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[1]
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Vivek Bharadwaj, Osman Asif Malik, Riley Murray, Laura Grigori, Aydin
Buluç, and James Demmel.
Fast exact leverage score sampling from Khatri-Rao products with
applications to tensor decomposition.
arXiv preprint arXiv:2301.12584, 2023.
[ bib |
arXiv ]
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[2]
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Vivek Bharadwaj, Osman Asif Malik, Riley Murray, Aydin Buluç, and
James Demmel.
Distributed-memory randomized algorithms for sparse tensor CP
decomposition.
arXiv preprint arXiv:2210.05105, 2022.
[ bib |
arXiv ]
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[3]
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Brian Wheatman, Randal Burns, Aydin Buluç, and Helen Xu.
Optimizing search layouts in packed memory arrays.
In Proceedings of the Symposium on Algorithm Engineering and
Experiments (ALENEX), pages 148-161. SIAM, 2023.
[ bib |
DOI |
.pdf ]
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[4]
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Oguz Selvitopi, Saliya Ekanayakey, Giulia Guidiz, Muaaz G Awanx, Georgios A
Pavlopoulos, Ariful Azadk, Nikos Kyrpides, Leonid Oliker, Katherine Yelickz,
and Aydin Buluç.
Extreme-scale many-against-many protein similarity search.
In International Conference for High Performance Computing,
Networking, Storage and Analysis (SC), pages 1-12. IEEE Computer Society,
2022.
[ bib |
arXiv ]
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[5]
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Yuxin Chen, Benjamin Brock, Serban Porumbescu, Aydin Buluç, Katherine
Yelick, and John D Owens.
Scalable irregular parallelism with GPUs: getting CPUs out of the
way.
In International Conference for High Performance Computing,
Networking, Storage and Analysis (SC), pages 708-723. IEEE Computer
Society, 2022.
[ bib |
DOI ]
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[6]
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Can Kızılkale, Farid Rashidi Mehrabadi, Erfan Sadeqi Azer, Eva
Pérez-Guijarro, Kerrie L. Marie, Maxwell P. Lee, Chi-Ping Day, Glenn
Merlino, Funda Ergün, Aydın Buluç, S. Cenk Sahinalp, and Salem
Malikić.
Fast intratumor heterogeneity inference from single-cell sequencing
data.
Nature Computational Science, 2(9):577-583, 2022.
[ bib |
DOI |
http ]
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[7]
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Sran Milaković, Oguz Selvitopi, Israt Nisa, Zoran Budimlić, and
Aydin Buluç.
Parallel algorithms for masked sparse matrix-matrix products.
In Proceedings of the 51st International Conference on Parallel
Processing, pages 1-11, 2022.
[ bib |
DOI |
arXiv |
.pdf ]
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[8]
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Giulia Guidi, Gabriel Raulet, Daniel Rokhsar, Leonid Oliker, Katherine Yelick,
and Aydin Buluç.
Distributed-memory parallel contig generation for de novo long-read
genome assembly.
In Proceedings of the 51st International Conference on Parallel
Processing, pages 1-11, 2022.
[ bib |
DOI ]
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[9]
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Yuxin Chen, Benjamin Brock, Serban Porumbescu, Aydin Buluç, Katherine
Yelick, and John Owens.
Atos: A task-parallel GPU scheduler for graph analytics.
In Proceedings of the 51st International Conference on Parallel
Processing, pages 1-11, 2022.
[ bib |
DOI ]
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[10]
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Vivek Bharadwaj, Aydin Buluç, and James Demmel.
Distributed-memory sparse kernels for machine learning.
In International Parallel and Distributed Processing Symposium
(IPDPS), pages 47-58. IEEE, 2022.
[ bib |
DOI |
arXiv ]
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[11]
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Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker,
Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco
Beghini, Denis Bertrand, Jaqueline J. Brito, C. Titus Brown, Jan Buchmann,
Aydin Buluç, Bo Chen, Rayan Chikhi, Philip T. L. C. Clausen, Alexandru
Cristian, Piotr Wojciech Dabrowski, Aaron E. Darling, Rob Egan, Eleazar
Eskin, Evangelos Georganas, Eugene Goltsman, Melissa A. Gray, Lars Hestbjerg
Hansen, Steven Hofmeyr, Pingqin Huang, Luiz Irber, Huijue Jia, Tue Sparholt
Jørgensen, Silas D. Kieser, Terje Klemetsen, Axel Kola, Mikhail
Kolmogorov, Anton Korobeynikov, Jason Kwan, Nathan LaPierre, Claire Lemaitre,
Chenhao Li, Antoine Limasset, Fabio Malcher-Miranda, Serghei Mangul,
Vanessa R. Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko,
Daniel R. Mende, Alessio Milanese, Niranjan Nagarajan, Jakob Nissen, Sergey
Nurk, Leonid Oliker, Lucas Paoli, Pierre Peterlongo, Vitor C. Piro, Jacob S.
