Training Next Generation AI Users and Developers at NCSA

no code implementations • 20 Jun 2024 • Daniel S. Katz, Volodymyr Kindratenko, Olena Kindratenko, Priyam Mazumdar

This article focuses on training work carried out in artificial intelligence (AI) at the National Center for Supercomputing Applications (NCSA) at the University of Illinois Urbana-Champaign via a research experience for undergraduates (REU) program named FoDOMMaT.

Leveraging Large Language Models to Build and Execute Computational Workflows

no code implementations • 12 Dec 2023 • Alejandro Duque, Abdullah Syed, Kastan V. Day, Matthew J. Berry, Daniel S. Katz, Volodymyr V. Kindratenko

The recent development of large language models (LLMs) with multi-billion parameters, coupled with the creation of user-friendly application programming interfaces (APIs), has paved the way for automatically generating and executing code in response to straightforward human queries.

Management

FAIR AI Models in High Energy Physics

no code implementations • 9 Dec 2022 • Javier Duarte, Haoyang Li, Avik Roy, Ruike Zhu, E. A. Huerta, Daniel Diaz, Philip Harris, Raghav Kansal, Daniel S. Katz, Ishaan H. Kavoori, Volodymyr V. Kindratenko, Farouk Mokhtar, Mark S. Neubauer, Sang Eon Park, Melissa Quinnan, Roger Rusack, Zhizhen Zhao

The findable, accessible, interoperable, and reusable (FAIR) data principles provide a framework for examining, evaluating, and improving how data is shared to facilitate scientific discovery.

Graph Neural Network scientific discovery +1

FAIR for AI: An interdisciplinary and international community building perspective

no code implementations • 30 Sep 2022 • E. A. Huerta, Ben Blaiszik, L. Catherine Brinson, Kristofer E. Bouchard, Daniel Diaz, Caterina Doglioni, Javier M. Duarte, Murali Emani, Ian Foster, Geoffrey Fox, Philip Harris, Lukas Heinrich, Shantenu Jha, Daniel S. Katz, Volodymyr Kindratenko, Christine R. Kirkpatrick, Kati Lassila-Perini, Ravi K. Madduri, Mark S. Neubauer, Fotis E. Psomopoulos, Avik Roy, Oliver Rübel, Zhizhen Zhao, Ruike Zhu

A foundational set of findable, accessible, interoperable, and reusable (FAIR) principles were proposed in 2016 as prerequisites for proper data management and stewardship, with the goal of enabling the reusability of scholarly data.

Management

A FAIR and AI-ready Higgs boson decay dataset

no code implementations • 4 Aug 2021 • Yifan Chen, E. A. Huerta, Javier Duarte, Philip Harris, Daniel S. Katz, Mark S. Neubauer, Daniel Diaz, Farouk Mokhtar, Raghav Kansal, Sang Eon Park, Volodymyr V. Kindratenko, Zhizhen Zhao, Roger Rusack

To enable the reusability of massive scientific datasets by humans and machines, researchers aim to adhere to the principles of findability, accessibility, interoperability, and reusability (FAIR) for data and artificial intelligence (AI) models.

Fairness

Research Software Sustainability and Citation

no code implementations • 11 Mar 2021 • Stephan Druskat, Daniel S. Katz, Ilian T. Todorov

Software citation contributes to achieving software sustainability in two ways: It provides an impact metric to incentivize stakeholders to make software sustainable.

Software Engineering

Sustaining Research Software via Research Software Engineers and Professional Associations

no code implementations • 2 Mar 2021 • Jeffrey C. Carver, Ian A. Cosden, Chris Hill, Sandra Gesing, Daniel S. Katz

Research software is a class of software developed to support research.

