## Archive of selected HPCLAB (scgroup) publications and presentations

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**Selected publications / reports / presentations
**

- [T] L. Wu, A. Stathopoulos, J. Laeuchli, V. Kalantzis, E. Gallopoulos, “Estimating the Trace of the Matrix Inverse by Interpolating from the Diagonal of an Approximate Inverse”, arXiv:1507.07227 [cs.NA], July 2015. Revised version in J. Computational Physics, 326:828-844, Dec. 2016, http://dx.doi.org/10.1016/j.jcp.2016.09.001.
- [T] E. Gallopoulos, P. Drineas, I. Ipsen and M. Mahoney, “RandNLA, Pythons, and the CUR for your data problems”, SIAM News, Jan./Feb. 2016.
- [N] E. Gallopoulos, B. Philippe and A.H. Sameh, “Parallelism in Matrix Computations”, Scientific Computation Series, Springer (2015). See the publisher book flyer, TOC, Preface. See also the authors’ page containing bibliographical updates and errata.

- [T] I. Venetis, A. Sobczyk, A. Kouris, A. Nakos, N. Nikoloutsakos and E. Gallopoulos, “A general tridiagonal solver for coprocessors: Adapting g-Spike for the Intel Xeon Phi”, PARCO 2015, Edinburgh, Sept. 2015. Ιn the conference proceedings, Parallel Computing: On the Road to Exascale, vol. 27 of Advances in Parallel Computing, edited by Joubert, G.R., Leather, H., Parsons, M., Peters, F., Sawyer, M., IOS Press, April 2016
- [T] I. Venetis, A. Kouris, A. Sobczyk, E. Gallopoulos and A.H. Sameh, “A direct tridiagonal solver based on Givens rotations for GPU-based architectures”, Parallel Computing available online April 2015. First version appeared as Technical Report CEID-HPCLAB-SCG-6/11-14. Nov. 2014. Revised March 2015, HPCLAB-TR-SCG(02)03-2015.

- [N] I. Venetis, N. Nikoloutsakos, E. Gallopoulos and I. Ekaterinaris, “Towards the Implementation of Wind Turbine Simulations on Many-Core Systems”, Proc. 53rd AIAA Aerospace Sciences Meeting, AIAA Science and Technology Forum 2015, Florida, Jan. 2015. Also HPCLAB-TR-SCG-09, Dec. 2014.
- [N] E. Gallopoulos, “Revisiting rapid elliptic solvers with matrix functions”, Structured Numerical Linear and Multilinear Algebra: Analysis, Algorithms and Applications (SLA 2014), Kalamata, Sept. 2014.
- [N] I. Venetis, N. Nikoloutsakos, E. Gallopoulos and I. Ekaterinaris, “Local stiffness matrix calculations for FSI: Applications on multiGPU systems”, NUMAN 2014, Chania, Sept. 2014.
- [N] I. Venetis, A. Kouris, A. Sobczyk, E. Gallopoulos and A.H. Sameh, “Revisiting the Spike-based framework for GPU banded solvers: A Givens rotation approach for tridiagonal systems in CUDA“, PMAA 2014, Lugano, July 2014.
- [T] E.M. Kontopoulou, D. Zeimpekis and E. Gallopoulos, “Randomized Algorithms: progress in TMG”, 2013 CFE-ERCIM

Meeting, London, Dec. 2013. - [T] C. Bekas, V. Kalantzis, A. Curioni and E. Gallopoulos, “Accelerating parallel data uncertainty quatification by solving linear systems with multiple right-hand sides”, CFE-ERCIM Meeting, London, Dec. 2013.
- [N] M. Predari, I. Koutis and E. Gallopoulos, “Computing the exact matrix pseudospectrum: The GRID method revisited”, Workshop in Control Theory and its Applications (in honor of G. Kalogeropoulos), Dept. of Mathematics, University of Athens, May 2013.

- [T] E.M. Kontopoulou, M. Predari and E. Gallopoulos, “Onomatology and content analysis of ergodic literature”, 24th