Porter, Simon Rasmussen, Evan R. Rees, Knut Reinert, Bernhard Renard,
Espen Mikal Robertsen, Gail L. Rosen, Hans-Joachim Ruscheweyh, Varuni Sarwal,
Nicola Segata, Enrico Seiler, Lizhen Shi, Fengzhu Sun, Shinichi Sunagawa,
Søren Johannes Sørensen, Ashleigh Thomas, Chengxuan Tong, Mirko
Trajkovski, Julien Tremblay, Gherman Uritskiy, Riccardo Vicedomini, Zhengyang
Wang, Ziye Wang, Zhong Wang, Andrew Warren, Nils Peder Willassen, Katherine
Yelick, Ronghui You, Georg Zeller, Zhengqiao Zhao, Shanfeng Zhu, Jie Zhu,
Ruben Garrido-Oter, Petra Gastmeier, Stephane Hacquard, Susanne
Häußler, Ariane Khaledi, Friederike Maechler, Fantin Mesny, Simona
Radutoiu, Paul Schulze-Lefert, Nathiana Smit, Till Strowig, Andreas Bremges,
Alexander Sczyrba, and Alice Carolyn McHardy.
Critical assessment of metagenome interpretation: the second round of
challenges.
Nature Methods, 19(4):429-440, 2022.
[ bib |
DOI |
http ]
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[12]
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Md Taufique Hussain, Guttu Sai Abhishek, Aydin Buluç, and Ariful Azad.
Parallel algorithms for adding a collection of sparse matrices.
In International Parallel and Distributed Processing Symposium
Workshops (IPDPSW), pages 285-294. IEEE, 2022.
[ bib |
arXiv ]
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[13]
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Benjamin Brock, Scott McMillan, Aydin Buluç, Timothy G Mattson, and
José E Moreira.
GraphBLAS: C++ iterators for sparse matrices.
In International Parallel and Distributed Processing Symposium
Workshops (IPDPSW), pages 238-246. IEEE, 2022.
[ bib |
DOI ]
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[14]
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Jeremy Kepner, Michael Jones, Daniel Andersen, Aydin Buluç, Chansup
Byun, K Claffy, Timothy Davis, William Arcand, Jonathan Bernays, David
Bestor, et al.
Temporal correlation of internet observatories and outposts.
In International Parallel and Distributed Processing Symposium
Workshops (IPDPSW), pages 247-254. IEEE, 2022.
[ bib ]
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[15]
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Aydin Buluç.
Sparse matrices powering three pillars of science: Simulation, data,
and learning.
In Proceedings of the International Symposium on Symbolic and
Algebraic Computation, pages 31-31, 2022.
[ bib ]
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[16]
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Ivan Kawaminami, Arminda Estrada, Youssef Elsakkary, Hayden Jananthan, Aydin
Buluç, Tim Davis, Daniel Grant, Michael Jones, Chad Meiners, Andrew
Morris, et al.
Large scale enrichment and statistical cyber characterization of
network traffic.
In High Performance Extreme Computing Conference (HPEC), pages
1-7. IEEE, 2022.
[ bib ]
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[17]
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Michael Jones, Jeremy Kepner, Daniel Andersen, Aydin Buluç, Chansup Byun,
K Claffy, Timothy Davis, William Arcand, Jonathan Bernays, David Bestor,
et al.
GraphBLAS on the edge: Anonymized high performance streaming of
network traffic.
In 2022 IEEE High Performance Extreme Computing Conference
(HPEC), pages 1-8. IEEE, 2022.
[ bib ]
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[18]
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Carl Yang, Aydin Buluç, and John D Owens.
GraphBLAST: A high-performance linear algebra-based graph framework
on the GPU.
ACM Transactions on Mathematical Software, 48(1):1-51, 2022.
[ bib |
DOI |
arXiv ]
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[19]
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Muaaz Awan, Steven Hofmeyr, Rob Egan, Nan Ding, Aydin Buluç, Jack
Deslippe, Leonid Oliker, and Katherine Yelick.
Accelerating large scale de novo metagenome assembly using GPUs.
In International Conference for High Performance Computing,
Networking, Storage and Analysis, SC'21, 2021.
[ bib |
http ]
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[20]
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Ariful Azad, Oguz Selvitopi, Md Taufique Hussain, John Gilbert, and Aydin
Buluç.
Combinatorial BLAS 2.0: Scaling combinatorial algorithms on
distributed-memory systems.
IEEE Transactions on Parallel and Distributed Systems,
33(4):989-1001, 2021.
[ bib |
DOI |
arXiv ]
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[21]
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Seher Acer, Ariful Azad, Erik Boman, Aydin Buluç, Karen Devine, Nitin
Gawande, Sayan Ghosh, Mahantesh Halappanavar, Arif Khan, Ananth Kalyanaraman,
Marco Minutoli, Alex Pothen, Sivasankaran Rajamanickam, Oguz Selvitopi,
Nathan Tallent, and Antonino Tumeo.
EXAGRAPH: Graph and combinatorial methods for enabling exascale
applications.
International Journal of High Performance Computing Applications
(IJHPCA), 35(6):553-571, 2021.
[ bib ]
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[22]
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Oguz Selvitopi, Benjamin Brock, Israt Nisa, Alok Tripathy, Katherine Yelick,
and Aydin Buluç.
Distributed-memory parallel algorithms for sparse times
tall-skinny-dense matrix multiplication.
In Proceedings of the ACM International Conference on
Supercomputing (ICS), pages 431-442, 2021.
[ bib |
.pdf ]
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[23]
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Prashant Pandey, Brian Wheatman, Helen Xu, and Aydin Buluç.