Software Engineering

A Fresh Look at FAIR for Research Software

no code implementations • 26 Jan 2021 • Daniel S. Katz, Morane Gruenpeter, Tom Honeyman, Lorraine Hwang, Mark D. Wilkinson, Vanessa Sochat, Hartwig Anzt, Carole Goble, for FAIR4RS Subgroup 1

This document captures the discussion and deliberation of the FAIR for Research Software (FAIR4RS) subgroup that took a fresh look at the applicability of the FAIR Guiding Principles for scientific data management and stewardship for research software.

Software Engineering

Nine Best Practices for Research Software Registries and Repositories: A Concise Guide

2 code implementations • 24 Dec 2020 • Task Force on Best Practices for Software Registries, :, Alain Monteil, Alejandra Gonzalez-Beltran, Alexandros Ioannidis, Alice Allen, Allen Lee, Anita Bandrowski, Bruce E. Wilson, Bryce Mecum, Cai Fan Du, Carly Robinson, Daniel Garijo, Daniel S. Katz, David Long, Genevieve Milliken, Hervé Ménager, Jessica Hausman, Jurriaan H. Spaaks, Katrina Fenlon, Kristin Vanderbilt, Lorraine Hwang, Lynn Davis, Martin Fenner, Michael R. Crusoe, Michael Hucka, Mingfang Wu, Neil Chue Hong, Peter Teuben, Shelley Stall, Stephan Druskat, Ted Carnevale, Thomas Morrell

Scientific software registries and repositories serve various roles in their respective disciplines.

Digital Libraries Computers and Society

Accelerated, Scalable and Reproducible AI-driven Gravitational Wave Detection

no code implementations • 15 Dec 2020 • E. A. Huerta, Asad Khan, Xiaobo Huang, Minyang Tian, Maksim Levental, Ryan Chard, Wei Wei, Maeve Heflin, Daniel S. Katz, Volodymyr Kindratenko, Dawei Mu, Ben Blaiszik, Ian Foster

The development of reusable artificial intelligence (AI) models for wider use and rigorous validation by the community promises to unlock new opportunities in multi-messenger astrophysics.

Distributed Computing Gravitational Wave Detection

Convergence of Artificial Intelligence and High Performance Computing on NSF-supported Cyberinfrastructure

no code implementations • 18 Mar 2020 • E. A. Huerta, Asad Khan, Edward Davis, Colleen Bushell, William D. Gropp, Daniel S. Katz, Volodymyr Kindratenko, Seid Koric, William T. C. Kramer, Brendan McGinty, Kenton McHenry, Aaron Saxton

Significant investments to upgrade and construct large-scale scientific facilities demand commensurate investments in R&D to design algorithms and computing approaches to enable scientific and engineering breakthroughs in the big data era.

Enabling real-time multi-messenger astrophysics discoveries with deep learning

no code implementations • 26 Nov 2019 • E. A. Huerta, Gabrielle Allen, Igor Andreoni, Javier M. Antelis, Etienne Bachelet, Bruce Berriman, Federica Bianco, Rahul Biswas, Matias Carrasco, Kyle Chard, Minsik Cho, Philip S. Cowperthwaite, Zachariah B. Etienne, Maya Fishbach, Francisco Förster, Daniel George, Tom Gibbs, Matthew Graham, William Gropp, Robert Gruendl, Anushri Gupta, Roland Haas, Sarah Habib, Elise Jennings, Margaret W. G. Johnson, Erik Katsavounidis, Daniel S. Katz, Asad Khan, Volodymyr Kindratenko, William T. C. Kramer, Xin Liu, Ashish Mahabal, Zsuzsa Marka, Kenton McHenry, Jonah Miller, Claudia Moreno, Mark Neubauer, Steve Oberlin, Alexander R. Olivas, Donald Petravick, Adam Rebei, Shawn Rosofsky, Milton Ruiz, Aaron Saxton, Bernard F. Schutz, Alex Schwing, Ed Seidel, Stuart L. Shapiro, Hongyu Shen, Yue Shen, Leo Singer, Brigitta M. Sipőcz, Lunan Sun, John Towns, Antonios Tsokaros, Wei Wei, Jack Wells, Timothy J. Williams, JinJun Xiong, Zhizhen Zhao

Multi-messenger astrophysics is a fast-growing, interdisciplinary field that combines data, which vary in volume and speed of data processing, from many different instruments that probe the Universe using different cosmic messengers: electromagnetic waves, cosmic rays, gravitational waves and neutrinos.

