Publications

@article{brink2023thicket,
title={Thicket: Seeing the Performance Experiment Forest for the Individual Run Trees},
author={Brink, Stephanie and McKinsey, Michael and Boehme, David and Scully-Allison, Connor and Lumsden, Ian and Hawkins, Daryl and Burgess, Treece and Lama, Vanessa and Luettgau, Jakob and Isaacs, Katherine E and others},
journal={High-Performance Parallel and Distributed Computing (HPDC 2023)},
volume={6},
number={7},
pages={23},
year={2023}
}

@article{patel2023reproducibility,
title={Reproducibility of the first image of a black hole in the galaxy M87 from the event horizon telescope (EHT) collaboration},
author={Patel, Ria and Roachell, Brandan and Caino-Lores, Silvina and Ketron, Ross and Leonard, Jacob and Tan, Nigel and Vahi, Karan and Brown, Duncan A and Deelman, Ewa and Taufer, Michela},
journal={Computing in Science \& Engineering},
year={2023},
publisher=IEEE
}

@article{afle2023reproducing,
title={Reproducing the results for NICER observation of PSR J0030+ 0451},
author={Afle, Chaitanya and Miles, Patrick R and Caino-Lores, Silvina and Capano, Collin D and Tews, Ingo and Vahi, Karan and Deelman, Ewa and Taufer, Michela and Brown, Duncan A},
journal={arXiv preprint arXiv:2304.01035},
year=2023
}

@article{bhowmick2023survey,
title={A Survey of Graph Comparison Methods with Applications to Nondeterminism in High-Performance Computing},
author={Bhowmick, Sanjukta and Bell, Patrick and Taufer, Michela},
journal={The International Journal of High Performance Computing Applications},
pages={10943420231166610},
year={2023},
publisher={SAGE Publications Sage UK: London, England}
}

@article{zhou2023orchestration,
title={Orchestration of materials science workflows for heterogeneous resources at large scale},
author={Zhou, Naweiluo and Scorzelli, Giorgio and Luettgau, Jakob and Kancharla, Rahul R and Kane, Joshua J and Wheeler, Robert and Croom, Brendan P and Newell, Pania and Pascucci, Valerio and Taufer, Michela},
journal={The International Journal of High Performance Computing Applications},
pages={10943420231167800},
year={2023},
publisher={SAGE Publications Sage UK: London, England}
}

@inproceedings{caino2023runtime,
title={Runtime Steering of Molecular Dynamics Simulations Through In Situ Analysis and Annotation of Collective Variables},
author={Caino-Lores, Silvina and Cuendet, Michel and Marquez, Jack and Kots, Ekaterina and Estrada, Trilce and Deelman, Ewa and Weinstein, Harel and Taufer, Michela},
booktitle={Proceedings of the Platform for Advanced Scientific Computing Conference},
pages={1--11},
year={2023}
}

@inproceedings{olaya2023enabling,
title={Enabling Scalability in the Cloud for Scientific Workflows: An Earth Science Use Case},
author={Olaya, Paula and Luettgau, Jakob and Roa, Camila and Llamas, Ricardo and Vargas, Rodrigo and Wen, Sophia and Chung, I-Hsin and Seelam, Seetharami and Park, Yoonho and Lofstead, Jay and others},
booktitle={2023 IEEE 16th International Conference on Cloud Computing (CLOUD)},
pages={383--393},
year={2023},
organization={IEEE}
}

@inproceedings{luettgau2023development,
title={Development of Large-Scale Scientific Cyberinfrastructure and the Growing Opportunity to Democratize Access to Platforms and Data},
author={Luettgau, Jakob and Scorzelli, Giorgio and Pascucci, Valerio and Taufer, Michela},
booktitle={International Conference on Human-Computer Interaction},
pages={378--389},
year={2023},
organization={Springer}
}

@inproceedings{tan2023scalable,
title={Scalable Incremental Checkpointing using GPU-Accelerated De-Duplication},
author={Tan, Nigel and Luettgau, Jakob and Marquez, Jack and Teranishi, Keita and Morales, Nicolas and Bhowmick, Sanjukta and Cappello, Franck and Taufer, Michela and Nicolae, Bogdan},
booktitle={Proceedings of the 52nd International Conference on Parallel Processing},
pages={665--674},
year={2023}
}