Terrace: A hierarchical graph container for skewed dynamic graphs.
In Proceedings of the 2021 International Conference on
Management of Data (SIGMOD), pages 1372-1385, 2021.
[ bib |
code |
.pdf ]
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[24]
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Giulia Guidi, Marquita Ellis, Daniel Rokhsar, Katherine Yelick, and Aydin
Buluç.
BELLA: Berkeley efficient long-read to long-read aligner and
overlapper.
In SIAM Conference on Applied and Computational Discrete
Algorithms (ACDA21), pages 123-134. SIAM, 2021.
[ bib |
DOI |
code |
bioRxiv |
.pdf ]
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[25]
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Aydin Buluç, Tamara G Kolda, Stefan M Wild, Mihai Anitescu, Anthony
DeGennaro, John Jakeman, Chandrika Kamath, Miles E Lopes, Per-Gunnar
Martinsson, Kary Myers, et al.
Randomized algorithms for scientific computing (RASC).
2021.
DOE Report.
[ bib |
DOI |
arXiv |
http ]
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[26]
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Md Taufique Hussain, Oguz Selvitopi, Aydin Buluç, and Ariful Azad.
Communication-avoiding and memory-constrained sparse matrix-matrix
multiplication at extreme scale.
In International Parallel and Distributed Processing Symposium
(IPDPS), pages 90-100. IEEE, 2021.
[ bib |
arXiv ]
|
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[27]
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Israt Nisa, Prashant Pandey, Marquita Ellis, Leonid Oliker, Aydin
Buluç, and Katherine Yelick.
Distributed-memory k-mer counting on GPUs.
In International Parallel and Distributed Processing Symposium
(IPDPS), pages 527-536. IEEE, 2021.
[ bib |
DOI |
code |
.pdf ]
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[28]
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Giulia Guidi, Oguz Selvitopi, Marquita Ellis, Leonid Oliker, Katherine Yelick,
and Aydin Buluç.
Parallel string graph construction and transitive reduction for de
novo genome assembly.
In International Parallel and Distributed Processing Symposium
(IPDPS), pages 517-526. IEEE, 2021.
[ bib |
code |
arXiv ]
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[29]
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Marquita Ellis, Aydin Buluç, and Katherine Yelick.
Scaling generalized n-body problems, a case study from genomics.
In 50th International Conference on Parallel Processing (ICPP),
2021.
[ bib |
.pdf ]
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[30]
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Marquita Ellis, Aydin Buluç, and Katherine Yelick.
Asynchrony versus bulk-synchrony for a generalized n-body problem
from genomics.
In Proceedings of the 26th ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming (PPOPP), pages 465-466, 2021.
[ bib ]
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[31]
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Giulia Guidi, Marquita Ellis, Aydin Buluç, Katherine Yelick, and David
Culler.
10 years later: Cloud computing is closing the performance gap.
In Companion of the ACM/SPEC International Conference on
Performance Engineering, pages 41-48, 2021.
[ bib |
DOI |
arXiv ]
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[32]
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Benjamin Brock, Aydin Buluç, Timothy G Mattson, Scott McMillan, and
José E Moreira.
Introduction to GraphBLAS 2.0.
In International Parallel and Distributed Processing Symposium
Workshops (IPDPSW), pages 253-262. IEEE, 2021.
[ bib |
DOI ]
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[33]
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Jeremy Kepner, Michael Jones, Daniel Andersen, Aydin Buluç, Chansup
Byun, K Claffy, Timothy Davis, William Arcand, Jonathan Bernays, David
Bestor, et al.
Spatial temporal analysis of 40,000,000,000,000 internet darkspace
packets.
In 2021 IEEE High Performance Extreme Computing Conference
(HPEC), pages 1-8. IEEE, 2021.
[ bib ]
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[34]
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Alok Tripathy, Katherine Yelick, and Aydin Buluç.
Reducing communication in graph neural network training.
In International Conference for High Performance Computing,
Networking, Storage and Analysis, SC'20, 2020.
[ bib |
code |
arXiv ]
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[35]
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Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi, Georgios Pavlopoulos, Ariful
Azad, and Aydin Buluç.
Distributed many-to-many protein sequence alignment using sparse
matrices.
In International Conference for High Performance Computing,
Networking, Storage and Analysis, SC'20, 2020.
[ bib |
code |
.pdf ]
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[36]
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Nicolas Swenson, Aditi S Krishnapriyan, Aydin Buluç, Dmitriy Morozov,
and Katherine Yelick.
PersGNN: Applying topological data analysis and geometric deep
learning to structure-based protein function prediction.
In Learning Meaningful Representations of Life (LMRL) workshop
at NeurIPS, 2020.
[ bib |
arXiv ]
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[37]
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Muaaz G Awan, Jack Deslippe, Aydin Buluç, Oguz Selvitopi, Steven Hofmeyr,
Leonid Oliker, and Katherine Yelick.
ADEPT: a domain independent sequence alignment strategy for gpu
architectures.
BMC bioinformatics, 21(1):1-29, 2020.
[ bib ]
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[38]
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Ariful Azad, Aydin Buluç, Xiaoye S Li, Xinliang Wang, and Johannes
Langguth.
A distributed-memory algorithm for computing a heavy-weight perfect
matching on bipartite graphs.