BIG-bench Machine Learning Deep Learning +2

Deep Learning for Multi-Messenger Astrophysics: A Gateway for Discovery in the Big Data Era

no code implementations • 1 Feb 2019 • Gabrielle Allen, Igor Andreoni, Etienne Bachelet, G. Bruce Berriman, Federica B. Bianco, Rahul Biswas, Matias Carrasco Kind, Kyle Chard, Minsik Cho, Philip S. Cowperthwaite, Zachariah B. Etienne, Daniel George, Tom Gibbs, Matthew Graham, William Gropp, Anushri Gupta, Roland Haas, E. A. Huerta, Elise Jennings, Daniel S. Katz, Asad Khan, Volodymyr Kindratenko, William T. C. Kramer, Xin Liu, Ashish Mahabal, Kenton McHenry, J. M. Miller, M. S. Neubauer, Steve Oberlin, Alexander R. Olivas Jr, Shawn Rosofsky, Milton Ruiz, Aaron Saxton, Bernard Schutz, Alex Schwing, Ed Seidel, Stuart L. Shapiro, Hongyu Shen, Yue Shen, Brigitta M. Sipőcz, Lunan Sun, John Towns, Antonios Tsokaros, Wei Wei, Jack Wells, Timothy J. Williams, JinJun Xiong, Zhizhen Zhao

We discuss key aspects to realize this endeavor, namely (i) the design and exploitation of scalable and computationally efficient AI algorithms for Multi-Messenger Astrophysics; (ii) cyberinfrastructure requirements to numerically simulate astrophysical sources, and to process and interpret Multi-Messenger Astrophysics data; (iii) management of gravitational wave detections and triggers to enable electromagnetic and astro-particle follow-ups; (iv) a vision to harness future developments of machine and deep learning and cyberinfrastructure resources to cope with the scale of discovery in the Big Data Era; (v) and the need to build a community that brings domain experts together with data scientists on equal footing to maximize and accelerate discovery in the nascent field of Multi-Messenger Astrophysics.

Astronomy Management +1

Building a Sustainable Structure for Research Software Engineering Activities

1 code implementation • 11 Jul 2018 • Jeremy Cohen, Daniel S. Katz, Michelle Barker, Robert Haines, Neil Chue Hong

The profile of research software engineering has been greatly enhanced by developments at institutions around the world to form groups and communities that can support effective, sustainable development of research software.

Software Engineering

BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

1 code implementation • 11 Jan 2018 • Maria Luiza Mondelli, Thiago Magalhães, Guilherme Loss, Michael Wilde, Ian Foster, Marta Mattoso, Daniel S. Katz, Helio J. C. Barbosa, Ana Tereza R. Vasconcelos, Kary Ocaña, Luiz M. R. Gadelha Jr

This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application.