ACM conference on Hypertext and social media “Narrative and Hypertext” Workshop, May 2013. - [T] G. Kollias, E. Gallopoulos and A. Grama, “Surfing the network for ranking by multidamping”, IEEE Trans. Knowledge and Data Engineering, (published online Jan.2013).
- [T] V. Kalantzis, C. Bekas, A. Curioni and E. Gallopoulos, “Accelerating data uncertainty quantification by solving linear systems with multiple right-hand sides”, Numerical Algorithms, 62(4):637-653, 2013, DOI 10.1007/s11075-012-9687-2.
- [N] with V. Kalantzis, F. Saied and A. Sameh, “Accelerating Spike algorithms for the solution of sparse linear systems with multiple right-hand sides”, presented by V. Kalantzis at NumAn 2012, Ioannina, Sept. 2012.
- [N] E. Gallopoulos, “Matrix methods for some problems in data analysis”, keynote address, NumAn 2012, Ioannina, Sept. 2012.
- [N] with M. Predari and I. Koutis, “Inclusion-exclusion algorithms for revealing pseudospectra”, presented by M. Predari at NumAn 2012, Ioannina, Sept. 2012.
- [T] E.M. Kontopoulou, M. Predari, T. Kostakis and E. Gallopoulos, “Graph and matrix metrics to analyze ergodic literature for children”, Proc. 23rd ACM conference on Hypertext and social media (HT’12, Milwaukee), pp. 133-142, June 2012. Winner of the ACMSIGWEB 2012 Hypertext Ted Nelson Newcomer Award.
- [T] I. Duff, E. Gallopoulos, D. di Serafino and B. Ucar, “Topic 10: Parallel Numerical Algorithms”, preface to the

session, EURO-PAR 2012, Lecture Notes in Computer Science, 2012, Volume 7484/2012, p. 550. - [T] G. Kollias, E. Gallopoulos and A. Grama, “Rank computations with parallel random surfers”, 15th SIAM Conf. on Parallel Processing for Scientific Computing, Feb. 2012, Savannah, GA.
- [T] V. Kalantzis, C. Bekas, A. Curioni and E. Gallopoulos, “Estimating the diagonal of matrix inverses in parallel”, 15th

SIAM Conf. Parallel Processing for Scientific Computing, Feb. 2012, Savannah, GA. - [Τ] M.W. Berry, K.A. Gallivan, E. Gallopoulos, A. Grama, B. Philippe, Y. Saad and F. Saied eds., “High Performance Scientific Computing: Algorithms and Applications“, Springer ISBN 978-1-4471-2436-8 (Print) 978-1-4471-2437-5 (Online), Jan. 2012.

- [T] K. Gallivan, E. Gallopoulos, A. Grama, B.Philippe, E. Polizzi, Y. Saad, F. Saied, and D.Sorensen, “Parallel Numerical Computing from Illiac IV to Exascale -The Contributions of Ahmed H. Sameh”, in “High Performance Scientific Computing: Algorithms and Applications“, M. Berry et al. eds., Springer, Jan. 2012.
- [N] V. Kalantzis, C. Bekas, A. Curioni and E. Gallopoulos, “A matrix-free projection method for estimating the diagonal of a matrix inverse”, TR HPCLAB-SCG 2/12-11. Also presentation and abstract at International Conference on Scientific Computing, S. Margherita di Pula, Sardenia, Oct. 2011.
- [N] G.D. Kollias and E. Gallopoulos, “Functional rankings with multidamping: Generalizing PageRank with inhomogeneous matrix products”. TR HPCLAB-SCG 01/09-11.
- [T] V. Kalofolias and E. Gallopoulos, “Computing Symmetric Nonnegative Rank Factorizations”, Linear Algebra and its Applications, 436 (2012), pp. 421-435. Published online 3/11/2011.
- [N] E. Gallopoulos, “Rapid Elliptic Solvers”, In Encyclopedia of Parallel Computing, D. Padua ed., Springer, pp. 1719-1728, 2011. Also TR HPCLAB-SCG 1/06-10.
- [T] E. Gallopoulos (joint work with G. Kollias), “’Variations on PageRank’: Generalizing PageRank, multidamping and inhomogeneous matrix products”, Center for Computational and Applied Mathematics Seminar, Dept. Math., Purdue University, May 2011.
- [T] K. Georgiou, G. Kollias and E. Gallopoulos, “A versatile system for asynchronous iterations: From multithreaded simulations to Grid experiments”. In “Parallel Computing: From Multicores and GPU’s to Petascale”. B. Chapman, et al. eds., pp. 238-245, IOS Press, 2010. Selected for publication amongst papers presented at PARCO 2009 (Sept. 2009, Lyon, France).
- [T] D. Zeimpekis and E. Gallopoulos, “Document Clustering using NMF based on Spectral Information”. Revised version In Proc. Text Mining 2008 held in conjunction with the 8th SIAM Int’l. Conf. Data Mining (SDM 2008, Atlanta, GA). Also TR HPCLAB-SCG, CEID, University of Patras, Jan. 2008.
- [T] D. Zeimpekis and E. Gallopoulos, “Principal Direction Divisive Partitioning with Kernels and k-Means Steering”. In Survey of Text Mining II: Clustering, Classification and Retrieval, Michael W. Berry and Malu Castellanos eds., pp. 45-64, ISBN: 978-1-84800-045-2, Springer, 2008.
- [T] D. Zeimpekis and E. Gallopoulos, “Text to Matrix Generator (TMG) Manual”, TR HPCLAB-SCG 09/05-07, May 2007. Also in html.