@inproceedings{roa2023geotiled,
title={GEOtiled: A Scalable Workflow for Generating Large Datasets of High-Resolution Terrain Parameters},
author={Roa, Camila and Olaya, Paula and Llamas, Ricardo and Vargas, Rodrigo and Taufer, Michela},
booktitle={Proceedings of the 32nd International Symposium on High-Performance Parallel and Distributed Computing},
pages={311--312},
year={2023}
}

@inproceedings{luettgau2023studying,
title={Studying Latency and Throughput Constraints for Geo-Distributed Data in the National Science Data Fabric},
author={Luettgau, Jakob and Martinez, Heberth and Tarcea, Glenn and Scorzelli, Giorgio and Pascucci, Valerio and Taufer, Michela},
booktitle={Proceedings of the 32nd International Symposium on High-Performance Parallel and Distributed Computing},
pages={325--326},
year={2023}
}

@inproceedings{channing2023composable,
title={Composable Workflow for Accelerating Neural Architecture Search Using In Situ Analytics for Protein Classification},
author={Channing, Georgia and Patel, Ria and Olaya, Paula and Rorabaugh, Ariel and Miyashita, Osamu and Caino-Lores, Silvina and Schuman, Catherine and Tama, Florence and Taufer, Michela},
booktitle={Proceedings of the 52nd International Conference on Parallel Processing},
pages={1--1},
year={2023}
}

@article{do2023performance,
title={Performance assessment of ensembles of in situ workflows under resource constraints},
author={Do, Tu Mai Anh and Pottier, Lo{\"\i}c and Ferreira da Silva, Rafael and Ca{\'\i}no-Lores, Silvina and Taufer, Michela and Deelman, Ewa},
journal={Concurrency and Computation: Practice and Experience},
volume={35},
number={20},
pages={e7111},
year={2023},
publisher={Wiley Online Library}
}

@inproceedings{sahni2023online,
title={Online Boosted Gaussian Learners for In-Situ Detection and Characterization of Protein Folding States in Molecular Dynamics Simulations},
author={Sahni, Harshita and Carrillo-Cabada, Hector and Kots, Ekaterina and Caino-Lores, Silvina and Marquez, Jack and Deelman, Ewa and Cuendet, Michel and Weinstein, Harel and Taufer, Michela and Estrada, Trilce},
booktitle={2023 IEEE 19th International Conference on e-Science (e-Science)},
pages={1--10},
year={2023},
organization={IEEE}
}

@misc{taufer2023recognition,
title={Recognition of Outstanding Future Generation Computer Systems Reviewers for 2022},
author={Taufer, Michela},
year={2023}
}

@article{olaya2022building,
title={Building trust in earth science findings through data traceability and results explainability},
author={Olaya, Paula and Kennedy, Dominic and Llamas, Ricardo and Valera, Leobardo and Vargas, Rodrigo and Lofstead, Jay and Taufer, Michela},
journal={IEEE Transactions on Parallel and Distributed Systems},
volume={34},
number={2},
pages={704--717},
year={2022},
publisher={IEEE}
}

@ARTICLE{elsevier-ccpe-tu-2022,
author = {Tu Mai Anh Do, Loïc Pottier, Rafael Ferreira da Silva, Silvina Caíno-Lores, and Michela Taufer and Ewa Deelman},
journal = {{Journal of Concurrency and Computation: Practice and Experience (CCPE)}},
title = {{Performance Assessment of Ensembles of In Situ Workflows under Resource Constraints}},
year = {2022},
volume = {},
number = {},
pages = {},
note = {{\it (Accepted)}},
}

@article{doi:10.1128/msystems.00312-22,
author = {Nicholas C. Mucci and Katarina A. Jones and Mengyi Cao and Michael R. Wyatt and Shane Foye and Sarah J. Kauffman and Gregory R. Richards and Michela Taufer and Yoshito Chikaraishi and Shawn A. Steffan and Shawn R. Campagna and Heidi Goodrich-Blair and Christopher R. Anderton },
title = {{Apex Predator Nematodes and Meso-Predator Bacteria Consume Their Basal Insect Prey through Discrete Stages of Chemical Transformations}},
journal = {{mSystems}},
volume = {0},
number = {0},
pages = {e00312-22},
year = {2022},
doi = {10.1128/msystems.00312-22},
}

