Publications
Scientific Papers, Journals, Presentations, Posters, and Technical Reports
2024
- Callaghan, S., Maechling, P. J., Silva, F., Su, M.-H., Milner, K. R., Graves, R. W., Olsen, K. B., Cui, Y., Vahi, K., Kottke, A., Goulet, C. A., Deelman, E., Jordan, T. H., & Ben-Zion, Y. (2024). Corrigendum: Using open-science workflow tools to produce SCEC CyberShake physics-based probabilistic seismic hazard models. Frontiers in High Performance Computing, 2. https://doi.org/10.3389/fhpcp.2024.1497384
[BibTex] - Catalfamo, A., Aral, A., Brandic, I., Deelman, E., & Villari, M. (2024). Machine Learning Workflows in the Computing Continuum for Environmental Monitoring. Computational Science – ICCS 2024: 24th International Conference, Malaga, Spain, July 2–4, 2024, Proceedings, Part V, 368–382. https://doi.org/10.1007/978-3-031-63775-9_27
[BibTex] - Cranganore, S. S., De Maio, V., Brandic, I., & Deelman, E. (2024). Paving the way to hybrid quantum–classical scientific workflows. Future Generation Computer Systems, 158, 346–366. https://doi.org/https://doi.org/10.1016/j.future.2024.04.030 (Funding Acknowledgments: NSF 2331153)
[BibTex] - Hasan, M., Kee, K. F., Okunloye, O., & Deelman, E. (2024). Decision Strategies during a Science Crisis: How Science Organizations Made Adaptations during the Pandemic. https://wearecrisiscomm.com/2024-icrcc-proceedings/enzc7642/
[BibTex] - Jin, H., Papadimitriou, G., Raghavan, K., Zuk, P., Balaprakash, P., Wang, C., Mandal, A., & Deelman, E. (2024). Large Language Models for Anomaly Detection in Computational Workflows: from Supervised Fine-Tuning to In-Context Learning. https://arxiv.org/abs/2407.17545
[BibTex] - Poczekajlo, P., Moroz, L., Deelman, E., & Gepner, P. (2024). Modified CORDIC Algorithm for Givens Rotator. In L. Franco, C. de Mulatier, M. Paszynski, V. V. Krzhizhanovskaya, J. J. Dongarra, & P. M. A. Sloot (Eds.), Computational Science – ICCS 2024 (pp. 101–114). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-63778-0_8
[BibTex] - Raghavan, K., Papadimitriou, G., Jin, H., Mandal, A., Kiran, M., Balaprakash, P., & Deelman, E. (2024). Advancing Anomaly Detection in Computational Workflows with Active Learning. https://arxiv.org/abs/2405.06133
[BibTex] - Roa, C., Rynge, M., Olaya, P., Vahi, K., Miller, T., Griffioen, J., Knuth, S., Goodhue, J., Hudak, D., Romanella, A., Llamas, R., Vargas, R., Livny, M., Deelman, E., & Taufer, M. (2024). End-to-end Integration of Scientific Workflows on Distributed Cyberinfrastructures: Challenges and Lessons Learned with an Earth Science Application. Proceedings of the IEEE/ACM 16th International Conference on Utility and Cloud Computing. https://doi.org/10.1145/3603166.3632142 (Funding Acknowledgments: NSF 1664162, 1841758, 2028923, 2103845, 2103836, 2138811, 2223704, 2330582, 2331152, 2334945, 2138286)
[BibTex] - Safri, H., Papadimitriou, G., & Deelman, E. (2024). Dynamic Tracking, MLOps, and Workflow Integration: Enabling Transparent Reproducibility in Machine Learning. 2024 IEEE 20th International Conference on e-Science (e-Science), 1–10. https://doi.org/10.1109/e-Science62913.2024.10678658
[BibTex] - Safri, H., Papadimitriou, G., Desprez, F., & Deelman, E. (2024). A Workflow Management System Approach To Federated Learning: Application to Industry 4.0. 2024 20th International Conference on Distributed Computing in Smart Systems and the Internet of Things (DCOSS-IoT). https://doi.org/https://doi.org/10.1109/DCOSS-IoT61029.2024.00047 (Funding Acknowledgments: DE-SC0022328 and NSF 2138286, 2106147)
[BibTex] - Seidel, E., Randles, A., Arthur, R., Bergman, K., Carlson, B., Deelman, E., Grout, R., Hendrickson, B., & Reed, D. (2024). 2024 Advanced Scientific Computing Advisory Committee (ASCR): Facilities Subcommittee Recommendations. https://doi.org/10.2172/2370379
