Publications

2021 -- :

Kalyan Kumar Garepaty, Daniel Lokshtanov, Hemanta K. Maji and Alex Pothen The chromatic number of squares of random Erdos-Renyi graphs, Journal of Combinatorics, 14(4), pp. 507-537, 2023.

Abida Sanjana Shemonti, Alex Pothen, Terry Powley, Bartek Rajwa (and others) A novel statistical methodology for quantifying the spatial arrangement of axons in peripheral nerves, Frontiers in Neuroscience, 17, 32pp., 2023.

Hanjing Xu, Samudra Dasgupta, Alex Pothen and Arnab Banerjee, Dynamic Asset Allocation with expected shortfall via quantum annealing, Entropy, 25(3), 541, 20pp., 2023.

Siddhartha Shankar Das, Ashutosh Dutta, Sumit Purohit, Edoardo Serra, Mahantesh Halappanavar, and Alex Pothen, Towards automatic mapping of vulnerabilities to attack patterns using Large Language Models, Proceedings of the IEEE International Symosium on Technologies for Homeland Security (HST), pp. 1-7, 2022.
Awarded the best paper prize at the conference.

Pasqua D'Ambra, Fabio Durastante, S M Ferdous, Salvatore Philippone, Mahantesh Halappanavar and Alex Pothen, AMG Preconditioners based on parallel hybrid coarsening exploiting multi-objective graph matching, Proc. 31st Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP), pp. 59-67, 2023.

S M Ferdous, Alex Pothen, Arif Khan, Ajay Panyala and Mahantesh Halappanavar A parallel approximation algorithm for maximizing submodular b-matching, Proceedings of the First SIAM Conference on Applied and Computational Combinatorial Algorithms (ACDA), pp. 45-56, July 2021.

Ahmed Al-Herz and Alex Pothen A 2/3-approximation algorithm for vertex-weighted matching, Discrete Applied Mathematics, 308, pp. 46-67, 2022. (Publshed on line Oct. 19, 2019.)

Siddhartha Shankar Das, Edoardo Serra, Mahantesh Halappanavar, Alex Pothen, and Ehab El-Shaer V2W-BERT: A framework for effective hierarchical multiclass classification of software vulnerabilities, Proceedings of the IEEE Conference on Data Science and Advanced Analytics (DSAA), pp. 45-56, 11 pp., 2021.
Awarded the best paper prize at the conference.

S Acer, A. Azad, E. Boman, et al. ExaGraph: Graph and combinatorial methods for enabling Exascale applications, SAGE International Journal of High Performance Computing Applications, 2021.

2016 -- 2020:

Ahmed Al-Herz and Alex Pothen A parallel 2/3- approximation algorithm for vertex-weighted matching, Proceedings of SIAM CSC20, Feb. 2020.

Xin Cheng, Hemanta K. Maji and Alex Pothen Graphs with tunable chromatic numbers for parallel coloring, Proceedings of SIAM CSC20, Seattle, Feb. 2020.

Alex Pothen, S M Ferdous, and Fredrik Manne Approximation Algorithms in Combinatorial Scientific Computing, Acta Numerica, 28, pp. 541-633, 2019.

Arif Khan, Alex Pothen, S M Ferdous, Mahantesh Halappanavar and Antonino Tumeo Adaptive anonymization of data using b-Edge cover, Proceedings of Supercomputing, Nov. 2018.

Florin Dobrian, Mahantesh Halappanvar, Alex Pothen and Ahmed Al-Herz, An approximation algorithm for vertex-weighted matching in bipartite graphs, SIAM Journal on Scientific Computing, 41(1), A566-591, 2019.

Arif Khan, Alex Pothen and S M Ferdous, Parallel Algorithms through Approximation: b-Edge cover, Proceedings of IPDPS, May 2018.

S M Ferdous, Alex Pothen, and Arif Khan, New approximation algorithms for Minimum Weighted Edgecover, Proceedings of the Seventh SIAM Workshop on Combinatorial Scientific Computing (CSC18), June 2018.

Yu-Hong Yeung, Alex Pothen, Mahantesh Halappanavar and Zhenyu Huang, AMPS: An augmented matrix formulation for principal submatrix updates with application to power grids, SIAM J. Scientific Computing, 39(5), S809-827, 2017.