SIAM Journal on Scientific Computing, 42(4):C143-C168, 2020.
[ bib |
DOI |
arXiv |
.pdf ]
|
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[39]
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Steven Hofmeyr, Rob Egan, Evangelos Georganas, C Alex Copeland, Robert Riley,
Alicia Clum, Emiley Eloe-Fadrosh, Simon Roux, Eugene Goltsman, Aydin
Buluç, Daniel Rokhsar, Leonid Oliker, and Katherine Yelick.
Terabase-scale metagenome coassembly with MetaHipMer.
Scientific reports, 2020.
[ bib |
DOI ]
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[40]
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Yongzhe Zhang, Ariful Azad, and Aydin Buluç.
Parallel algorithms for finding connected components using linear
algebra.
Journal of Parallel and Distributed Computing, 2020.
[ bib |
DOI |
.pdf ]
|
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[41]
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Yu-Hang Tang, Oguz Selvitopi, Doru Popovici, and Aydin Buluç.
A high-throughput solver for marginalized graph kernels on GPU.
In Proceedings of the IPDPS, 2020.
[ bib |
arXiv |
.pdf ]
|
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[42]
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Oguz Selvitopi, Md Taufique Hussain, Ariful Azad, and Aydin Buluç.
Optimizing high performance Markov clustering for pre-exascale
architectures.
In Proceedings of the IPDPS, 2020.
[ bib |
code |
arXiv |
.pdf ]
|
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[43]
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Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio,
Steven Hofmeyr, Aydin Buluç, Leonid Oliker, and Katherine Yelick.
LOGAN: High-performance GPU-based x-drop long-read alignment.
In Proceedings of the IPDPS, 2020.
[ bib |
code |
arXiv |
.pdf ]
|
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[44]
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Katherine Yelick, Aydin Buluç, Muaaz Awan, Ariful Azad, Benjamin
Brock, Rob Egan, Saliya Ekanayake, Marquita Ellis, Evangelos Georganas,
Giulia Guidi, et al.
The parallelism motifs of genomic data analysis.
Philosophical Transactions of the Royal Society A,
378(2166):20190394, 2020.
[ bib |
DOI |
arXiv ]
|
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[45]
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Francesco Peverelli, Lorenzo Di Tucci, Marco D. Santambrogio, Nan Ding, Steven
Hofmeyr, Aydin Buluç, Leonid Oliker, and Katherine Yelick.
GPU accelerated partial order multiple sequence alignment for long
reads self-correction.
In IEEE International Workshop on High Performance Computational
Biology (HiCOMB), 2020.
[ bib |
code |
bioRxiv |
.pdf ]
|
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[46]
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Benjamin Brock, Aydin Buluç, Timothy Mattson, Scott McMillan, José
Moreira, Roger Pearce, Oguz Selvitopi, and Trevor Steil.
Considerations for a distributed GraphBLAS API.
In GrAPL: Workshop on Graphs, Architectures, Programming, and
Learning (IPDPSW), 2020.
[ bib |
.pdf ]
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[47]
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Benjamin Brock, Aydin Buluç, Timothy Mattson, Scott McMillan, and
José Moreira.
A roadmap for the GraphBLAS C++ API.
In GrAPL: Workshop on Graphs, Architectures, Programming, and
Learning (IPDPSW), 2020.
[ bib |
.pdf ]
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[48]
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Yusuke Nagasaka, Satoshi Matsuoka, Ariful Azad, and Aydin Buluç.
Performance optimization, modeling and analysis of sparse
matrix-matrix products on multi-core and many-core processors.
Parallel Computing, 90:102545, 2019.
[ bib |
DOI |
.pdf ]
|
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[49]
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Benjamin Brock, Yuxin Chen, Jiakun Yan, John D. Owens, Aydin Buluç,
and Katherine Yelick.
RDMA vs. RPC for implementing distributed data structures.
In IEEE/ACM 9th Workshop on Irregular Applications:
Architectures and Algorithms (IA3), 2019.
[ bib |
arXiv ]
|
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[50]
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Ben Brock, Aydin Buluç, and Katherine Yelick.
BCL: A cross-platform distributed data structures library.
In 48th International Conference on Parallel Processing (ICPP),
Kyoto, Japan, 2019.
[ bib |
code |
arXiv |
.pdf ]
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[51]
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Marquita Ellis, Giulia Guidi, Aydin Buluç, Leonid Oliker, and Katherine
Yelick.
diBELLA: Distributed long read to long read alignment.
In 48th International Conference on Parallel Processing (ICPP),
Kyoto, Japan, 2019.
[ bib |
arXiv |
.pdf ]
|
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[52]
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Santosh Pandey, Xiaoye Sherry Li, Aydin Buluç, Jiejun Xu, and Hang Liu.
H-INDEX: Hash-indexing for parallel triangle counting on GPUs.
In IEEE High Performance Extreme Computing Conference (HPEC),
pages 1-7. IEEE, 2019.
[ bib |
.pdf ]
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[53]
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Timothy Mattson, Timothy A. Davis, Manoj Kumar, Aydin Buluç, Scott
McMillan, José Moreira, and Carl Yang.
LAGraph: A community effort to collect graph algorithms built on
top of the GraphBLAS.
In GrAPL: Workshop on Graphs, Architectures, Programming, and
Learning (IPDPSW), 2019.