[BibTex] - Wyrzykowski, R., & Deelman, E. (2024). Guest Editor’s note: Special issue on challenges and solutions for porting applications to next-generation high performance computing systems. The International Journal of High Performance Computing Applications, 38(1), 3–4. https://doi.org/10.1177/10943420231224509
[BibTex]
2023
- Afle, C., Miles, P. R., Caino-Lores, S., Capano, C. D., Tews, I., Vahi, K., Deelman, E., Taufer, M., & Brown, D. A. (2023). Reproducing the results for NICER observation of PSR J0030+0451. (Funding Acknowledgments: NSF 2207264, 2041977, 2041901, 2028923, 2028930, 1841399, and 1941443; DOE DE-AC52-06NA25396 )
[BibTex] - Caino-Lores, S., Cuendet, M., Marquez, J., Kots, E., Estrada, T., Deelman, E., Weinstein, H., & Taufer, M. (2023). Runtime Steering of Molecular Dynamics Simulations Through In Situ Analysis and Annotation of Collective Variables. Proceedings of the Platform for Advanced Scientific Computing Conference. https://doi.org/10.1145/3592979.3593420 (Funding Acknowledgments: NSF 1741057, 1841758, 2138811 and 2223704)
[BibTex] - Caino-Lores, S., Cuendet, M., Marquez, J., Kots, E., Estrada, T., Deelman, E., Weinstein, H., & Taufer, M. (2023). Runtime Steering of Molecular Dynamics Simulations Through In Situ Analysis and Annotation of Collective Variables. Proceedings of the Platform for Advanced Scientific Computing Conference. https://doi.org/10.1145/3592979.3593420 (Funding Acknowledgments: NSF 1741057, 1841758, 2138811, 2223704; ORLCF CSC427; XSEDE TG-CIS200053; IBM Shared University Research Award)
[BibTex] - Deelman, E. (2023). How is Artificial Intelligence Changing Science? 2023 IEEE 19th International Conference on e-Science (e-Science), 1–4. https://doi.org/10.1109/e-Science58273.2023.10254913 (Funding Acknowledgments: DOE DE-SC0022328 and NSF 1664162, 2138286)
[BibTex] - Dongarra, J., Deelman, E., Hey, T., Matsuoka, S., Sarakar, V., Bell, G., Foster, I., Keyes, D., & Kranzlmueller, D. et-al. (2023). Can the United States Maintain Its Leadership in High-Performance Computing?-A report from the ASCAC Subcommittee on American Competitiveness and Innovation to the ASCR Office. OSTI. https://doi.org/10.2172/1989107
[BibTex] - Esquivel Morel, A., Calyam, P., Qu, C., Gafurov, D., Wang, C., Thareja, K., Mandal, A., Lyons, E., Zink, M., Papadimitriou, G., & Deelman, E. (2023). Network Services Management using Programmable Data Planes for Visual Cloud Computing. 2023 International Conference on Computing, Networking and Communications (ICNC), 130–136. https://doi.org/10.1109/ICNC57223.2023.10074183 (Funding Acknowledgments: NSF 1950873, 2018074)
[BibTex] - Gesing, S., Deelman, E., Hildreth, M., Makhija, R., McDowell, M. A., Meyers, N. K., & Thain, D. (2023). VisDict: Improving Communication Via a Visual Dictionary in a Science Gateway. Computing in Science & Engineering, 25(2), 7–11. https://doi.org/10.1109/MCSE.2023.3275711 (Funding Acknowledgments: NSF 2216851, 2100561, and 2100636 )
[BibTex] - Grote, A., Lyons, E., Thareja, K., Papadimitriou, G., Deelman, E., Mandal, A., Calyam, P., & Zink, M. (2023). FlyPaw: Optimized Route Planning for Scientific UAVMissions. 2023 IEEE 19th International Conference on e-Science (e-Science), 1–10. https://doi.org/10.1109/e-Science58273.2023.10254831 (Funding Acknowledgments: NSF 2018074, 1939334)
[BibTex] - Jin, H., Raghavan, K., Papadimitriou, G., Wang, C., Mandal, A., Kiran, M., Deelman, E., & Balaprakash, P. (2023). Graph neural networks for detecting anomalies in scientific workflows. The International Journal of High Performance Computing Applications. https://doi.org/10.1177/10943420231172140 (Funding Acknowledgments: DOE DE-SC0022328, DE-AC02-06CH11357)
[BibTex] - Mahmud, I., Papadimitriou, G., Wang, C., Kiran, M., Mandal, A., & Deelman, E. (2023). Elephants Sharing the Highway: Studying TCP Fairness in Large Transfers over High Throughput Links. Proceedings of the SC ’23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis, 806–818. https://doi.org/10.1145/3624062.3624594 (Funding Acknowledgments: DOE DE-SC0022328. Best Paper Award.)