@ARTICLE{sage-ijhpca-wyatt-2022,
author = {Michael R. Wyatt II+, and Stephen Herbein, and Todd Gamblin, and Michela Taufer},
journal = {{International Journal of High Performance Computing Applications (IJHPCA)}},
title = {{AI4IO: A Suite of AI-Based Tools for IO-Aware Scheduling}},
year = {2022},
volume = {36},
number = {3},
pages = {370-387},
doi = {10.1177/10943420221079765},
}

@article{rorabaugh2022highfrequency,
author = {Ariel Keller Rorabaugh and Silvina Caíno-Lores and Travis Johnston and Michela Taufer},
title = {{High frequency accuracy and loss data of random neural networks trained on image datasets}},
journal = {Data in Brief},
volume = {40},
pages = {107780},
year = {2022},
issn = {2352-3409},
doi = {10.1016/j.dib.2021.107780},
url = {https://doi.org/10.1016/j.dib.2021.107780},
}

@ARTICLE{9674227,
author={Keller Rorabaugh, Ariel and Caíno-Lores, Silvina and Johnston, Travis and Taufer, Michela},
journal={{IEEE Transactions on Parallel and Distributed Systems}},
title={{Building High-Throughput Neural Architecture Search Workflows via a Decoupled Fitness Prediction Engine}},
year={2022},
volume={33},
number={11},
pages={2913-2926},
doi={10.1109/TPDS.2022.3140681}}

@ARTICLE{sage-ijhpca-herbein-2022,
author = {S. Herbein and T. Patki and D. H. Ahn and S. Mobo and C. Hathaway and S. Caíno-Lores and J. Corbett and D. Domyancic and T. R. W. Scogland and B. R. de Supinski and M. Taufer},
journal = {{International Journal of High Performance Computing Applications (IJHPCA)}},
title = {{An Analytical Performance Model of Generalized Multi-Level Scheduling}},
year = {2022},
volume = {36},
number = {3},
pages = {289-306},
doi = {10.1177/10943420211051039},
}

@ARTICLE {bird2022vpic,
author = {R. Bird and N. Tan and S. V. Luedtke and S. Harrell and M. Taufer and B. Albright},
journal = {{IEEE Transactions on Parallel & Distributed Systems}},
title = {{VPIC 2.0: Next Generation Particle-in-Cell Simulations}},
year = {2022},
volume = {33},
number = {04},
issn = {1558-2183},
pages = {952-963},
doi = {10.1109/TPDS.2021.3084795},
publisher = {IEEE Computer Society},
month = {apr}
}

@article{bell2021anacinx,
author = {Patrick Bell and Kae Suarez and Dylan Chapp and Nigel Tan and Sanjukta Bhowmick and Michela Taufer},
title = {{ANACIN-X: A software framework for studying non-determinism in MPI applications}},
journal = {Software Impacts},
volume = {10},
pages = {100151},
year = {2021},
issn = {2665-9638},
doi = {10.1016/j.simpa.2021.100151},
url = {https://doi.org/10.1016/j.simpa.2021.100151},
}

@ARTICLE {brown2021reproducing,
author = {D. A. Brown and K. Vahi and M. Taufer and V. Welch and E. Deelman},
journal = {{Computing in Science & Engineering}},
title = {{Reproducing GW150914: The First Observation of Gravitational Waves From a Binary Black Hole Merger}},
year = {2021},
volume = {23},
number = {02},
issn = {1558-366X},
pages = {73-82},
doi = {10.1109/MCSE.2021.3059232},
publisher = {IEEE Computer Society},
month = {mar}
}

@article{do2021lightweight,
title={{A lightweight method for evaluating in situ workflow efficiency}},
author={Tu Mai Anh Do and Lo{\"i}c Pottier and Silvina Ca{\'i}no-Lores and Rafael Ferreira da Silva and Michel A. Cuendet and Harel Weinstein and Trilce Estrada and Michela Taufer and Ewa Deelman},
journal={{J. Comput. Sci.}},
year={2021},
volume={48},
pages={101259}
}