Mu Wang, Guang Lin, and Alex Pothen, Using Automatic Differentiation for compressive sensing in uncertainty quantification, Optimization Methods and Software, Published Online, 14 pp., Aug. 2017. DOI: 10.1080/10556788.2017.1359267

Ariful Azad, Aydin Buluc and Alex Pothen, Computing Maximum Cardinality Matchings in Parallel on Bipartite Graphs via Tree Grafting, IEEE Transactions on Distributed and Parallel Systems, 28(1), pp. 44-59, 2017.

Tianying Wu, Vaithianathan "Mani" Venkatasubramanian, and Alex Pothen, Fast parallel stochastic subspace algorithms for large-scale ambient oscillation monitoring, IEEE Transactions on Smart Grid, 8(3), pp. 1494-1503, 2017.

Ariful Azad, Bartek Rajwa and Alex Pothen, Immunophenotype discovery, hierarchical organization, and template-based classification of flow cytometry samples, Frontiers in Oncology, 6, 20pp., August 2016. DOI: 10.3389/fonc.2016.00188

Arif Khan and Alex Pothen, A new 3/2-approximation algorithm for the b-Edgecover problem, Proceedings of Seventh SIAM Workshop on Combinatorial Scientific Computing (CSC16), pp. 52-61, Nov. 2016.

Arif Khan, Alex Pothen, Md. Mostofa Ali Patwary, Mahantesh Halappanavar, Nadathur Rajagopalan Satish, Narayanan Sundaram, and Pradeep Dubey, Designing scalable b-Matching algorithms on distributed memory multiprocessors via approximation, Proceedings of Supercomputing (SC16), ACM/IEEE, 11 pages, Nov. 2016.

Mu Wang, Assefaw H. Gebremedhin, and Alex Pothen, Capitalizing on Live Variables: Efficient Hessian computations for Automatic Differentiation, Mathematical Programming Computation, 8(4), pp. 393-433, Dec. 2016.

Mu Wang, Alex Pothen, and Paul Hovland, Edge Pushing is equivalent to vertex elimination for computing Hessians, Proceedings of the Seventh SIAM Workshop on Combinatorial Scientific Computing (CSC16), pp. 102-111, Nov. 2016.

Yu-Hong Yeung, Jessica Crouch and Alex Pothen, Interactively cutting and constraining nodes in a mesh by augmented matrices, ACM Transactions on Graphics, 35, Article 18, 17 pp., 2016. Presented at SIGGRAPH 2016, Anaheim CA, July 2016. Here is a video of our results (MP4 format)

Arif Khan, Alex Pothen, Md Mostofa Ali Patwary, Nadathur Satish, Narayanan Sundaram, Fredrik Manne, Mahantesh Halappanavar and Pradeep Dubey, Efficient Approximation Algorithms for Weighted b-Matching, SIAM Journal on Scientific Computing, 38(5), S593-S619, 2016.

Ariful Azad, Bartek Rajwa and Alex Pothen, FlowVS: Channel-Specific Variance Stabilization in Flow Cytometry, BMC Bioinformatics, 17:291, 15 pp., 2016.

Tianying Wu S. Arash Nezam Sarmadi, Vaithianathan "Mani" Venkatasubramanian, Alex Pothen and Ananth Kalyanaraman, Fast SVD computations for synchrophasor algorithms, IEEE PES Transactions on Power Systems, 31(2), 1651-1652, March 2016.

2011 -- 2015:

Mahantesh Halappanavar, Alex Pothen, Fredrik Manne, Ariful Azad, Johannes Langguth and Arif Khan, Codesign Lessons Learned from Implementing Graph Matching Algorithms on Multithreaded Architectures, IEEE Computer, pp. 46-55, August 2015.

Ariful Azad, Aydin Buluc and Alex Pothen, A parallel tree grafting algorithm for computing maximum cardinality matchings in bipartite graphs, Proceedings of IPDPS, pp. 1075- 1084, 2015.

Assefaw H. Gebremedhin, Duc Nguyen, Mostofa Ali Patwary, and Alex Pothen, ColPack: Graph coloring software for derivative computation and beyond, ACM Transactions on Mathematical Software, 40 (1), 30 pp., 2013.