[BibTex] - Morel, A. E., Gafurov, D., Calyam, P., Wang, C., Thareja, K., Mandal, A., Lyons, E., Zink, M., Papadimitriou, G., & Deelman, E. (2023). Experiments on Network Services for Video Transmission using FABRIC Instrument Resources. IEEE INFOCOM 2023 - IEEE Conference on Computer Communications Workshops (INFOCOM WKSHPS), 1–6. https://doi.org/10.1109/INFOCOMWKSHPS57453.2023.10225817 (Funding Acknowledgments: NSF CNS-1950873, CNS-1647182 and OAC-2018074)
[BibTex] - Morel, A. E., Qu, C., Calyam, P., Wang, C., Thareja, K., Mandal, A., Lyons, E., Zink, M., Papadimitriou, G., & Deelman, E. (2023). FlyNet: Drones on the Horizon. IEEE Internet Computing, 27(3), 35–43. https://doi.org/10.1109/MIC.2023.3260440 (Funding Acknowledgments: NSF 1950873, 1647182, 2018074)
[BibTex] - Murillo, A., Brower, D., Hossain, S., Kee, K., Mandal, A., Nabrzyski, J., Scott, E., Virdone, N., Ewing, R., & Deelman, E. (2023). Broadening Student Engagement To Build the Next Generation of Cyberinfrastructure Professionals. Practice and Experience in Advanced Research Computing, 470–473. https://doi.org/10.1145/3569951.3597567 (Funding Acknowledgments: NSF 2127548)
[BibTex] - Papadimitriou, G., Jin, H., Wang, C., Raghavan, K., Mandal, A., Balaprakash, P., & Deelman, E. (2023). Flow-Bench: A Dataset for Computational Workflow Anomaly Detection. https://doi.org/10.48550/ARXIV.2306.09930
[BibTex] - Papadimitriou, G., Wang, C., Lyons, E., Thareja, K., Ruth, P., Villalobos, J. J., Rodero, I., Deelman, E., Zink, M., & Mandal, A. (2023). Dynamic Network-Centric Multi-cloud Platform for Real-Time and Data-Intensive Science Workflows. In F. Darema, E. P. Blasch, S. Ravela, & A. J. Aved (Eds.), Handbook of Dynamic Data Driven Applications Systems: Volume 2 (pp. 835–868). Springer International Publishing. https://doi.org/10.1007/978-3-031-27986-7_32 (Funding Acknowledgments: NSF 1826997)
[BibTex] - Rynge, M., Vahi, K., Alam, M. Z., Deelman, E., Miller, T., Livny, M., Knuth, S., Griffioen, J., Goodhue, J., Hudak, D., Ma, J., Pasquale, A., & Fein, L. (2023). ACCESS Pegasus: Bringing Workflows to the ACCESS Masses. Practice and Experience in Advanced Research Computing, 478–480. https://doi.org/10.1145/3569951.3597590 (Funding Acknowledgments: NSF 2138286, 1664162)
[BibTex] - Sahni, H., Carrillo-Cabada, H., Kots, E., Caino-Lores, S., Marquez, J., Deelman, E., Cuendet, M., Weinstein, H., Taufer, M., & Estrada, T. (2023). Online Boosted Gaussian Learners for In-Situ Detection and Characterization of Protein Folding States in Molecular Dynamics Simulations. 2023 IEEE 19th International Conference on e-Science (e-Science), 1–10. https://doi.org/10.1109/e-Science58273.2023.10254895 (Funding Acknowledgments: NSF 1757207, 1741057, 1841758, 2138811 and 2223704)
[BibTex]
2022
- Abhinit, I., Adams, E. K., Alam, K., Chase, B., Deelman, E., Gorenstein, L., Hudson, S., Islam, T., Larson, J., Lentner, G., Mandal, A., Navarro, J.-L., Nicolae, B., Pouchard, L., Ross, R., Roy, B., Rynge, M., Serebrenik, A., Vahi, K., … Filgueira, R. (2022). Novel Proposals for FAIR, Automated, Recommendable, and Robust Workflows. 2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS), 84–92. https://doi.org/10.1109/WORKS56498.2022.00016 (Funding Acknowledgments: NSF 1839900 and DOE DE-AC02-06CH11357, DE-AC05-00OR22725)
[BibTex] - Casanova, H., Ching Wong, Y., Pottier, L., & Ferreira da Silva, R. (2022). On the Feasibility of Simulation-driven Portfolio Scheduling for Cyberinfrastructure Runtime Systems. 2022 Job Scheduling Strategies for Parallel Processing (JSSPP), To appear. (Funding Acknowledgments: NSF 2106059 and 2106147, DOE DE-AC05-00OR22725)
[BibTex] - Choudhary, K., Nersisyan, N., Lin, E., Chandrasekaran, S., Mayani, R., Pottier, L., Murillo, A. P., Virdone, N. K., Kee, K., & Deelman, E. (2022). Application of Edge-to-Cloud Methods Toward Deep Learning. 2022 IEEE 18th International Conference on e-Science (e-Science), 415–416. https://doi.org/10.1109/eScience55777.2022.00065 (Funding Acknowledgments: NSF 2127548)