- [T] K. Georgiou, G. Kollias and E. Gallopoulos, “Grid-enabling a Problem Solving Environment: Implementation and Everyday Use“. To appear in Proc. CoreGRID Workshop on Grid Programming Model, Grid and P2P Systems Architecture, and Grid Systems, Tools and Environments, Springer Lecture Notes (proceedings papers selected

after the Workshop (held at Institute of Computer Science, Foundation for Research and Technology, Crete, June 12-13, 2007). Original version HPCLAB-SCG 08/05-07. Also presented at “Enabling Grids for E-sciencE”: EGEE07-Budapest-Poster Session. - [N] T. Kostakis and E. Gallopoulos, “The 88 Ntolmadakia” eigenvector and beyond: Link Analysis and Linear Algebra on children’s books”, HPCLAB-SCG 07/04-07, presented at 1st Greek Panhellenic Student Conference “EYRHKA 2007” held with 11th Panhellenic Conference on Informatics (PCI 2007), Patras, May 2007.
- [T] A. Zouzias and E. Gallopoulos, “From k-plane to Projective Clustering”, HPCLAB-SCG 06/04-07, presented at 1st Greek Panhellenic Student Conference “EYRHKA 2007” held with 11th Panhellenic Conference on Informatics (PCI

2007), Patras, May 2007. - [T] G. Kollias and E. Gallopoulos, “Multiranking simulation framework for link-based ranking”, Schloss Dagstuhl Seminar “Web Information Retrieval and Linear Algebra Algorithms”, Feb. 11-16, 2007. Presentation TR HPCLAB-SCG

05/02-07. - [T] G. Kollias, E. Gallopoulos and D. Szyld, “Asynchronous Computation of PageRank”, Schloss Dagstuhl Seminar “Web Information Retrieval and Linear Algebra Algorithms”, Feb. 11-16, 2007. Presentation HPCLAB-SCG 04/02-07.
- [T] D. Zeimpekis and E. Gallopoulos, “k-means steering of spectral divisive clustering algorithms”. In Proc. Text

Mining 2007 held in conjunction with the 7th SIAM Int’l. Conf. Data Mining (SDM 2007, April 28, Minneapolis, MN). Also TR HPCLAB-SCG 03/01-07, CEID, University of Patras, Feb. 2007. - [T] D. Zeimpekis, A. Zouzias and E. Gallopoulos, “TMG: A MATLAB toolbox for text indexing, retrieval and classification”, Demo session during 6th Int’l. conf. on Data Mining (ICDM’06), (ICDM’06), Dec. 2006.
- D. Zeimpekis and E. Gallopoulos, “Non-Linear Dimensional Reduction via Class Representatives for Text Classification”. Proc. 6th Int’l. conf. on Data Mining (ICDM’06), pp. 1172-1177, IEEE Computer Society,

Los Alamitos, Dec. 2006. Revised from TR HPCLAB-SCG 11/07-06, CEID,

University of Patras, July 2006. - G. Kollias and E. Gallopoulos, “Jylab: A System for Portable Scientific Computing over Distributed Platforms“.

In Proc. 2nd IEEE Int’l. Conf. on e-Science and Grid Computing (e-Science 2006): Session on Innovative and Collaborative Problem Solving, Dec. 2006. Revised from TR HPCLAB-SCG 10/07-06, CEID, University of Patras, July 2006. See also the Jylab Wiki. The paper received the top grade in the review process and was declared by the Workshop Program Committee as the keynote paper of the Workshop. - C. Boutsidis and E. Gallopoulos, “SVD based initialization: A head start for nonnegative matrix factorization”. TR HPCLAB-SCG-02/01-07 (supercedes HPCLAB-SCG-6/08-05). Revised in “Pattern Recognition“, 41(4):1350-1362, April 2008. Related presentation “Structured initialization for head start in nonnegative matrix factorization” at joint