Ariful Azad, Arif Khan, Bartek Rajwa, Saumyadipta Pyne and Alex Pothen, Classifying immunophenotypes with templates from Flow Cytometry, Proceedings of the ACM Conference on Bioinformatics and Computational Biology (BCB), 10 pages, 2013

Umit Catalyurek, John Feo, Assefaw H. Gebremedhin, Mahantesh Halappanavar, and Alex Pothen, Graph Coloring Algorithms for Multi-core and Massively Multithreaded Architectures, Parallel Computing, 38, 576-594, 2012.

Benjamin Letschert, Kshitij Kulshreshtha, Andrea Walther, Duc Nguyen, Assefaw Gebremedhin, and Alex Pothen, Exploiting sparsity in Automatic Differentiation on multicore architectures, Lecture Notes in Computer Science, 87, pp. 151-161, 2012. (Proceedings of AD 2012.)

Arif Khan, David Gleich, Mahantesh Halappanavar and Alex Pothen, A multithreaded algorithm for network alignment via approximate matching, Proceedings of Supercomputing 2012, 11 pp., IEEE and ACM Press.

Ariful Azad, Mahantesh Halappanavar, Siva Rajamanickam, Erik Boman, Arif Khan and Alex Pothen, Multithreaded algorithms for maximum matching in bipartite graphs, Proceedings of 26th IPDPS, pp. 860-872, 2012.

Mahantesh Halappanavar, John Feo, Oreste Villa, Florin Dobrian, and Alex Pothen, Approximate weighted matching on emerging manycore and multithreaded architectures, International Journal on High Performance Computing and Applications, 26, 413-430, 2012.

Ariful Azad, Saumyadipta Pyne and Alex Pothen, Matching phosphorylation response patterns of antigen-receptor-stimulated T cells via Flow Cytometry, BMC Bioinformatics, 13(Suppl 2): S10, 2012.

Mostofa Ali Patwary, Assefaw H. Gebremedhin and Alex Pothen, New multithreaded ordering and coloring algorithms for multicore architectures, Europar 2011, Lecture Notes in Computer Science, Vol. 6853, pp. 250-262, Springer, 2011.

Umit Catalyurek, Florin Dobrian, Assefaw Gebremedhin, Mahantesh Halappanavar, and Alex Pothen, Distributed memory algorithms for matching and coloring, Proceedings of IPDPS (Workshop on Parallel Computing and Optimization), 2011.

Bruce Hendrickson and Alex Pothen, Combinatorial Scientific Computing: Past Successes, Current Challenges and Future Opportunities, Chapter 1 in Combinatorial Scientific Computing, Uwe Naumann and Olaf Schenk (eds.), CRC Press/Chapman and Hall, Dec. 2011.

2006 -- 2010:

Ariful Azad, Johannes Langguth, Youhan Fang, Alan Qi and Alex Pothen, Identifying Rare Cell Populations in Comparative Flow Cytometry, Workshop on Algorithms in Bioinformatics (WABI) 2010, Lecture Notes in Bioinformatics, 6293, pp. 162-175, 2010.

E. Ramadan, C. Osgood, and A. Pothen, Discovering overlapping modules and bridge proteins in proteomic networks, Proceedings of the First ACM Conference on Bioinformatics and Computational Biology, pp. 366-369, 2010.

A.H. Gebremedhin, A. Pothen, A. Tarafdar, and A. Walther, Efficient computation of sparse Hessians using coloring and Automatic Differentiation, INFORMS Journal on Computing, 21(2), pp. 209-223, 2009.

A.H. Gebremedhin, A. Pothen, and A. Walther, Exploiting Sparsity in Jacobian Computation via Coloring and Automatic Differentiation: a Case Study in a Simulated Moving Bed process, In C. Bischof et al. (Eds.): Proceeding of AD2008, The 5th Int'l Conference on AD, Lecture Notes in Computational Science and Engineering 64, pp. 339-349, 2008, Springer.