[BibTex] - Coleman, T., Casanova, H., Pottier, L., Kaushik, M., Deelman, E., & Ferreira da Silva, R. (2022). WfCommons: A framework for enabling scientific workflow research and development. Future Generation Computer Systems, 128, 16–27. https://doi.org/10.1016/j.future.2021.09.043 (Funding Acknowledgments: NSF 1923539, 2016610, 2016619, 2103489, 2103508, 1923621, 1664162, DOE DE-SC0012636)
[BibTex] - Cranganore, S. S., De Maio, V., Brandic, I., Do, T. M. A., & Deelman, E. (2022). Molecular Dynamics Workflow Decomposition for Hybrid Classic/Quantum Systems. 2022 IEEE 18th International Conference on e-Science (e-Science), 346–356. https://doi.org/10.1109/eScience55777.2022.00048 (Funding Acknowledgments: NSF 1664162 and 1741040)
[BibTex] - Do, T. M. A., Pottier, L., Ferreira da Silva, R., Caı́no-Lores Silvina, Taufer, M., & Deelman, E. (2022). Performance assessment of ensembles of in situ workflows under resource constraints. Concurrency and Computation: Practice and Experience. https://doi.org/10.1002/cpe.7111 (Funding Acknowledgments: NSF 1664162)
[BibTex] - Do, T. M. A., Pottier, L., Yildiz, O., Vahi, K., Krawczuk, P., Peterka, T., & Deelman, E. (2022). Accelerating Scientific Workflows on HPC Platforms with In Situ Processing. 2022 IEEE/ACM 22nd International Symposium on Cluster, Cloud and Internet Computing (CCGrid), 1–10. https://doi.org/10.1109/CCGrid54584.2022.00009 (Funding Acknowledgments: NSF 1664162, DOE DE-AC02-06CH11357, DE-AC02-05CH11231, DE-SC0012636 and DE-SC0022328)
[BibTex] - Do, T. M. A., Pottier, L., da Silva, R. F., Suter, F., Caíno-Lores, S., Taufer, M., & Deelman, E. (2022). Co-scheduling Ensembles of In Situ Workflows. 2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS), 43–51. https://doi.org/10.1109/WORKS56498.2022.00011 (Funding Acknowledgments: NSF 1741040, 1741057, 1841758 and DOE DE-AC05-00OR22725)
[BibTex] - Gesing, S., Deelman, E., Ferreira da Silva, R., Hildreth, M., McDowell, M. A., Meyers, N., Taylor, I., & Tain, D. (2022). VisDict: A Visual Dictionary in a Science Gateway. In Gateways 2022. Zenodo. https://doi.org/10.5281/zenodo.7098353 (Funding Acknowledgments: NSF 2216851)
[BibTex] - Hacker, T., Smith, P., Brunson, D., Arafune, L., Cheatham, T., & Deelman, E. (2022). Building the Research Innovation Workforce: Challenges and Recommendations from a Virtual Workshop to Advance the Research Computing Community*. Practice and Experience in Advanced Research Computing. https://doi.org/10.1145/3491418.3530288 (Funding Acknowledgments: NSF 2036534)
[BibTex] - Hamed, A. A., Jonczyk, J., Alam, M. Z., Deelman, E., & Lee, B. S. (2022). Mining Literature-Based Knowledge Graph for Predicting Combination Therapeutics: A COVID-19 Use Case. 2022 IEEE International Conference on Knowledge Graph (ICKG), 79–86. https://doi.org/10.1109/ICKG55886.2022.00018
[BibTex] - Honoré, V., Do, T. M. A., Pottier, L., Da Silva, R. F., Deelman, E., & Suter, F. (2022). SIM-SITU: A Framework for the Faithful Simulation of in situ Processing. 2022 IEEE 18th International Conference on e-Science (e-Science), 182–191. https://doi.org/10.1109/eScience55777.2022.00032 (Funding Acknowledgments: DOE DE-AC05-00OR22725)
[BibTex] - Jin, H., Raghavan, K., Papadimitriou, G., Wang, C., Mandal, A., Krawczuk, P., Pottier, L., Kiran, M., Deelman, E., & Balaprakash, P. (2022). Workflow Anomaly Detection with Graph Neural Networks. 2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS), 35–42. https://doi.org/10.1109/WORKS56498.2022.00010 (Funding Acknowledgments: DOE DE-SC0022328, DE-AC02-06CH11357)