[ bib |
.pdf ]
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[54]
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Muhammad Osama, Minh Truong, Carl Yang, Aydin Buluç, and John D Owens.
Graph coloring on the GPU.
In GrAPL: Workshop on Graphs, Architectures, Programming, and
Learning (IPDPSW), 2019.
[ bib |
.pdf ]
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[55]
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Ariful Azad and Aydin Buluç.
LACC: a linear-algebraic algorithm for finding connected components
in distributed memory.
In Proceedings of the IPDPS, 2019.
[ bib |
code |
.pdf ]
|
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[56]
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Evangelos Georganas, Rob Egan, Steven Hofmeyr, Eugene Goltsman, Bill Arndt,
Andrew Tritt, Aydin Buluç, Leonid Oliker, and Katherine Yelick.
Extreme scale de novo metagenome assembly.
In Proceedings of the International Conference for High
Performance Computing, Networking, Storage, and Analysis (SC), page 10. IEEE
Press, 2018.
Best Paper Nominee.
[ bib |
code |
arXiv |
.pdf ]
|
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[57]
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Amir Gholami, Ariful Azad, Peter Jin, Kurt Keutzer, and Aydin Buluç.
Integrated model, batch, and domain parallelism in training neural
networks.
In SPAA'18: 30th ACM Symposium on Parallelism in Algorithms and
Architectures, 2018.
[ bib |
arXiv |
.pdf ]
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[58]
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Carl Yang, Aydin Buluç, and John D Owens.
Implementing push-pull efficiently in GraphBLAS.
In 47th International Conference on Parallel Processing (ICPP),
2018.
[ bib |
code |
arXiv |
.pdf ]
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[59]
|
Carl Yang, Aydin Buluç, and John D Owens.
Design principles for sparse matrix multiplication on the GPU.
In 24th International European Conference on Parallel and
Distributed Computing (Euro-Par), 2018.
Distinguished Paper and Best Artifact Award.
[ bib |
code |
arXiv |
.pdf ]
|
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[60]
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Yusuke Nagasaka, Satoshi Matsuoka, Ariful Azad, and Aydin Buluc.
High-performance sparse matrix-matrix products on Intel KNL and
multicore architectures.
In 47th International Conference on Parallel Processing
Workshops (ICPPW), 2018.
[ bib |
code |
arXiv |
.pdf ]
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[61]
|
Ariful Azad, Georgios A. Pavlopoulos, Christos A. Ouzounis, Nikos C. Kyrpides,
and Aydin Buluç.
HipMCL: A high-performance parallel implementation of the Markov
clustering algorithm for large-scale networks.
Nucleic Acids Research (NAR), 2018.
[ bib |
DOI |
code ]
|
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[62]
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Penporn Koanantakool, Alnur Ali, Ariful Azad, Aydin Buluç, Dmitriy
Morozov, Sang-Yun Oh, Leonid Oliker, and Katherine Yelick.
Communication-avoiding optimization methods for distributed
massive-scale sparse inverse covariance estimation.
In The 21st International Conference on Artificial Intelligence
and Statistics (AISTATS), 2018.
[ bib |
code |
.pdf ]
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[63]
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Yang You, Aydin Buluç, and James Demmel.
Scaling deep learning on GPU and Knights Landing clusters.
In Proceedings of the International Conference for High
Performance Computing, Networking, Storage and Analysis (SC'17), 2017.
[ bib |
DOI |
code |
.pdf ]
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[64]
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Ariful Azad and Aydin Buluç.
A work-efficient parallel sparse matrix-sparse vector multiplication
algorithm.
In Proceedings of the IPDPS, 2017.
[ bib |
code |
.pdf ]
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[65]
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Aydin Buluç, Timothy Mattson, Scott McMillan, Jose Moreira, and Carl
Yang.
Design of the GraphBLAS API for C.
In IEEE Workshop on Graph Algorithm Building Blocks, IPDPSW,
2017.
[ bib |
.pdf ]
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[66]
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Ariful Azad, Mathias Jacquelin, Aydin Buluç, and Esmond G. Ng.
The reverse Cuthill-McKee algorithm in distributed-memory.
In Proceedings of the IPDPS, 2017.
[ bib |
code |
.pdf ]
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[67]
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Marquita Ellis, Evangelos Georganas, Rob Egan, Steven Hofmeyr, Aydin
Buluç, Brandon Cook, Leonid Oliker, and Katherine Yelick.
Performance characterization of de novo genome assembly on leading
parallel systems.
In Europar - International European Conference on Parallel and
Distributed Computing, 2017.
[ bib |
.pdf ]
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[68]
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Ariful Azad and Aydin Buluç.
Towards a GraphBLAS library in Chapel.
In Intl. Parallel & Distributed Processing Symposium Workshops
(IPDPSW), 2017.
[ bib |
.pdf ]
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[69]
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Ariful Azad, Aydin Buluç, and Alex Pothen.
Computing maximum cardinality matchings in parallel on bipartite
graphs via tree-grafting.
IEEE Transactions on Parallel and Distributed Systems (TPDS)),
28(1):44-59, 2017.
[ bib |
DOI |
code |
.pdf ]
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[70]
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Timothy G Mattson, Carl Yang, Scott McMillan, Aydin Buluç, and José E
Moreira.
