# Ariful Azad

Ariful
Azad

Research Scientist

Web: https://azad.lbl.gov

059-4024H ( M/S 59R4104 )

One Cyclotron Rd

Berkeley,
CA
94720-8142
## Biographical Sketch

Ariful Azad is a Research Scientist in the Computational Research Division at the Lawrence Berkeley National Laboratory (LBNL). His research interests include parallel graph algorithms, high performance computing, combinatorial scientific computing and bioinformatics. Ariful finished his Ph.D. in Computer Science from Purdue University in 2014 and his bachelor degree in Computer Science and Engineering from Bangladesh University of Engineering and Technology (BUET) in 2006.

» Visit Ariful Azad's personal web page for more information.

## Current Projects

- EDGAR: Energy-efficient Data and Graph Algorithms Research
- ExaBiome: Exascale Solutions for Microbiome Analysis
- Parallel Combinatorial Algorithms
- PGAS Graph Analysis Library

## Software

## Journal Articles

### Katherine Yelick, Aydın Buluç, Muaaz Awan, Ariful Azad, Benjamin Brock, Rob Egan, Saliya Ekanayake, Marquita Ellis, Evangelos Georganas, Giulia Guidi, Steven Hofmeyr, Oguz Selvitopi, Cristina Teodoropol, Leonid Oliker, "The parallelism motifs of genomic data analysis", Philosophical Transactions of The Royal Society A: Mathematical, Physical and Engineering Sciences, 2020,

### Ariful Azad, Georgios A. Pavlopoulos, Christos A. Ouzounis, Nikos C. Kyrpides, Aydin Buluç, "HipMCL: A high-performance parallel implementation of the Markov cluster algorithm for large scale networks", Nucleic Acids Research, April 2018,

### Ariful Azad, Grey Ballard, Aydin Buluc, James Demmel, Laura Grigori, Oded Schwartz, Sivan Toledo, Samuel Williams, "Exploiting multiple levels of parallelism in sparse matrix-matrix multiplication", SIAM Journal on Scientific Computing, 38(6), C624–C651, November 2016, doi: 10.1137/15M104253X

- Download File: SISC-SpGEMM.pdf (pdf: 1.5 MB)

### Ariful Azad, Bartek Rajwa, Alex Pothen, "Immunophenotype Discovery, Hierarchical Organization, and Template-based Classification of Flow Cytometry Samples", Frontiers in Oncology, August 31, 2016,

- Download File: frontier-immunophenotypes.pdf (pdf: 15 MB)

### Ariful Azad, Bartek Rajwa, Alex Pothen, "flowVS: Channel-Specic Variance Stabilization in Flow Cytometry", BMC Bioinformatics, June 2016,

### Ariful Azad, Aydın Buluç, "A matrix-algebraic formulation of distributed-memory maximal cardinality matching algorithms in bipartite graphs", Parallel Computing, June 2016,

### Ariful Azad, Aydın Buluç, Alex Pothen, "Computing Maximum Cardinality Matchings in Parallel on Bipartite Graphs via Tree-Grafting", IEEE Transactions on Parallel and Distributed Systems (TPDS), May 2016,

- Download File: matchingGraft-TPDS.pdf (pdf: 1.4 MB)

### Mahantesh Halappanavar, Alex Pothen, Ariful Azad, Fredrik Manne, Johannes Langguth, Arif Khan, "Codesign Lessons Learned from Implementing Graph Matching on Multithreaded Architectures", IEEE Computer, August 2015,

### J Langguth, A Azad, M Halappanavar, F Manne, "On parallel push–relabel based algorithms for bipartite maximum matching", Parallel Computing, January 2014,

### N. Aghaeepour, G. Finak, D. Dougall, A. Hadj-Khodabakhshi, P. Mah, G. Obermoser, J. Spidlen, I. Taylor, S. A Wuensch, J. Bramson, C. Eaves, A. P. Weng, E. Fortuno III, K. Ho, T. Kollmann, W. Rogers, S. Rosa, B. Dalal, A. Azad, A. Pothen, A. Brandes, H. Bretschneider, R. Bruggner, R. Finck, R. Jia, N. Zimmerman, M. Linderman, D. Dill, G. Nolan, C. Chan, F. Khettabi, K. Neill, M. Chikina, A. Gupta, P. Shooshtari, H. Zare, P. Jager, M. Jiang, J. Keilwagen, J. M. Maisog, P. Majek, J. Vilcek, T. Manninen, H. Huttunen, P. Ruusuvuori, M. Nykter, G. J. McLachlan, K. Wang, I. Naim, G. Sharma, R. Nikolic, S. Pyne, Y. Qian, P. Qiu, J. Quinn, A. Roth, R. Norel, G. Stolovitzky, P. Meyer, J. Saez-Rodriguez, M. Bhattacharjee, M. Biehl, P. Bucher, K. Bunte, B. .Camillo, S. Dimitrieva, J. Grau, I. Grosse, S. Posch, N. Guex, J. Keilwagen, M. Kursa, B. Liu, M. Maienschein-Cline, T. Manninen, G. J. McLachlan, P. Seifert, M. Strickert, J. Vilar, H. Hoos, T. Mosmann, R. Brinkman, R. Gottardo, and R. Scheuermann, "Critical Assessment of Automated Flow Cytometry Analysis Techniques", Nature Methods, 2013,