[BibTex] - Knuth, S. L., Ma, J., Adams, J. C., Chalker, A., Deelman, E., Freeborn, L., Gazula, V., Goodhue, J., Griffioen, J., Hudak, D., Pasquale, A., Perkins, D., Romanella, A., & Rynge, M. (2022). The Multi-Tier Assistance, Training, and Computational Help (MATCH) Project, a Track 2 NSF ACCESS Initiative. The Journal of Computational Science Education, 13(2), 17–20. https://doi.org/https://doi.org/10.22369/issn.2153-4136/13/2/4 (Funding Acknowledgments: NSF 2138286)
[BibTex] - Murillo, A., Deelman, E., Nabrzyski, J., & Pottier, L. (2022). Broadening Student Participation in Cyberinfrastructure Research and Development. Practice and Experience in Advanced Research Computing. https://doi.org/10.1145/3491418.3535175 (Funding Acknowledgments: NSF 2127548 and 1842042)
[BibTex] - Murillo, A. P., Deelman, E., Nabrzyski, J., & Pottier Loı̈c. (2022). Broadening Student Participation in Cyberinfrastructure Research and Development. Practice and Experience in Advanced Research Computing. https://doi.org/10.1145/3491418.3535175 (Funding Acknowledgments: NSF 2127548, 1842042)
[BibTex] - Osinski, T., Rynge, M., Hong, J. K., Vahi, K., Chu, R., Sul, C., Deelman, E., & Kim, B.-D. (2022). An automated Cryo-EM computational environment on the HPC system using Pegasus WMS. 2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS), 60–67. https://doi.org/10.1109/WORKS56498.2022.00013 (Funding Acknowledgments: NSF 1664162)
[BibTex] - Patel, R., Roachell, B., Caíno-Lores, S., Ketron, R., Leonard, J., Tan, N., Vahi, K., Brown, D. A., Deelman, E., & Taufer, M. (2022). Reproducibility of the First Image of a Black Hole in the Galaxy M87 From the Event Horizon Telescope Collaboration. Computing in Science & Engineering, 24(5), 42–52. https://doi.org/10.1109/MCSE.2023.3241105 (Funding Acknowledgments: NSF 2041977, 1941443, 2041901, 1664162 and 2041878)
[BibTex] - Tanaka, R., Papadimitriou, G., Viswanath, S. C., Wang, C., Lyons, E., Thareja, K., Qu, C., Esquivel, A., Deelman, E., Mandal, A., Calyam, P., & Zink, M. (2022). Automating Edge-to-cloud Workflows for Science: Traversing the Edge-to-cloud Continuum with Pegasus. 2022 22nd IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid), 826–833. https://doi.org/10.1109/CCGrid54584.2022.00098 (Funding Acknowledgments: NSF 2018074, 1664162. Best Paper Award.)
[BibTex] - Xin, Y., Fu, S.-W., Mandal, A., Tanaka, R., Rynge, M., Vahi, K., & Deelman, E. (2022). Data Integrity Error Localization in Networked Systems with Missing Data. ICC 2022 - IEEE International Conference on Communications, 341–346. https://doi.org/10.1109/ICC45855.2022.9838996 (Funding Acknowledgments: NSF 1839900)
[BibTex]
2021
- Brown, D., Vahi, K., Taufer, M., Welch, V., & Deelman, E. (2021). Reproducing GW150914: the first observation of gravitational waves from a binary black hole merger. Computing in Science & Engineering. https://doi.org/10.1109/MCSE.2021.3059232 (Funding Acknowledgments: NSF 1664162, NSF 1823405)
[BibTex] - Burkat, K., Pawlik, M., Balis, B., Malawski, M., Vahi, K., Rynge, M., da Silva, R. F., & Deelman, E. (2021). Serverless Containers – Rising Viable Approach to Scientific Workflows. 2021 IEEE 17th International Conference on EScience (EScience), 40–49. https://doi.org/10.1109/eScience51609.2021.00014
[BibTex] - Casanova, H., Deelman, E., Gesing, S., Hildreth, M., Hudson, S., Koch, W., Larson, J., McDowell, M. A., Meyers, N., Navarro, J.-L., Papadimitriou, G., Tanaka, R., Taylor, I., Thain, D., Wild, S. M., Filgueira, R., & da Silva, R. F. (2021). Emerging Frameworks for Advancing Scientific Workflows Research, Development, and Education. 2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS), 74–80. https://doi.org/10.1109/WORKS54523.2021.00015 (Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162)
[BibTex] - Casanova, H., Tanaka, R., Koch, W., & Ferreira da Silva, R. (2021). Teaching Parallel and Distributed Computing Concepts in Simulation with WRENCH. Journal of Parallel and Distributed Computing. https://doi.org/10.1016/j.jpdc.2021.05.009 (Funding Acknowledgments: NSF 1923539, NSF 1642335)