GraphBLAS C API: Ideas for future versions of the specification.
In IEEE High Performance Extreme Computing Conference (HPEC),
2017.
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[71]
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Hasan Metin Aktulga, Md. Afibuzzaman, Samuel Williams, Aydin Buluç,
Meiyue Shao, Chao Yang, Esmond G. Ng, Pieter Maris, and James P. Vary.
A high performance block eigensolver for nuclear configuration
interaction calculations.
IEEE Transactions on Parallel and Distributed Systems (TPDS)),
2017.
[ bib |
DOI |
.pdf ]
|
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[72]
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Evangelos Georganas, Marquita Ellis, Rob Egan, Steven Hofmeyr, Aydin
Buluç, Brandon Cook, Leonid Oliker, and Katherine Yelick.
MerBench: PGAS benchmarks for high performance genome assembly.
In Proceedings of the Second Annual PGAS Applications Workshop,
page 5. ACM, 2017.
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[73]
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Evangelos Georganas, Steven Hofmeyr, Rob Egan, Aydin Buluc, Leonid Oliker,
Daniel Rokhsar, and Katherine Yelick.
Extreme-scale de novo genome assembly.
2017.
To appear as a chapter in Exascale Scientific Applications:
Programming Approaches for Scalability, Performance, and Portability (CRC
Press).
[ bib |
arXiv ]
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[74]
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Ariful Azad, Grey Ballard, Aydin Buluç, James Demmel, Laura Grigori,
Oded Schwartz, Sivan Toledo, and Samuel Williams.
Exploiting multiple levels of parallelism in sparse matrix-matrix
multiplication.
SIAM Journal on Scientific Computing (SISC), 38(6):C624-C651,
2016.
[ bib |
DOI |
code |
arXiv |
.pdf ]
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[75]
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Ariful Azad and Aydin Buluç.
A matrix-algebraic formulation of distributed-memory maximal
cardinality matching algorithms in bipartite graphs.
Parallel Computing, 2016.
[ bib |
DOI |
code ]
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[76]
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Ariful Azad and Aydin Buluç.
Distributed-memory algorithms for maximum cardinality matching in
bipartite graphs.
In Proceedings of the IPDPS. IEEE, 2016.
[ bib |
code |
.pdf ]
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[77]
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Penporn Koanantakool, Ariful Azad, Aydin Buluç, Dmitriy Morozov,
Sang-Yun Oh, Leonid Oliker, and Katherine Yelick.
Communication-avoiding parallel sparse-dense matrix-matrix
multiplication.
In Proceedings of the IPDPS, 2016.
[ bib |
.pdf ]
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[78]
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Veronika Strnadova-Neeley, Aydin Buluc, John R Gilbert, Leonid Oliker, and
Weimin Ouyang.
LiRa: A new likelihood-based similarity score for collaborative
filtering.
arXiv preprint arXiv:1608.08646, 2016.
[ bib |
arXiv ]
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[79]
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Jeremy Kepner, Peter Aaltonen, David Bader, Aydin Buluç, Franz
Franchetti, John Gilbert, Dylan Hutchison, Manoj Kumar, Andrew Lumsdaine,
Henning Meyerhenke, Scott McMillan, José Moreira, John Owens, Carl Yang,
Marcin Zalewski, and Timothy Mattson.
Mathematical foundations of the GraphBLAS.
In IEEE High Performance Extreme Computing (HPEC), 2016.
[ bib |
.pdf ]
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[80]
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Aydin Buluç, Henning Meyerhenke, Ilya Safro, Peter Sanders, and
Christian Schulz.
Recent advances in graph partitioning.
In Algorithm Engineering - Selected Results and Surveys, volume
9220. Lecture Notes in Computer Science, 2016.
[ bib |
DOI |
arXiv ]
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[81]
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Ariful Azad and Aydin Buluç.
Distributed-memory algorithms for maximal cardinality matching using
matrix algebra.
In IEEE International Conference on Cluster Computing
(CLUSTER), 2015.
(full paper).
[ bib |
.pdf ]
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[82]
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Evangelos Georganas, Aydin Buluç, Jarrod Chapman, Steven Hofmeyr,
Chaitanya Aluru, Rob Egan, Leonid Oliker, Daniel Rokhsar, and Katherine
Yelick.
HipMer: An extreme-scale de novo genome assembler.
In International Conference for High Performance Computing,
Networking, Storage and Analysis (SC'15), 2015.
[ bib |
.pdf ]
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[83]
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Veronika Strnadova-Neeley, Aydin Buluç, Joseph Gonzalez, Jarrod Chapman,
John Gilbert, and Leonid Oliker.
Efficient data reduction for large-scale genetic mapping.
In ACM Conference on Bioinformatics, Computational Biology, and
Health Informatics (ACM BCB), 2015.
[ bib |
.pdf ]
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[84]
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Aydin Buluç, Scott Beamer, Kamesh Madduri, Krste Asanović, and David
Patterson.
Distributed-memory breadth-first search on massive graphs.
In D. Bader, editor, Parallel Graph Algorithms. CRC Press,
Taylor-Francis, 2016 (in press).
[ bib |
.pdf ]
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[85]
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Ariful Azad, Aydin Buluç, and Alex Pothen.