### Ariful Azad, Saumyadipta Pyne, Alex Pothen, "Matching phosphorylation response patterns of antigen-receptor-stimulated T cells via flow cytometry", BMC Bioinformatics, 2012,

## Conference Papers

### Oguz Selvitopi*, Saliya Ekanayake*, Giulia Guidi, Georgios Pavlopoulos, Ariful Azad, Aydın Buluç, "Distributed Many-to-Many Protein Sequence Alignment Using Sparse Matrices", Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis (SC’20)., 2020,

(*:joint first authors)

### P Koanantakool, A Ali, A Azad, A Buluç, D Morozov, L Oliker, KA Yelick, S-Y Oh, "Communication-Avoiding Optimization Methods for Distributed Massive-Scale Sparse Inverse Covariance Estimation.", Proceedings of Machine Learning Research, PMLR, 2018, 84:1376--1386,

### Ariful Azad, Aydin Buluc, "Towards a GraphBLAS Library in Chapel", IPDPS Workshops, Orlando, FL, May 2017,

- Download File: GraphBLAS-Chapel.pdf (pdf: 368 KB)

### Ariful Azad, Aydin Buluc, "A work-efficient parallel sparse matrix-sparse vector multiplication algorithm", IEEE International Parallel & Distributed Processing Symposium (IPDPS), Orlando, FL, May 2017,

- Download File: SpMSpV-ipdps17.pdf (pdf: 422 KB)

### Ariful Azad, Mathias Jacquelin, Aydin Bulu\cc, Esmond G Ng, "The reverse Cuthill-McKee algorithm in distributed-memory", Parallel and Distributed Processing Symposium (IPDPS), 2017 IEEE International, January 2017, 22--31,

- Download File: RCM-ipdps17.pdf (pdf: 1.1 MB)

### Ariful Azad, Aydin Buluç, "Distributed-Memory Algorithms for Maximum Cardinality Matching in Bipartite Graphs", IEEE International Parallel & Distributed Processing Symposium (IPDPS), May 2016,

- Download File: MaximumMatchingDist-IPDPS16.pdf (pdf: 620 KB)

### P Koanantakool, A Azad, A Buluc, D Morozov, SY Oh, L Oliker, K Yelick, "Communication-Avoiding Parallel Sparse-Dense Matrix-Matrix Multiplication", Proceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium, IPDPS 2016, January 2016, 842--853, doi: 10.1109/IPDPS.2016.117

### Ariful Azad, Aydin Buluc, "Distributed-Memory Algorithms for Maximal Cardinality Matching using Matrix Algebra", IEEE Cluster, Chicago, IL, September 2015,

- Download File: maximalMatching-distribute.pdf (pdf: 659 KB)

### Ariful Azad, Aydin Buluc, John Gilbert, "Parallel Triangle Counting and Enumeration using Matrix Algebra", Workshop on Graph Algorithms Building Blocks (GABB), in conjunction with IPDPS, IEEE, May 2015,

- Download File: triangles-gabb.pdf (pdf: 384 KB)

### Ariful Azad, Aydin Buluç, Alex Pothen, "A Parallel Tree Grafting Algorithm for Maximum Cardinality Matching in Bipartite Graphs", International Parallel and Distributed Processing Symposium (IPDPS), May 2015,

- Download File: matchingGraft.pdf (pdf: 518 KB)

### A. Azad, A. Khan, B. Rajwa, S. Pyne, A. Pothen, "Classifying Immunophenotypes with Templates from Flow Cytometry", ACM BCB, 2013, doi: 10.1145/2506583.2506627

### A. Azad, M. Halappanavar, S. Rajamanickam, A. Khan, E. Boman, A. Pothen, "Multithreaded Algorithms for Maximum Matching in Bipartite Graphs", IPDPS, May 2012, doi: 10.1109/IPDPS.2012.82

### Ariful Azad, Alex Pothen, "Multithreaded algorithms for matching in graphs with application to data analysis in flow cytometry", IPDPSW, May 2012, doi: 10.1109/IPDPSW.2012.310

## Presentation/Talks

### Ariful Azad, Aydın Buluç, Distributed-memory algorithms for cardinality matching using matrix algebra, SIAM Conference on Parallel Processing for Scientific Computing (PP), Paris, France, April 2016,

- Download File: Azad-SIAM-PP16.pdf (pdf: 1.3 MB)

### A. Azad, G. Ballard, A. Buluc, J. Demmel, J. Gilbert, L. Grigori, O. Schwartz, S. Toledo, S. Williams, Parallel Sparse Matrix-Matrix Multiplication and Its Use in Triangle Counting and Enumeration, SIAM ALA, October 26, 2015,

- Download File: SIAM-LA-2015-SpGEMM.pdf (pdf: 3 MB)
- Download File: SIAM-LA-2015-SpGEMM.pptx (pptx: 2.5 MB)