GAMM-SIAM Conference on Applied Linear Algebra, Duesseldorf, Germany, July 2006. Presentation TR HPCLAB-SCG 8/07-06. - [N] G. Kollias and E. Gallopoulos, “PageRank computations for compressed link-structures”, Abstract at joint GAMM-SIAM Conference on Applied Linear Algebra, Duesseldorf, Germany, July 2006. Also (presentation) TR HPCLAB-SCG 7/07-06, CEID, University of Patras.
- [T] I. Antonellis and E. Gallopoulos, “Tensor based text representation: a new dimension in IR”, Poster presented at Workshop on Algorithms for Modern Massive Data Sets, Stanford University and Yahoo! Research. Also Report (presentation) TR HPCLAB-SCG 6/06-06.
- [T] C. Boutsidis and E. Gallopoulos in collaboration with P. Zhang and R.J. Plemmons, “PALSIR : A new approach to Nonnegative Tensor Factorization”, Poster presented at Workshop on Algorithms for Modern Massive Data Sets, Stanford University and Yahoo! Research. Also Report (presentation) TR HPCLAB-SCG 5/06-06.
- [T] S. Hatzimihail and E. Gallopoulos, “Can Information Retrieval aid Iterative Methods?”, 9th Copper Mountain Conf. Iterative Methods, April 2006. Report (presentation) TR HPCLAB-SCG 4/04-06.
- [T] D.K. Tasoulis, D. Zeimpekis, E. Gallopoulos and M.N. Vrahatis, “Oriented k-windows: A PCA driven clustering method”. In “Advances in Web Intelligence and Data Mining“, M. Last, P.S. Szcepaniak, Z. Volkovich and A. Kandel eds., Springer Studies in Computational Intelligence, v. 23, pp. 319-328, 2006, Springer. Revised from TR HPCLAB-SCG 2/02-06, CEID, University of Patras, Feb. 2006.
- [T] I. Antonellis and E. Gallopoulos, “Exploring term-document matrices from matrix models in text mining”, Proc. SIAM Text Mining 2006 Workshop, held in conjunction with the 6th SIAM Int’l. Conf. Data Mining (SDM 2006, April 20-22). Also TR HPCLAB-SCG 3/02-06, CEID, University of Patras, Feb. 2006. (Supercedes TR HPCLAB-SCG 1/01-06, Jan. 2006).
- [T] C. Boutsidis and E. Gallopoulos, “On SVD-based initialization for nonnegative matrix factorization”, TR HPCLAB-SCG-6/08-05, CEID, University of Patras”, Oct. 2005. Superceded by TR HPCLAB-SCG 2/01-07.
- [T] G. Kollias, E. Gallopoulos and D. Szyld, “Asynchronous iterative computations with Web information retrieval structures: The PageRank case”. In Parallel Computing: Current & Future issues of High-End Computing (NIC Series Volume 33): Proc. PARCO’05 (Malaga, Sept. 2005) , G.R. Joubert, et al. eds. pp. 309-317, Oct. 2006. Also TR HPCLAB-SCG 5/08-05, CEID, University of Patras, Aug. 2005.
- [T] E. Gallopoulos, “Some Computational Linear Algebra Algorithms and Tools for Information retrieval”, TR HPCLAB-SCG 4/05-05, CEID, University of Patras, presented at the Algorithmic Techniques in Data Mining Workshop, Karmiel, May 2005.
- [T] C. Bekas, V. Bogeas, K. Petrakos and E. Gallopoulos, ” Computing Pseudospectra of Parameter-Dependent Matrices”, presented at the XVIth Householder Symposium, Seven Springs, Pennsylvania, May 2005 (extended abstract). Also TR HPCLAB-SCG 3/05-05, CEID, University of Patras.
- [T] D. Zeimpekis and E. Gallopoulos, “Design of a MATLAB toolbox for term-document matrix generation”, TR HPCLAB-SCG 2/02-05, CEID, University of Patras, Februry 2005. In Proc. Workshop on Clustering High Dimensional Data and its Applications, (held in conjunction with 5th SIAM Int’l Conf. Data Mining), I.S. Dhillon, J. Kogan and J.