[BibTex] - Coleman, T., Casanova, H., & Ferreira da Silva, R. (2021). WfChef: Automated Generation of Accurate Scientific Workflow Generators. 17th IEEE EScience Conference. (Funding Acknowledgments: NSF 1923539, NSF 2016619)
[BibTex] - Coleman, T., Casanova, H., Gwartney, T., & Ferreira da Silva, R. (2021). Evaluating energy-aware scheduling algorithms for I/O-intensive scientific workflows. International Conference on Computational Science (ICCS), 183–197. https://doi.org/10.1007/978-3-030-77961-0_16 (Funding Acknowledgments: NSF 1923539, NSF 2016619)
[BibTex] - Deelman, E., Ferreira da Silva, R., Vahi, K., Rynge, M., Mayani, R., Tanaka, R., Whitcup, W., & Livny, M. (2021). The Pegasus Workflow Management System: Translational Computer Science in Practice. Journal of Computational Science, 52, 101200. https://doi.org/10.1016/j.jocs.2020.101200 (Funding Acknowledgments: NSF 1664162)
[BibTex] - Deelman, E., Mandal, A., Murillo, A. P., Nabrzyski, J., Pascucci, V., Ricci, R., Baldin, I., Sons, S., Christopherson, L., Vardeman, C., Ferreira da Silva, R., Wyngaard, J., Petruzza, S., Rynge, M., Vahi, K., Whitcup, W. R., Drake, J., & Scott, E. (2021). Blueprint: Cyberinfrastructure Center of Excellence. Zenodo. https://doi.org/10.5281/zenodo.4587866
[BibTex] - Do, H.-D., Hayot-Sasson, V., Ferreira da Silva, R., Steele, C., Casanova, H., & Glatard, T. (2021). Modeling the Linux page cache for accurate simulation of data-intensive applications. IEEE Cluster. (Funding Acknowledgments: NSF 1923539)
[BibTex] - Do, T. M. A., Pottier, L., Caíno-Lores, S., Ferreira da Silva, R., Cuendet, M. A., Weinstein, H., Estrada, T., Taufer, M., & Deelman, E. (2021). A Lightweight Method for Evaluating In Situ Workflow Efficiency. Journal of Computational Science, 48, 101259. https://doi.org/10.1016/j.jocs.2020.101259 (Funding Acknowledgments: NSF 1741040, DOE DE-SC0012636)
[BibTex] - Do, T. M. A., Pottier Loı̈c, Ferreira da Silva, R., Caı́no-Lores Silvina, Taufer, M., & Deelman, E. (2021). Assessing Resource Provisioning and Allocation of Ensembles of In Situ Workflows. 50th International Conference on Parallel Processing Workshop. https://doi.org/10.1145/3458744.3474051 (Funding Acknowledgments: NSF 1741040, DOE SC0012636)
[BibTex] - Ferreira da Silva, R., Casanova, H., Chard, K., Altintas, I., Badia, R. M., Balis, B., Coleman, T., Coppens, F., Di Natale, F., Enders, B., Fahringer, T., Filgueira, R., Fursin, G., Garijo, D., Goble, C., Howell, D., Jha, S., Katz, D. S., Laney, D., … Wolf, M. (2021). A Community Roadmap for Scientific Workflows Research and Development. 2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS), 81–90. https://doi.org/10.1109/WORKS54523.2021.00016
[BibTex] - Ferreira da Silva, R., Casanova, H., Chard, K., Coleman, T., Laney, D., Ahn, D., Jha, S., Howell, D., Soiland-Reys, S., Altintas, I., Thain, D., Filgueira, R., Babuji, Y., Badia, R. M., Balis, B., Caino-Lores, S., Callaghan, S., Coppens, F., Crusoe, M. R., … Wozniak, J. (2021). Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development. Zenodo. https://doi.org/10.5281/zenodo.4915801
[BibTex] - Ferreira da Silva, R., Casanova, H., Chard, K., Laney, D., Ahn, D., Jha, S., Goble, C., Ramakrishnan, L., eerson, L., Enders, B., Thain, D., Altintas, I., Babuji, Y., Badia, R., Bonazzi, V., Coleman, T., Crusoe, M., Deelman, E., Di Natale, F., … Wozniak, J. (2021). Workflows Community Summit: Bringing the Scientific Workflows Community Together. Zenodo. https://doi.org/10.5281/zenodo.4606958
[BibTex] - Gesing, S., Ferreira da Silva, R., Deelman, E., Hildreth, M., McDowell, M. A., Meyers, N., Taylor, I., & Tain, D. (2021). VisDict: Enhancing the Communication between Workflow Providers and User Communities via a Visual Dictionary. 2021 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS).