@ARTICLE {carrillocabada2021graphic,
author = {H. Carrillo-Cabada and J. Benson and A. M. Razavi and B. Mulligan and M. A. Cuendet and H. Weinstein and M. Taufer and T. Estrada},
journal = {{IEEE/ACM Transactions on Computational Biology and Bioinformatics}},
title = {{A Graphic Encoding Method for Quantitative Classification of Protein Structure and Representation of Conformational Changes}},
year = {2021},
volume = {18},
number = {04},
issn = {1557-9964},
pages = {1336-1349},
doi = {10.1109/TCBB.2019.2945291},
publisher = {IEEE Computer Society},
month = {jul}
}

@article{llamas2020spatial,
title={{Spatial gap-filling of ESA CCI satellite-derived soil moisture based on geostatistical techniques and multiple regression}},
author={Llamas, Ricardo M and Guevara, Mario and Rorabaugh, Danny and Taufer, Michela and Vargas, Rodrigo},
journal={Remote Sensing},
volume={12},
number={4},
pages={665},
year={2020},
publisher={Multidisciplinary Digital Publishing Institute}
}

@inproceedings{ian_escience22,
author = {Ian Lumsden and Jakob Luettgau and Vanessa Lama and Connor Scully-Allison and Stephanie Brink and Katherine E. Isaacs and Olga Pearce and {\bf Michela Taufer}},
title = {{Enabling Call Path Querying in Hatchet to Identify Performance Bottlenecks in Scientific Applications}},
booktitle = {Proceedings of the 18th IEEE International Conference on e-Science (eScience)},
pages = {1--10},
address = {Salt Lake City, Utah, USA},
date = {October 10-14, 2022},
year = {2022},
publisher = {{IEEE} Computer Society},
}

@inproceedings{polaya_escience22,
author = {Paula Olaya and Silvina Caino-Lores and Vanessa Lama and Ria Patel and Ariel Keller Rorabaugh and Osamu Miyashita and Florence Tama and {\bf Michela Taufer}},
title = {{Identifying Structural Properties of Proteins from X-ray Free Electron Laser Diffraction Patterns}},
booktitle = {Proceedings of the 18th IEEE International Conference on e-Science (eScience)},
pages = {1--10},
address = {Salt Lake City, Utah, USA},
date = {October 10-14, 2022},
year = {2022},
publisher = {{IEEE} Computer Society},
}

@inproceedings{domenic_escience22,
author = {Kennedy, Dominic and Olaya, Paula and Lofstead, Jay and Vargas, Rodrigo and Taufer, Michela},
title = {{Augmenting Singularity to Generate Fine-grained Workflows, Record Trails, and Data Provenance}},
booktitle = {Proceedings of the 18th IEEE International Conference on e-Science (eScience)},
pages = {1--2},
address = {Salt Lake City, Utah, USA},
date = {October 10-14, 2022},
year = {2022},
publisher = {IEEE Computer Society},
note = {{\it (Short paper)}},
}

@inproceedings{yeom_escience22,
author = {Yeom, Jae-Seung and Ahn, Dong H. and Lumsden, Ian and Luettgau, Jakob and Caino-Lores, Silvina and Taufer, Michela},
title = {{Ubique: A New Model for Untangling Inter-task Data Dependence in Complex HPC Workflows}},
booktitle = {Proceedings of the 18th IEEE International Conference on e-Science (eScience)},
pages = {1--2},
address = {Salt Lake City, Utah, USA},
date = {October 10-14, 2022},
year = {2022},
publisher = {IEEE Computer Society},
note = {{\it (Short paper)}},
}

@inproceedings{glenn_escience22,
author = {Tarcea, Glenn and Puchala, Brian and Berman, Tracy and Scorzelli, Giorgio and Pascucci, Valerio and Taufer, Michela and Allison, John},
title = {{The Materials Commons Data Repository}},
booktitle = {Proceedings of the 18th IEEE International Conference on e-Science (eScience)},
pages = {1--2},
address = {Salt Lake City, Utah, USA},
date = {October 10-14, 2022},
year = {2022},
publisher = {IEEE Computer Society},
note = {{\it (Short paper)}},
}

@inproceedings{ria_escience22,
author = {Patel, Ria and Rorabaugh, Ariel Keller and Olaya, Paula and Caino-Lores, Silvina and Channing, Georgia and Schuman, Catherine and Miyashita, Osamu and Tama, Florence and Taufer, Michela},
title = {{A Methodology to Generate Efficient Neural Networks for Classification of Scientific Datasets}},
booktitle = {Proceedings of the 18th IEEE International Conference on e-Science (eScience)},
pages = {1--2},
address = {Salt Lake City, Utah, USA},
date = {October 10-14, 2022},
year = {2022},
publisher = {IEEE Computer Society},
note = {{\it (Short paper)}},
}