A parallel tree grafting algorithm for maximum cardinality matching
in bipartite graphs.
In Proceedings of the IPDPS, 2015.
[ bib |
DOI |
.pdf ]
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[86]
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Evangelos Georganas, Aydin Buluç, Jarrod Chapman, Leonid Oliker, Daniel
Rokhsar, and Katherine Yelick.
meraligner: A fully parallel sequence aligner.
In Proceedings of the IPDPS, 2015.
[ bib |
.pdf ]
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[87]
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Ariful Azad, Aydin Buluç, and John R Gilbert.
Parallel triangle counting and enumeration using matrix algebra.
In Proceedings of the IPDPSW, Workshop on Graph Algorithm
Building Blocks (GABB), pages 804 - 811, 2015.
[ bib |
DOI |
.pdf ]
|
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[88]
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Jarrod Chapman, Martin Mascher, Aydin Buluç, Kerrie Barry, Evangelos
Georganas, Adam Session, Veronika Strnadova, Jerry Jenkins, Sunish Sehgal,
Leonid Oliker, Jeremy Schmutz, Katherine Yelick, Uwe Scholz, Robbie Waugh,
Jesse Poland, Gary Muehlbauer, Nils Stein, and Daniel Rokhsar.
A whole-genome shotgun approach for assembling and anchoring the
hexaploid bread wheat genome.
Genome Biology, 16(26), 2015.
[ bib |
DOI |
.pdf ]
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[89]
|
Adam Lugowski, Shoaib Kamil, Aydin Buluç, Samuel Williams, Erika
Duriakova, Leonid Oliker, Armando Fox, and John Gilbert.
Parallel processing of filtered queries in attributed semantic
graphs.
Journal of Parallel and Distributed Computing (JPDC)),
79-80:115-131, 2015.
[ bib |
DOI |
.pdf ]
|
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[90]
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J. Kepner, D. Bader, A. Buluç, J. Gilbert, J. Kepner, T. Mattson, and
H. Meyerhenke.
Graphs, matrices, and the GraphBLAS: Seven good reasons.
In The International Conference on Computational Science
(ICCS), 2015.
[ bib |
DOI |
arXiv ]
|
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[91]
|
Evangelos Georganas, Aydin Buluç, Jarrod Chapman, Leonid Oliker, Daniel
Rokhsar, and Katherine Yelick.
Parallel de bruijn graph construction and traversal for de novo
genome assembly.
In Proceedings of the International Conference for High
Performance Computing, Networking, Storage and Analysis (SC'14), 2014.
[ bib |
.pdf ]
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[92]
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V. Strnadova, A. Buluç, J. Gonzalez, S. Jegelka, J. Chapman, J. Gilbert,
D. Rokhsar, and L. Oliker.
Efficient and accurate clustering for large-scale genetic mapping.
In The IEEE International Conference on Bioinformatics and
Biomedicine (BIBM'14), 2014.
Regular paper.
[ bib |
.pdf ]
|
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[93]
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Aydin Buluç, John Gilbert, and Sivan Toledo.
Computing shortest paths using sparse Gaussian elimination.
In SIAM Workshop on Network Science (NS14), 2014.
(extended abstract).
[ bib |
.pdf ]
|
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[94]
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D. Bader, A. Buluç, J. Gilbert, J. Gonzalez, J. Kepner, and T. Mattson.
The Graph BLAS effort and its implications for Exascale.
In SIAM Workshop on Exascale Applied Mathematics Challenges and
Opportunities (EX14), 2014.
(extended abstract).
[ bib |
.pdf ]
|
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[95]
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H. Metin Aktulga, Aydin Buluç, Samuel Williams, and Chao Yang.
Optimizing sparse matrix-multiple vectors multiplication for nuclear
configuration interaction calculations.
In Proceedings of the IPDPS. IEEE Computer Society, 2014.
[ bib |
.pdf ]
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[96]
|
T. Mattson, D. Bader, J. Berry, A. Buluç, J. Dongarra, C. Faloutsos,
J. Feo, J. Gilbert, J. Gonzalez, B. Hendrickson, J. Kepner, C. Leiserson,
A. Lumsdaine, D. Padua, S. Poole, S. Reinhardt, M. Stonebraker, S. Wallach,
and A. Yoo.
Standards for graph algorithm primitives.
In High Performance Extreme Computing Conference (HPEC '13).
IEEE, 2013.
(position paper).
[ bib |
.pdf ]
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[97]
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Grey Ballard, Aydin Buluç, James Demmel, Laura Grigori, Benjamin
Lipshitz, Oded Schwartz, and Sivan Toledo.
Communication optimal parallel multiplication of sparse random
matrices.
In SPAA 2013: The 25th ACM Symposium on Parallelism in
Algorithms and Architectures, Montreal, Canada, 2013.
[ bib |
DOI |
.pdf ]
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[98]
|
Aydin Buluç, Erika Duriakova, Armando Fox, John Gilbert, Shoaib Kamil,
Adam Lugowski, Leonid Oliker, and Samuel Williams.
High-productivity and high-performance analysis of filtered semantic
graphs.
In Proceedings of the IPDPS. IEEE Computer Society, 2013.
[ bib |
DOI |
.pdf ]
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[99]
|
Edgar Solomonik, Aydin Buluç, and James Demmel.
Minimizing communication in all-pairs shortest paths.