[BibTex] - Gil, Y., Garijo, D., Khider, D., Knoblock, C. A., Ratnakar, V., Osorio, M., Vargas, H., Pham, M., Pujara, J., Shbita, B., Vu, B., Chiang, Y.-Y., Feldman, D., Lin, Y., Song, H., Kumar, V., Khandelwal, A., Steinbach, M., Tayal, K., … Shu, L. (2021). Artificial Intelligence for Modeling Complex Systems: Taming the Complexity of Expert Models to Improve Decision Making. ACM Transactions on Interactive Intelligent Systems, 11(2). (Funding Acknowledgments: DARPA W911NF-18-1-0027)
[BibTex] - Hataishi, E., Dutot, P.-F., Ferreira da Silva, R., & Casanova, H. (2021). GLUME: A Strategy for Reducing Workflow Execution Times on Batch-Scheduled Platforms. Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP). (Funding Acknowledgments: NSF 1923539)
[BibTex] - Hayes, C., Kulkarni, C., Milman, E. D., Okunloye, O., Olshansky, A., Oruche, R., Kee, K., Moreira, P. C. S., Vardeman, C., Coleman, T., Do, T. M. A., Jain, A., Krawczuk, P., Lam, K., Nagarkar, S., Papadimitriou, G., Subramanya, S., White, R., Whitcup, W., … Deelman, E. (2021). 2021 SciTech and Friends Research Symposium. Zenodo. https://doi.org/10.5281/zenodo.4847543
[BibTex] - Ketron, R., Leonard, J., Roachell, B., Patel, R., White, R., Caíno-Lores, S., Tan, N., Miles, P., Vahi, K., Deelman, E., Brown, D., & Taufer, M. (2021). A Case Study in Scientific Reproducibility from the Event Horizon Telescope (EHT). 2021 IEEE 17th International Conference on EScience (EScience), 249–250. https://doi.org/10.1109/eScience51609.2021.00045 (Funding Acknowledgments: NSF 2041977, 2041901, 2041878)
[BibTex] - Krawczuk, P., Nagarkar, S., & Deelman, E. (2021). CrisisFlow: Multimodal Representation Learning Workflow for Crisis Computing. 2021 IEEE 17th International Conference on EScience (EScience), 264–266. https://doi.org/10.1109/eScience51609.2021.00052 (Funding Acknowledgments: NSF 1664162)
[BibTex] - Krawczuk, P., Papadimitriou, G., Nagarkar, S., Kiran, M., Mandal, A., & Deelman, E. (2021). Anomaly Detection in Scientific Workflows using End-to-End Execution Gantt Charts and Convolutional Neural Networks. Practice and Experience in Advanced Research Computing. https://doi.org/10.1145/3437359.3465597 (Funding Acknowledgments: DOE DESC0012636)
[BibTex] - Krawczuk, P., Papadimitriou, G., Tanaka, R., Do, T. M. A., Subramany, S., Nagarkar, S., Jain, A., Lam, K., Mandal, A., Pottier, L., & Deelman, E. (2021). A Performance Characterization of Scientific Machine Learning Workflows. 2021 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS), 58–65. https://doi.org/10.1109/WORKS54523.2021.00013 (Funding Acknowledgments: DOE DE-SC0012636, DE-SC0022328, NSF 1664162)
[BibTex] - Lyons, E., Saplakoglu, H., Zink, M., Thareja, K., Mandal, A., Qu, C., Wang, S., Calyam, P., Papadimitriou, G., Tanaka, R., & Deelman, E. (2021). FlyNet: A Platform to Support Scientific Workflows from the Edge to the Core for UAV Applications. Proceedings of the 14th IEEE/ACM International Conference on Utility and Cloud Computing. https://doi.org/10.1145/3468737.3494098 (Funding Acknowledgments: NSF 2018074)
[BibTex] - Lyons, E., Seo, D.-J., Kim, S., Habibi, H., Papadimitriou, G., Tanaka, R., Deelman, E., Zink, M., & Mandal, A. (2021). Predicting Flash Floods in the Dallas-Fort Worth Metroplex Using Workflows and Cloud Computing. 2021 IEEE 17th International Conference on EScience (EScience), 259–261. https://doi.org/10.1109/eScience51609.2021.00050 (Funding Acknowledgments: NSF 1826997, 2018074, 1664162)
[BibTex] - Papadimitriou, G., & Deelman, E. (2021). A Lightweight GPU Monitoring Extension for Pegasus Kickstart. 2021 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS). https://doi.org/10.5281/zenodo.5915106 (Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162)
[BibTex] - Papadimitriou, G., Lyons, E., Wang, C., Thareja, K., Tanaka, R., Ruth, P., Rodero, I., Deelman, E., Zink, M., & Mandal, A. (2021). Fair sharing of network resources among workflow ensembles. Cluster Computing. https://doi.org/10.1007/s10586-021-03457-3 (Funding Acknowledgments: NSF 1826997)
[BibTex] - Papadimitriou, G., Wang, C., Vahi, K., Ferreira da Silva, R., Mandal, A., Zhengchun, L., Mayani, R., Rynge, M., Kiran, M., Lynch, V. E., Kettimuthu, R., Deelman, E., Vetter, J. S., & Foster, I. (2021). End-to-End Online Performance Data Capture and Analysis for Scientific Workflows. Future Generation Computer Systems, 117, 387–400. https://doi.org/10.1016/j.future.2020.11.024 (Funding Acknowledgments: DOE DE-SC0012636. Best Paper Award and Editor’s Choice Article)