@inproceedings{DBLP:conf/cluster/OlayaHPDC22, author = { Paula Olaya and Jakob Luettgau and Naweiluo Zhou and Giorgio Scorzelli and Jay Lofstead and Valerio Pascucci and {\bf Michela Taufer} },
title = {{NSDF-FUSE: A Testbed for Studying Object Storage via FUSE File Systems}},
booktitle = {Proceedings of the 31st International ACM Symposium on High-Performance Parallel and Distributed Computing (HPDC)},
publisher = {{IEEE} Computer Society},
pages = {1--2},
address = {Minneapolis, Minnesota},
month = {June},
year = {2022},
note = {{\it (Short paper)}},
}

@inproceedings{DBLP:conf/cluster/LuettgauHPDC22,
author = { Jakob Luettgau and Paula Olaya and Naweiluo Zhou and Giorgio Scorzelli and Valerio Pascucci and Michela Taufer},
title = {{NSDF-Cloud: Enabling Ad-Hoc Compute Clusters Across Academic and Commercial Clouds}},
booktitle = {Proceedings of the 31st International ACM Symposium on High-Performance Parallel and Distributed Computing (HPDC)},
publisher = {{ACM}},
pages = {1--2},
address = {Minneapolis, Minnesota},
month = {June},
year = {2022},
note = {{\it (Short paper)}},
}

@INPROCEEDINGS {taufer2021roadmapdevelopers,
author = {M. Taufer and E. Deelman and R. Silva and T. Estrada and M. Hall and M. Livny},
booktitle = {{2021 IEEE International Conference on Cluster Computing (CLUSTER)}},
title = {{A Roadmap to Robust Science for High-throughput Applications: The Developers' Perspective}},
year = {2021},
pages = {807-808},
doi = {10.1109/Cluster48925.2021.00068},
url = {https://doi.ieeecomputersociety.org/10.1109/Cluster48925.2021.00068},
publisher = {{IEEE} Computer Society},
month = {sep}
}

@INPROCEEDINGS{ketron2021casestudy,
author={Ketron, R. and Leonard, J. and Roachell, B. and Patel, R. and White, R. and Caíno-Lores, S. and Tan, N. and Miles, P. and Vahi, K. and Deelman, E. and Brown, D. and Taufer, M.},
booktitle={{2021 IEEE 17th International Conference on eScience (eScience)}},
title={{A Case Study in Scientific Reproducibility from the Event Horizon Telescope (EHT)}}
, year={2021},
pages={249-250},
doi={10.1109/eScience51609.2021.00045}
}

@INPROCEEDINGS{taufer2021roadmapscientists,
author={Taufer, M. and Deelman, E. and da Silva, R. Ferreira and Estrada, T. and Hall, M.},
booktitle={{2021 IEEE 17th International Conference on eScience (eScience)}},
title={{A Roadmap to Robust Science for High-throughput Applications: The Scientists’ Perspective}},
year={2021},
pages={247-248},
doi={10.1109/eScience51609.2021.00044}
}

@inproceedings{do2021assessing, author = {Do, Tu Mai Anh and Pottier, Lo\"{\i}c and Ferreira da Silva, Rafael and Ca\'{\i}no-Lores, Silvina and Taufer, Michela and Deelman, Ewa},
title = {{Assessing Resource Provisioning and Allocation of Ensembles of In Situ Workflows}},
year = {2021},
isbn = {9781450384414},
publisher = {Association for Computing Machinery},
url = {https://doi.org/10.1145/3458744.3474051},
doi = {10.1145/3458744.3474051},
booktitle = {{50th International Conference on Parallel Processing Workshop}},
articleno = {38},
numpages = {10},
}

@inproceedings{Tan2021OptimizeMU,
title={{Optimize Memory Usage in Vector Particle-In-Cell (VPIC) to Break the 10 Trillion Particle Barrier in Plasma Simulations}},
author={Nigel Tan and Robert Francis Bird and Guangye Chen and Michela Taufer},
booktitle={{ICCS}},
year={2021}
}