is, such a graph $G$ satisfies the odd Hadwiger's conjecture.

math.CO↗

arXiv2015

A User Interface for Semantically Oriented Data Mining of Astronomy Repositories

We present a user-friendly, but powerful interface for the data mining of scientific repositories. We present the tool in use with actual astronomy data and show how it may be used to achieve many different types of powerful semantic queries. The tool itself hides the gory details of query formulation, and data retrieval from the user, and allows the user to create workflows which may be used to transform the data into a convenient form.

astro-ph.IM↗

arXiv2015

Knowledge Discovery Framework for the Virtual Observatory

We describe a framework that allows a scientist-user to easily query for information across all Virtual Observatory (VO) repositories and pull it back for analysis. This framework hides the gory details of meta-data remediation and data formatting from the user, allowing them to get on with search, retrieval and analysis of VO data as if they were drawn from a single source using a science based terminology rather than a data-centric one.

astro-ph.IM↗

arXiv2015

Significant problems in FITS limit its use in modern astronomical research

The Flexible Image Transport System (FITS) standard has been a great boon to astronomy, allowing observatories, scientists and the public to exchange astronomical information easily. The FITS standard is, however, showing its age. Developed in the late 1970s the FITS authors made a number of implementation choices for the format that, while common at the time, are now seen to limit its utility with modern data. The authors of the FITS standard could not appreciate the challenges which we would be facing today in astronomical computing. Difficulties we now face include, but are not limited to, having to address the need to handle an expanded range of specialized data product types (data models), being more conducive to the networked exchange and storage of data, handling very large datasets and the need to capture significantly more complex metadata and data relationships. There are members of the community today who find some (or all) of these limitations unworkable, and have decided to move ahead with storing data in other formats. This reaction should be taken as a wakeup call to the FITS community to make changes in the FITS standard, or to see its usage fall. In this paper we detail some selected important problems which exist within the FITS standard today. It is not our intention to prescribe specific remedies to these issues; rather, we hope to call attention of the FITS and greater astronomical computing communities to these issues in the hopes that it will spur action to address them.

astro-ph.IM↗

arXiv2015

Development of a VO Registry Subject Ontology using Automated Methods

We report on our initial work to automate the generation of a domain ontology using subject fields of resources held in the Virtual Observatory registry. Preliminary results are comparable to more generalized ontology learning software currently in use. We expect to be able to refine our solution to improve both the depth and breadth of the generated ontology.

astro-ph.IM↗

arXiv2015

Learning from FITS: Limitations in use in modern astronomical research

The Flexible Image Transport System (FITS) standard has been a great boon to astronomy, allowing observatories, scientists and the public to exchange astronomical information easily. The FITS standard, however, is showing its age. Developed in the late 1970s, the FITS authors made a number of implementation choices that, while common at the time, are now seen to limit its utility with modern data. The authors of the FITS standard could not anticipate the challenges which we are facing today in astronomical computing. Difficulties we now face include, but are not limited to, addressing the need to handle an expanded range of specialized data product types (data models), being more conducive to the networked exchange and storage of data, handling very large datasets, and capturing significantly more complex metadata and data relationships. There are members of the community today who find some or all of these limitations unworkable, and have decided to move ahead with storing data in other formats. If this fragmentation continues, we risk abandoning the advantages of broad interoperability, and ready archivability, that the FITS format provides for astronomy. In this paper we detail some selected important problems which exist within the FITS standard today. These problems may provide insight into deeper underlying issues which reside in the format and we provide a discussion of some lessons learned. It is not our intention here to prescribe specific remedies to these issues; rather, it is to call attention of the FITS and greater astronomical computing communities to these problems in the hope that it will spur action to address them.

astro-ph.IM↗

arXiv2014

The Past, Present and Future of Astronomical Data Formats

The future of astronomy is inextricably entwined with the care and feeding of astronomical data products. Community standards such as FITS and NDF have been instrumental in the success of numerous astronomy projects. Their very success challenges us to entertain pragmatic strategies to adapt and evolve the standards to meet the aggressive data-handling requirements of facilities now being designed and built. We discuss characteristics that have made standards successful in the past, as well as desirable features for the future, and an open discussion follows.

astro-ph.IM↗

arXiv2014

Iris: an Extensible Application for Building and Analyzing Spectral Energy Distributions

Iris is an extensible application that provides astronomers with a user-friendly interface capable of ingesting broad-band data from many different sources in order to build, explore, and model spectral energy distributions (SEDs). Iris takes advantage of the standards defined by the International Virtual Observatory Alliance, but hides the technicalities of such standards by implementing different layers of abstraction on top of them. Such intermediate layers provide hooks that users and developers can exploit in order to extend the capabilities provided by Iris. For instance, custom Python models can be combined in arbitrary ways with the Iris built-in models or with other custom functions. As such, Iris offers a platform for the development and integration of SED data, services, and applications, either from the user's system or from the web. In this paper we describe the built-in features provided by Iris for building and analyzing SEDs. We also explore in some detail the Iris framework and software development kit, showing how astronomers and software developers can plug their code into an integrated SED analysis environment.