Emad Ramadan, Michael Ward, Xin Guo, Sarah Durkin, Adam Sawyer, Marcelo Viela, Chris Osgood, Alex Pothen and O. John Semmes, Physical and in silico approaches identify DNA-PK in a Tax DNA-damage response interactome, Retrovirology, 5:92, 13 pages, 2008

E.G. Boman, D. Bozdag, U. Catalyurek, K. Devine, A.H. Gebremedhin, P. Hovland and A. Pothen, Combinatorial Algorithms for Computational Science and Engineering, Journal of Physics: Conference Series 125 (2008) 012071, 5 pp. SciDAC 2008.

A. Gebremedhin, A. Tarafdar, F. Manne and A. Pothen, New Acyclic and Star Coloring Algorithms with Applications to Hessian Computation, SIAM Journal on Scientific Computing, Vol 29, No 3, pp 1042--1072, 2007.

A. Pothen, A.H. Gebremedhin, F. Dobrian, E.G. Boman, K.D. Devine, B.A. Hendrickson, P. Hovland, B. Norris, J. Utke, U. Catalyurek, M.M. Strout, Combinatorial Algorithms for Petascale Science, SciDAC Review, Issue 5, pp 26-35, Fall 2007.

E.G. Boman, D. Bozdag, U.V. Catalyurek, K.D. Devine, A.H. Gebremedhin, P.D. Hovland, A. Pothen, and M.M. Strout, Enabling high performance computational science through combinatorial algorithms, Proceedings of SciDAC 2007, Journal of Physics: Conference Series 78 (2007) 012058.

B. Hendrickson, and A. Pothen, Combinatorial Scientific Computing: The enabling power of discrete algorithms in computational science, Proceedings of the 7th International Meeting on High Performance Computing for Computational Science (VECPAR'06), Lecture Notes in Computer Science, Springer Verlag, 21 pp., 2006. (Invited paper)

A. Pinar, E. Chow and A. Pothen, Combinatorial Algorithms for Computing Column Space Bases that have Sparse Inverses, Electronic Transactions on Numerical Analysis, 22, pp. 122--145, 2006.

S. Bhomwick, E.G. Boman, K. Devine, A.H. Gebremedhin, B. Hendrickson, P. Hovland, T. Munson and A. Pothen, Combinatorial Algorithms Enabling Computational Science: Tales from the Front, Journal of Physics: Conference Series 46 (2006), 453-457, SciDAC 2006.

2001 -- 2005:

Assefaw Gebremedhin, Fredrik Manne and Alex Pothen, What Color is Your Jacobian? Graph Coloring for Computing Derivatives, SIAM Review, Vol. 47 (4), pp. 629--705, 2005.

E. Ramadan, C. Osgood, and A. Pothen, The architecture of a proteomic network in the yeast, Proceedings of CompLife2005, Lecture Notes in Bioinformatics, Vol. 3695, pp. 265--276, 2005.

Badr Al-Mutairy, Jolan E. Walter, Alex Pothen and Douglas K. Mitchell, Genomic mapping of genome-linked viral protein (VPg) and helicase of astroviruses, Virus Genes, 31 (1), pp. 21--30, 2005.
This paper computationally predicted a VPg gene in a human astrovirus, and now it has been experimentally confirmed! See
C. Fuentes, A. Bosch, R. M. Pinto and S. Guix, Identification of human astrovirus genome-linked protein (VPg) essential for virus infectivity, Journal of Virology, Vol. 86, 18, 10070-78, 2012.

F. Dobrian and A. Pothen, Oblio: Design and Performance, in State of the Art in Scientific Computing, J. Dongarra, K. Madsen and J. Wasniewski (eds.), Lecture Notes in Computer Science, 3732, pp. 758--767, 2005.

A. Pothen, Dedication to Alan George, Electronic Transactions on Numerical Analysis, Special Volume on Combinatorial Scientific Computing, 21, pp. vii--xviii, Dec. 2005.

M. Wagner, D. Naik, A. Pothen et al., Computational protein biomarker prediction: a case study for prostate cancer, BMC Bioinformatics, 5, 26 pp., March 2004.