In Proceedings of the IPDPS. IEEE Computer Society, 2013.
[ bib |
DOI |
.pdf ]
|
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[100]
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Scott Beamer, Aydin Buluç, Krste Asanović, and David Patterson.
Distributed memory breadth-first search revisited: Enabling bottom-up
search.
In Workshop on Multithreaded Architectures and Applications
(MTAAP), in conjunction with IPDPS. IEEE Computer Society, 2013.
[ bib |
DOI |
.pdf ]
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[101]
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Aydin Buluç and Kamesh Madduri.
Graph partitioning for scalable distributed graph computations.
In Graph Partitioning and Graph Clustering (Proc. 10th DIMACS
Implementation Challenge), volume 588 of Contemporary Mathematics,
pages 83-101. AMS, 2013.
[ bib |
.pdf ]
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[102]
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Adam Lugowski, David Alber, Aydin Buluç, John Gilbert, Steve Reinhardt,
Yun Teng, and Andrew Waranis.
A flexible open-source toolbox for scalable complex graph analysis.
In SIAM Conference on Data Mining (SDM), 2012.
[ bib |
.pdf ]
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[103]
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Aydin Buluç and John R. Gilbert.
Parallel sparse matrix-matrix multiplication and indexing:
Implementation and experiments.
SIAM Journal of Scientific Computing (SISC), 34(4):170 - 191,
2012.
[ bib |
DOI |
arXiv |
.pdf ]
|
|
[104]
|
Adam Lugowski, Aydin Buluç, John R. Gilbert, and Steve Reinhardt.
Scalable complex graph analysis with the knowledge discovery toolbox.
In ICASSP, Special session on “Big Data”, 2012.
[ bib |
.pdf ]
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[105]
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K Kandalla, A Buluc, H Subramoni, K Tomko, J Vienne, L Oliker, and DK Panda.
Can network-offload based non-blocking neighborhood MPI collectives
improve communication overheads of irregular graph algorithms?
In IEEE International Conference on Cluster Computing
Workshops, pages 222-230. IEEE, 2012.
[ bib |
DOI |
.pdf ]
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[106]
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Aydin Buluç and Kamesh Madduri.
Parallel breadth-first search on distributed memory systems.
In International Conference for High Performance Computing,
Networking, Storage and Analysis (SC'11), 2011.
[ bib |
DOI |
arXiv |
.pdf ]
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[107]
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Aydin Buluç, Samuel Williams, Leonid Oliker, and James Demmel.
Reduced-bandwidth multithreaded algorithms for sparse matrix-vector
multiplication.
In Proc. IPDPS, 2011.
[ bib |
.pdf ]
|
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[108]
|
Aydin Buluç and John R. Gilbert.
The Combinatorial BLAS: Design, implementation, and applications.
The International Journal of High Performance Computing
Applications, 25(4):496 - 509, 2011.
[ bib |
DOI |
.pdf ]
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[109]
|
Aydin Buluç, John R. Gilbert, and Viral B. Shah.
Implementing Sparse Matrices for Graph Algorithms.
In Jeremy Kepner and John R. Gilbert, editors, Graph Algorithms
in the Language of Linear Algebra. SIAM Press, 2011.
[ bib |
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[110]
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Aydin Buluç and John R. Gilbert.
New Ideas in Sparse Matrix-Matrix Multiplication.
In Jeremy Kepner and John R. Gilbert, editors, Graph Algorithms
in the Language of Linear Algebra. SIAM Press, 2011.
[ bib |
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[111]
|
Aydin Buluç, John R. Gilbert, and Ceren Budak.
Solving path problems on the GPU.
Parallel Computing, 36(5-6):241 - 253, 2010.
[ bib |
DOI |
.pdf ]
|
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[112]
|
Aydin Buluç and John R. Gilbert.
Highly parallel sparse matrix-matrix multiplication.
Technical Report UCSB-CS-2010-10, UCSB CS Department, June 2010.
[ bib |
.pdf ]
|
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[113]
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Aydin Buluç.
Linear Algebraic Primitives for Parallel Computing on Large
Graphs.
PhD thesis, University of California, Santa Barbara, CA, March 2010.
[ bib |
.pdf ]
|
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[114]
|
Aydin Buluç, Jeremy T. Fineman, Matteo Frigo, John R. Gilbert, and
Charles E. Leiserson.
Parallel sparse matrix-vector and matrix-transpose-vector
multiplication using compressed sparse blocks.
In Proc. SPAA, Calgary, Canada, August 2009.
[ bib |
.pdf ]
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[115]
|
Aydin Buluç and John R. Gilbert.
Challenges and advances in parallel sparse matrix-matrix
multiplication.
In The 37th International Conference on Parallel Processing
(ICPP'08), pages 503-510, Portland, Oregon, USA, September 2008.
[ bib |
DOI |
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[116]
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Aydin Buluç and John R. Gilbert.
On the Representation and Multiplication of Hypersparse Matrices.
In Proc. IPDPS, April 2008.
[ bib |
DOI |
.pdf ]
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[117]
|
Aydin Buluç and Erik G. Boman.
Towards scalable parallel hypergraph partitioning.
In CSRI Summer Proceedings, Albuquerque, NM and Livermore, CA,
2008.
[ bib |
.pdf ]
|