Distributed, Parallel, and Cluster Computing Databases

A Roadmap for HEP Software and Computing R&D for the 2020s

1 code implementation • 18 Dec 2017 • Johannes Albrecht, Antonio Augusto Alves Jr, Guilherme Amadio, Giuseppe Andronico, Nguyen Anh-Ky, Laurent Aphecetche, John Apostolakis, Makoto Asai, Luca Atzori, Marian Babik, Giuseppe Bagliesi, Marilena Bandieramonte, Sunanda Banerjee, Martin Barisits, Lothar A. T. Bauerdick, Stefano Belforte, Douglas Benjamin, Catrin Bernius, Wahid Bhimji, Riccardo Maria Bianchi, Ian Bird, Catherine Biscarat, Jakob Blomer, Kenneth Bloom, Tommaso Boccali, Brian Bockelman, Tomasz Bold, Daniele Bonacorsi, Antonio Boveia, Concezio Bozzi, Marko Bracko, David Britton, Andy Buckley, Predrag Buncic, Paolo Calafiura, Simone Campana, Philippe Canal, Luca Canali, Gianpaolo Carlino, Nuno Castro, Marco Cattaneo, Gianluca Cerminara, Javier Cervantes Villanueva, Philip Chang, John Chapman, Gang Chen, Taylor Childers, Peter Clarke, Marco Clemencic, Eric Cogneras, Jeremy Coles, Ian Collier, David Colling, Gloria Corti, Gabriele Cosmo, Davide Costanzo, Ben Couturier, Kyle Cranmer, Jack Cranshaw, Leonardo Cristella, David Crooks, Sabine Crépé-Renaudin, Robert Currie, Sünje Dallmeier-Tiessen, Kaushik De, Michel De Cian, Albert De Roeck, Antonio Delgado Peris, Frédéric Derue, Alessandro Di Girolamo, Salvatore Di Guida, Gancho Dimitrov, Caterina Doglioni, Andrea Dotti, Dirk Duellmann, Laurent Duflot, Dave Dykstra, Katarzyna Dziedziniewicz-Wojcik, Agnieszka Dziurda, Ulrik Egede, Peter Elmer, Johannes Elmsheuser, V. Daniel Elvira, Giulio Eulisse, Steven Farrell, Torben Ferber, Andrej Filipcic, Ian Fisk, Conor Fitzpatrick, José Flix, Andrea Formica, Alessandra Forti, Giovanni Franzoni, James Frost, Stu Fuess, Frank Gaede, Gerardo Ganis, Robert Gardner, Vincent Garonne, Andreas Gellrich, Krzysztof Genser, Simon George, Frank Geurts, Andrei Gheata, Mihaela Gheata, Francesco Giacomini, Stefano Giagu, Manuel Giffels, Douglas Gingrich, Maria Girone, Vladimir V. Gligorov, Ivan Glushkov, Wesley Gohn, Jose Benito Gonzalez Lopez, Isidro González Caballero, Juan R. González Fernández, Giacomo Govi, Claudio Grandi, Hadrien Grasland, Heather Gray, Lucia Grillo, Wen Guan, Oliver Gutsche, Vardan Gyurjyan, Andrew Hanushevsky, Farah Hariri, Thomas Hartmann, John Harvey, Thomas Hauth, Benedikt Hegner, Beate Heinemann, Lukas Heinrich, Andreas Heiss, José M. Hernández, Michael Hildreth, Mark Hodgkinson, Stefan Hoeche, Burt Holzman, Peter Hristov, Xingtao Huang, Vladimir N. Ivanchenko, Todor Ivanov, Jan Iven, Brij Jashal, Bodhitha Jayatilaka, Roger Jones, Michel Jouvin, Soon Yung Jun, Michael Kagan, Charles William Kalderon, Meghan Kane, Edward Karavakis, Daniel S. Katz, Dorian Kcira, Oliver Keeble, Borut Paul Kersevan, Michael Kirby, Alexei Klimentov, Markus Klute, Ilya Komarov, Dmitri Konstantinov, Patrick Koppenburg, Jim Kowalkowski, Luke Kreczko, Thomas Kuhr, Robert Kutschke, Valentin Kuznetsov, Walter Lampl, Eric Lancon, David Lange, Mario Lassnig, Paul Laycock, Charles Leggett, James Letts, Birgit Lewendel, Teng Li, Guilherme Lima, Jacob Linacre, Tomas Linden, Miron Livny, Giuseppe Lo Presti, Sebastian Lopienski, Peter