astro-ph.IM↗

arXiv2013

Starch metabolism and antiflorigenic signals modulate the juvenile-to-adult phase transition in Arabidopsis

The physiology and genetics underlying juvenility is poorly understood. Here we exploit Arabidopsis as a system to understand the mechanisms that regulate floral incompetence during juvenility. Using an experimental assay that allows the length of juvenility to be estimated, and mutants impaired in different pathways, we show that multiple inputs influence juvenility. Juvenile phase lengths of wild type (WT) accessions Col-0, Ler-0 and Ws-4 are shown to differ, with Col-0 having the shortest and Ws-4 the longest length. Plants defective in sugar signalling [gin1-1, gin2-1, gin6 (abi4)] and floral repressor mutants [hst1, tfl1, tfl2 (lhp1)] showed shortened juvenile phase lengths, compared to their respective WTs. Mutants defective in starch anabolism (adg1-1, pgm1) and catabolism (sex1, sex4, bam3) showed prolonged juvenile phase lengths compared to Col-0. Examination of diurnal metabolite changes in adg1-1 and sex1 mutants indicates that their altered juvenile phase length may be due to lack of starch turnover, which influences carbohydrate availability. In this article we propose a model in which a variety of signals including floral activators and repressors modulate the juvenile-to-adult phase transition. The role of carbohydrates may be in their capacity as nutrients, osmotic regulators, signalling molecules and/ or through their interaction with phytohormonal networks.

q-bio.BM↗

arXiv2012

Managing Distributed Software Development in the Virtual Astronomical Observatory

The U.S. Virtual Astronomical Observatory (VAO) is a product-driven organization that provides new scientific research capabilities to the astronomical community. Software development for the VAO follows a lightweight framework that guides development of science applications and infrastructure. Challenges to be overcome include distributed development teams, part-time efforts, and highly constrained schedules. We describe the process we followed to conquer these challenges while developing Iris, the VAO application for analysis of 1-D astronomical spectral energy distributions (SEDs). Iris was successfully built and released in less than a year with a team distributed across four institutions. The project followed existing International Virtual Observatory Alliance inter-operability standards for spectral data and contributed a SED library as a by-product of the project. We emphasize lessons learned that will be folded into future development efforts. In our experience, a well-defined process that provides guidelines to ensure the project is cohesive and stays on track is key to success. Internal product deliveries with a planned test and feedback loop are critical. Release candidates are measured against use cases established early in the process, and provide the opportunity to assess priorities and make course corrections during development. Also key is the participation of a stakeholder such as a lead scientist who manages the technical questions, advises on priorities, and is actively involved as a lead tester. Finally, frequent scheduled communications (for example a bi-weekly tele-conference) assure issues are resolved quickly and the team is working toward a common vision

astro-ph.IM↗

arXiv2011

IVOA Recommendation: Vocabularies in the Virtual Observatory Version 1.19

This document specifies a standard format for vocabularies based on the W3C's Resource Description Framework (RDF) and Simple Knowledge Organization System (SKOS). By adopting a standard and simple format, the IVOA will permit different groups to create and maintain their own specialised vocabularies while letting the rest of the astronomical community access, use, and combine them. The use of current, open standards ensures that VO applications will be able to tap into resources of the growing semantic web. The document provides several examples of useful astronomical vocabularies.

astro-ph.IM↗

arXiv2011

Ultra-Broadband Coherent Supercontinuum Frequency Comb

We present detailed studies of the coherence properties of an ultra-broadband super-continuum, enabled by a new approach involving continuous wave laser sources to independently probe both the amplitude and phase noise quadratures across the entire spectrum. The continuum coherently spans more than 1.5 octaves, supporting Hz-level comparison of ultrastable lasers at 698 nm and 1.54 μm. We present the first numerical simulation of the accumulated comb coherence in the limit of many pulses, in contrast to the single-pulse level, with systematic experimental verification. The experiment and numerical simulations reveal the presence of quantum-seeded broadband amplitude noise without phase coherence degradation, including the discovery of a dependence of the super-continuum coherence on the fiber fractional Raman gain.

physics.optics↗

arXiv2007

Modeling atmospheric effects of the September 1859 Solar Flare

We have modeled atmospheric effects, especially ozone depletion, due to a solar proton event which probably accompanied the extreme magnetic storm of 1-2 September 1859. We use an inferred proton fluence for this event as estimated from nitrate levels in Greenland ice cores. We present results showing production of odd nitrogen compounds and their impact on ozone. We also compute rainout of nitrate in our model and compare to values from ice core data.

astro-ph↗