Ghosh eds., pp. 38-48, April 2005, Newport Beach, California. (Also software– same as in next item). - [T] D. Zeimpekis and E. Gallopoulos, “TMG: A MATLAB Toolbox for generating term-document matrices from text collections” TR HPCLAB-SCG 1/01-05 In “Grouping Multidimensional Data: Recent Advances in Clustering”, J. Kogan, C. Nicholas and M. Teboulle, eds., pp. 187-210, Springer, 2005. TMG Software
- [T] D. Zeimpekis and E. Gallopoulos, “CLSI: A Flexible Approximation Scheme from Clustered Term-Document Matrices”, Proc. SIAM 2005 Data Mining Conf. H. Kargupta, J. Srivastava, C. Kamath and A. Goodman, eds., pp. 631-635, April 2005, Newport Beach, California. For an extended version, see TR HPCLAB-SCG 2/10-04.
- C. Bekas, E. Kokiopoulou and E. Gallopoulos, “The design of a distributed MATLAB-based environment for computing pseudospectra”. Special issue on “Complex Problem-Solving Environments for Grid Computing” of Future Generation Computer Systems, 21(6):930-941, April 2005.
- [T] D. Zeimpekis and E. Gallopoulos “PDDP(l): Towards a flexible principal direction divisive partitioning clustering algorithm”, in Proc. IEEE ICDM ’03 Workshop on Clustering Large Data Sets, pp. 26-35, D. Boley, I. Dhillon, J. Ghosh and J. Kogan eds., Melbourne, Florida, Nov. 2003.
- [N] C. Bekas, E. Gallopoulos and V. Simoncini, “Transfer Functions and Path Following for Computing Pseudospectra“. Extended abstract in the (electronic) Proc. SIAM Conf. in Applied Linear Algebra, July 2003.
- [T] E. Kokiopoulou, C. Bekas and E. Gallopoulos, “Computing smallest singular triplets with implicitly restarted Lanczos bidiagonalization”. In Applied Numerical Mathematics, 49(1), April 2004, pp. 39-61. Also TR HPCLAB-TR-17-02-03, Feb. 2003. Extended abstract in (electronic) Proc. SIAM Conf. in Applied Linear Algebra, July 2003.
- [T] C. Bekas, E. Kokiopoulou, E. Gallopoulos and V. Simoncini, “Parallel Computation of Pseudospectra using Transfer Functions on a MATLAB-MPI Cluster Platform”. In D. Kranzlm?ller, P. Kacsuk, J. Dongarra, J.

Volkert (Eds.): Recent Advances in Parallel Virtual Machine and Message Passing Interface, Proc.9th European PVM/MPI Users’ Group Meeting, Springer-Verlag, LNCS Vol. 2474, pp. 199-207, Linz, Austria, September 29-October 2, 2002. - [T] C. Bekas and E. Gallopoulos, “Parallel Computation of Pseudospectra by Fast Descent”. Parallel Computing, v. 28, pp. 223-242, 2002.
- [T] I. Koutis and E. Gallopoulos, “Exclusion disks for computing pseudospectra”, unpublished manuscript, HPCLab, CEID, University of Patras Technical Report, 2002. Also available via the Oxford Pseudospectra Gateway.
- [T] C. Bekas, E. Kokiopoulou, I. Koutis and E. Gallopoulos, “Towards the Parallel Computation of Matrix Pseudospectra”. In Proc. 15th ACM International Conference of Supercomputing (ICS’01: Sorrento, June 17-21, 2001).
- [T] E.N. Houstis, J.R. Rice, E. Gallopoulos and R. Bramley editors, Enabling Technologies for Computational Science: Frameworks, Middleware and Environments, Kluwer Academic Publishers, Boston, March 2000.
- [T] L. DeRose, B. Marsolf, K. Gallivan, E. Gallopoulos and D. Padua, “Design issues in a MATLAB-based environment for numerical programs”. In Enabling Technologies for Computational Science: Frameworks, Middleware and

Environments, E. Houstis et al. eds., pp. 315-326, Kluwer Academic Pub., Boston, March 2000. - [T] C. Bekas and E. Gallopoulos, “Cobra: Parallel path following for computing the matrix pseudospectrum”. Parallel Computing, v. 27, pp. 1879-1896, 2001.
- [N] K. Gallivan, B. Marsolf and E. Gallopoulos, “The interactive restructuring of MATLAB Programs using the FALCON environment”. In Innovative Architecture for Future Generation High-Performance Processors and Systems, Alex Veidenbaum and Kazuki Joe eds., pp. 3-12, IEEE Computer Society Press, 1998 (ISBN 0-8186-8424-0).
- [T] V. Simoncini and E. Gallopoulos, “Transfer functions and resolvent norm approximation of large matrices”. Electronic Transactions in Numerical Analysis (ETNA), 7:190-201, 1998. Abstract and links to paper also available directly from ETNA. Revised version of LHPCA Tech. Rept. 010298, Dept. of Computer Engineering and Informatics, University of Patras, Feb. 1998.
- [N] C. Bekas and E. Gallopoulos, “Cobra: A hybrid method for computing the matrix pseudospectrum”. LHPCA Tech. Rept. 010198, Dept. of Computer Engineering and Informatics, University of Patras, Jan. 1998. In Proc. 1998 Copper Mountain Conference on Iterative Methods, April 1998.