Emad Ramadan, Arijit Tarafdar, and A. Pothen, A hypergraph model for the yeast protein complex network, Proceedings of the IEEE Workshop on High Performance Computational Biology, April 2004. (Presented at the HICOMB Workshop, Santa Fe, NM, IEEE)

A. Pothen and S. Toledo, Elimination structures in scientific computing, In Handbook on Data Structures and Applications, Chapter 59, 29 pp., Dinesh Mehta and Sartaj Sahni, editors, Chapman and Hall /CRC, 2004.

Michael Wagner, Dayanand Naik, and A. Pothen, Protocols for disease classification from mass spectrometry data, Proteomics, Vol 3 (9), pp. 1692--1698, Sep 2003. (Presented at the First Annual Proteomics Datamining Conference at the Duke Medical School)

Florin Dobrian and A. Pothen, A comparison between three external memory algorithms for factoring sparse matrices, Proceedings of the SIAM Conference on Applied Linear Algebra, 11 pp, July 2003.

Pinar Heggernes, Stan Eisenstat, Gary Kumfert and A. Pothen, The computational complexity of the minimum degree algorithm, Proceedings of the Norwegian Conference on Computer Science NIK, 2002.

David Hysom and A. Pothen, Level-based Incomplete LU factorization: Graph Model and Algorithms, Tech Report UCRL-JC-150789, Lawrence Livermore National Labs, 19 pp., Nov 2002.

D. Hysom and A. Pothen, A scalable parallel algorithm for incomplete factor preconditioning, SIAM Journal on Scientific Computing, 22(6), 2194--2215, 2001.

Florin Dobrian and A. Pothen, The Design of I/O efficient Sparse Direct Solvers, Proceedings of Supercomputing 2001, IEEE and ACM.

Florin Dobrian, External memory algorithms for factoring sparse matrices, PhD Thesis, Old Dominion University, Dec. 2001.

David Hysom, New parallel and sequential algorithms for incomplete factor preconditioners, PhD Thesis, Old Dominion University, Dec. 2001.

1996 -- 2000:

F. Dobrian and A. Pothen, Oblio: a sparse direct solver library for serial and parallel computations, Technical Report describing the OBLIO software library, 2000.

F. Dobrian, G. Kumfert and A. Pothen, The Design of Sparse Direct Solvers using Object-Oriented Techniques , In Modern Software Tools in Scientific Computing, A. M. Bruaset, H. P. Langtangen and E. Quak (eds.), pp. 89--131, Springer-Verlag, 2000.

Gary Karl Kumfert, An object-oriented algorithmic laboratory for ordering sparse matrices, PhD Thesis, Old Dominion University, Dec. 2000.

D. Hysom and A. Pothen, Efficient Parallel Computation of ILU(k) Preconditioners, Proceedings of Supercomputing '99 (CDROM), 1999.

G. Kumfert and A. Pothen, An object-oriented collection of minimum degree algorithms: design, implementation, and experience,s In Computing in Object-oriented Parallel Environments, Lecture Notes in Computer Science 1505, D.~Caromel et al (eds.), pp. 95--106, Springer Verlag, 1998. (Proceedings of the Second International Symposium on Computing in Object-oriented Parallel Environments, Santa Fe, 1998.)

Florin Dobrian, Gary Kumfert, and Alex Pothen, Object-Oriented Design for Sparse Direct Solvers, In Computing in Object-oriented Parallel Environments, Lecture Notes in Computer Science 1505, D.~Caromel et al (eds.), pp. 207--214, Springer Verlag, 1998. (Proceedings of the Second International Symposium on Computing in Object-oriented Parallel Environments, Santa Fe, 1998.)

G. Kumfert and A. Pothen, Two improved algorithms for envelope and wavefront reduction, invited paper, BIT, 37(3), 559--590, 1997.

A. George and A. Pothen, An analysis of spectral envelope-reduction via quadratic assignment problems, SIAM Journal of Matrix Analysis and its Applications, 18(3), pp. 706--732, 1997.

A. Pothen, Graph partitioning algorithms with applications to scientific computing, In Parallel Numerical Algorithms, D. E. Keyes, A. H. Sameh and V. Venkatakrishnan (eds.), Kluwer Academic Press, 1996. (46 pages)

I. Stoica and A. Pothen, A robust and flexible microeconomic scheduler for parallel computers, Preprint, Dec 1996. Proceedings of Third International Conference on High Performance Computing, Thiruvananthapuram, India.