[BibTex] - Rangan, R., Watkins, A. M., Chacon, J., Kretsch, R., Kladwang, W., Zheludev, I. N., Townley, J., Rynge, M., Thain, G., & Das, R. (2021). De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures. Nucleic Acids Research, 49(6), 3092–3108. https://doi.org/10.1093/nar/gkab119
[BibTex] - Taufer, M., Deelman, E., Silva, R. F. da, Estrada, T., Hall, M., & Livny, M. (2021). A Roadmap to Robust Science for High-throughput Applications: The Developers’ Perspective. 2021 IEEE International Conference on Cluster Computing (CLUSTER), 807–808. https://doi.org/10.1109/Cluster48925.2021.00068 (Funding Acknowledgments: NSF 2028881, 2028923, 2028930, 2028955, 2028956)
[BibTex] - Taufer, M., Deelman, E., da Silva, R. F., Estrada, T., & Hall, M. (2021). A Roadmap to Robust Science for High-throughput Applications: The Scientists’ Perspective. 2021 IEEE 17th International Conference on EScience (EScience), 247–248. https://doi.org/10.1109/eScience51609.2021.00044 (Funding Acknowledgments: NSF 2028881, 2028923, 2028930, 2028955, 2028956)
[BibTex] - Tu, H., Papadimitriou, G., Kiran, M., Wang, C., Mandal, A., Deelman, E., & Menzies, T. (2021). Mining Workflows for Anomalous Data Transfers. 2021 2021 IEEE/ACM 18th International Conference on Mining Software Repositories (MSR) (MSR), 1–12. https://doi.org/10.1109/MSR52588.2021.00013 (Funding Acknowledgments: NSF 1826574, NSF 1931425, DOE DE-SC0012636)
[BibTex] - Xin, Y., Fu, S.-W., Mandal, A., Baldin, I., Tanaka, R., Rynge, M., Vahi, K., Deelman, E., Abhinit, I., & Von, W. (2021). Root Cause Analysis of Data Integrity Errors in Networked Systems with Incomplete Information. 2021 International Conference on Information and Communication Technology Convergence (ICTC), 735–740. https://doi.org/10.1109/ICTC52510.2021.9621124
[BibTex]
2020
- Adams, J. C., Back, G., Bala, P., Bane, M. K., Cameron, K., Casanova, H., Ellis, M., Ferreira da Silva, R., Jethwani, G., Koch, W., Lee, T., & Zhu, T. (2020). Lightning Talks of EduHPC 2020. 2020 IEEE/ACM Workshop on Education for High-Performance Computing (EduHPC), 59–64. https://doi.org/10.1109/EduHPC51895.2020.00013 (Funding Acknowledgments: NSF 1923539)
[BibTex] - Casanova, H., Ferreira da Silva, R., Gonzalez-Escribano, A., Koch, W., Torres, Y., & Bunde, D. P. (2020). Peachy Parallel Assignments (EduHPC 2020). 2020 IEEE/ACM Workshop on Education for High-Performance Computing (EduHPC), 53–58. https://doi.org/10.1109/EduHPC51895.2020.00012 (Funding Acknowledgments: NSF 1923539)
[BibTex] - Casanova, H., Ferreira da Silva, R., Tanaka, R., Pandey, S., Jethwani, G., Koch, W., Albrecht, S., Oeth, J., & Suter, F. (2020). Developing Accurate and Scalable Simulators of Production Workflow Management Systems with WRENCH. Future Generation Computer Systems, 112, 162–175. https://doi.org/10.1016/j.future.2020.05.030 (Funding Acknowledgments: NSF 1642335, NSF 1923539)
[BibTex] - Do, T. M. A., Pottier, L., Thomas, S., Ferreira da Silva, R., Cuendet, M. A., Weinstein, H., Estrada, T., Taufer, M., & Deelman, E. (2020). A Novel Metric to Evaluate In Situ Workflows. International Conference on Computational Science (ICCS), 538–553. https://doi.org/10.1007/978-3-030-50371-0_40 (Funding Acknowledgments: NSF 1741040)
[BibTex] - Ferreira da Silva, R., Casanova, H., Orgerie, A.-C., Tanaka, R., Deelman, E., & Suter, F. (2020). Characterizing, Modeling, and Accurately Simulating Power and Energy Consumption of I/O-intensive Scientific Workflows. Journal of Computational Science, 44, 101157. https://doi.org/10.1016/j.jocs.2020.101157 (Funding Acknowledgments: NSF 1642335, NSF 1923539, NSF 1664162, DOE DE-SC0012636)
[BibTex] - Ferreira da Silva, R., Pottier, L., Coleman, T., Deelman, E., & Casanova, H. (2020). WorkflowHub: Community Framework for Enabling Scientific Workflow Research and Development. 2020 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS), 49–56. https://doi.org/10.1109/WORKS51914.2020.00012 (Funding Acknowledgments: NSF 2016619, DOE DE-SC0012636, NSF 1664162, NSF 1923539)
[BibTex] - Kiran, M., Wang, C., Papadimitriou, G., Mandal, A., & Deelman, E. (2020). Detecting Anomalous Packets in Network Transfers: Investigations using PCA, Autoencoder and Isolation Forest in TCP. Machine Learning. https://doi.org/10.1007/s10994-020-05870-y (Funding Acknowledgments: DOE DESC0012636)
[BibTex] - Lyons, E., Westbrook, D., Grote, A., Papadimitriou, G., Thareja, K., Wang, C., Zink, M., Deelman, E., Mandal, A., & Ruth, P. (2020). An On-Demand Weather Avoidance System for Small Aircraft Flight Path Routing. In F. Darema, E. Blasch, S. Ravela, & A. Aved (Eds.), Dynamic Data Driven Application Systems (pp. 311–319). Springer International Publishing. https://doi.org/10.1007/978-3-030-61725-7_36 (Funding Acknowledgments: NSF 1826997, 2018074)
[BibTex]