Love, Adam Lyon, Nicolò Magini, Zachary L. Marshall, Edoardo Martelli, Stewart Martin-Haugh, Pere Mato, Kajari Mazumdar, Thomas McCauley, Josh McFayden, Shawn McKee, Andrew McNab, Rashid Mehdiyev, Helge Meinhard, Dario Menasce, Patricia Mendez Lorenzo, Alaettin Serhan Mete, Michele Michelotto, Jovan Mitrevski, Lorenzo Moneta, Ben Morgan, Richard Mount, Edward Moyse, Sean Murray, Armin Nairz, Mark S. Neubauer, Andrew Norman, Sérgio Novaes, Mihaly Novak, Arantza Oyanguren, Nurcan Ozturk, Andres Pacheco Pages, Michela Paganini, Jerome Pansanel, Vincent R. Pascuzzi, Glenn Patrick, Alex Pearce, Ben Pearson, Kevin Pedro, Gabriel Perdue, Antonio Perez-Calero Yzquierdo, Luca Perrozzi, Troels Petersen, Marko Petric, Andreas Petzold, Jónatan Piedra, Leo Piilonen, Danilo Piparo, Jim Pivarski, Witold Pokorski, Francesco Polci, Karolos Potamianos, Fernanda Psihas, Albert Puig Navarro, Günter Quast, Gerhard Raven, Jürgen Reuter, Alberto Ribon, Lorenzo Rinaldi, Martin Ritter, James Robinson, Eduardo Rodrigues, Stefan Roiser, David Rousseau, Gareth Roy, Grigori Rybkine, Andre Sailer, Tai Sakuma, Renato Santana, Andrea Sartirana, Heidi Schellman, Jaroslava Schovancová, Steven Schramm, Markus Schulz, Andrea Sciabà, Sally Seidel, Sezen Sekmen, Cedric Serfon, Horst Severini, Elizabeth Sexton-Kennedy, Michael Seymour, Davide Sgalaberna, Illya Shapoval, Jamie Shiers, Jing-Ge Shiu, Hannah Short, Gian Piero Siroli, Sam Skipsey, Tim Smith, Scott Snyder, Michael D. Sokoloff, Panagiotis Spentzouris, Hartmut Stadie, Giordon Stark, Gordon Stewart, Graeme A. Stewart, Arturo Sánchez, Alberto Sánchez-Hernández, Anyes Taffard, Umberto Tamponi, Jeff Templon, Giacomo Tenaglia, Vakhtang Tsulaia, Christopher Tunnell, Eric Vaandering, Andrea Valassi, Sofia Vallecorsa, Liviu Valsan, Peter Van Gemmeren, Renaud Vernet, Brett Viren, Jean-Roch Vlimant, Christian Voss, Margaret Votava, Carl Vuosalo, Carlos Vázquez Sierra, Romain Wartel, Gordon T. Watts, Torre Wenaus, Sandro Wenzel, Mike Williams, Frank Winklmeier, Christoph Wissing, Frank Wuerthwein, Benjamin Wynne, Zhang Xiaomei, Wei Yang, Efe Yazgan

Particle physics has an ambitious and broad experimental programme for the coming decades.

Computational Physics High Energy Physics - Experiment

Journal of Open Source Software (JOSS): design and first-year review

1 code implementation • 7 Jul 2017 • Arfon M. Smith, Kyle E. Niemeyer, Daniel S. Katz, Lorena A. Barba, George Githinji, Melissa Gymrek, Kathryn D Huff, Christopher R. Madan, Abigail Cabunoc Mayes, Kevin M Moerman, Pjotr Prins, Karthik Ram, Ariel Rokem, Tracy K. Teal, Roman Valls Guimera, Jacob T. VanderPlas

JOSS is a free and open-access journal that publishes articles describing research software.

Digital Libraries Software Engineering

Implementing Transitive Credit with JSON-LD

no code implementations • 18 Jul 2014 • Daniel S. Katz, Arfon M. Smith

Science and engineering research increasingly relies on activities that facilitate research but are not currently rewarded or recognized, such as: data sharing; developing common data resources, software and methodologies; and annotating data and publications.

Computers and Society Digital Libraries