1990 -- 1995:

S. T. Barnard, A. Pothen and H. D. Simon, A spectral algorithm for envelope reduction of sparse matrices, Numerical Linear Algebra with Applications, 2, pp. 317--334, 1995.

B. W. Peyton, A. Pothen and X. Yuan, A clique tree algorithm for partitioning a chordal graph into transitive subgraphs, Linear Algebra and its Applications, 223/224, pp. 553--588, 1995.

I. Stoica, H. Abdel-Wahab, and A.Pothen, A microeconomic scheduler for parallel computers, In Load-balancing and Job Scheduling for Parallel Computers, D. G. Feitelson and L. Rudolph (eds.), Lecture Notes in Computer Science, Vol. 949, Springer-Verlag, pp. 200--218, 1995.

R.A.Brualdi, A. Pothen and S. Friedland, The sparse basis problem and multilinear algebra, SIAM J. Matrix Anal. Applic., 16, pp. 1--20, 1995.

N.J. Higham and A.Pothen, Stability of the partitioned inverse method for parallel solution of sparse triangular systems, SIAM J. Sci. Computing, 15, 139--148, 1994.

A. Pothen, Predicting the structure of sparse orthogonal factors, Lin. Alg. Applic., 194 (1993), 183--204.

B. W. Peyton, A. Pothen and X. Yuan, Partitioning a chordal graph into transitive subgraphs for parallel sparse triangular solution, Linear Algebra and its Applications, 192, pp. 329--354, 1993.

F. L. Alvarado, A. Pothen and R. S. Schreiber, Highly parallel sparse triangular solution, In Graph Theory and Sparse Matrix Computation, IMA vol. in Appl. Math., 56, 141--158, 1993. (Springer Verlag)

A. Pothen and C.Sun, A mapping algorithm for parallel sparse Cholesky factorization, SIAM J. Sci. Computing, 14 (1993), 1253--1257.

A. Pothen and F. Alvarado, A fast reordering algorithm for parallel sparse triangular solution, SIAM Journal on Scientific and Statistical Computing, 13 (2), pp. 645--653, 1992.

A. Pothen, H. D. Simon, and K. Liou, Partitioning sparse matrices with eigenvectors of graphs, SIAM Journal on Matrix Analysis and its Applications, 11, pp. 430--452, 1990.

A. Pothen and C. Fan, Computing the block triangular form of a sparse matrix, ACM Transactions on Mathematical Software, 16 (4), pp. 303--324, 1990.

A. Pothen and C. Sun, Compact clique tree data structures in sparse matrix factorizations, SIAM Proceedings in Applied Mathematics, 46, pp. 180--204, 1990.

1986 -- 1989:

J. G. Lewis, B. W. Peyton, and A. Pothen, A fast algorithm for reordering sparse matrices for parallel factorization, SIAM Journal on Scientific and Statistical Computing, 10, pp. 1146--1173, 1989.

A. Pothen and P. Raghavan, Distributed orthogonal factorization: Givens and Householder algorithms, SIAM Journal on Scientific and Statistical Computing, 10, pp. 1113--1134, 1989.

A. Pothen, Sparse null basis computations in structural optimization, Numerische Mathematik, 55, pp. 501--519, 1989.

A. Pothen, The complexity of optimal elimination trees, Technical Report CS 88-16, Department of Computer Science, Penn State, April 1988.

A. Pothen, S. Jha, and U. B. Vemulapati, Orthogonal factorization on a distributed memory multiprocessor, Hypercube Multiprocessors 1987, pp. 587-596, SIAM, Philadelphia, 1987.

T. F. Coleman and A. Pothen, The null space problem II: algorithms, SIAM Journal on Algebraic and Discrete Methods, 8, pp. 544--563, 1987.

T. F. Coleman and A. Pothen, The null space problem I: complexity, SIAM Journal on Algebraic and Discrete Methods, 7, pp. 527--537, 1986.

A. Pothen and G. Basu, The single crystal spectra of tetrakis-thiourea nickel (II) chloride, Indian Journal on Chemistry, pp. 5-8, 1978.