Refereed  Publications

  1. Josiah Smalley, Suely Oliveira, A Comparison of Canny Edge Detection Implementations with Hadoop, to appear in IEEE Future of Information and Communication Conference Proceedings,  2018.

  2. Rahil Sharma and Suely Oliveira, Community Detection Algorithm for Big Social Networks using Hybrid Architecture, to appear in Big Data Research, 2017.

  3. Thamer Alsulaiman, Beth Osia, Anna Malkova and Suely Oliveira, Concurrent MMBIRFinder, to appear in IEEE 7th Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2017.

  4. S. Oliveira and Rahil Sharma, High Quality Multi-core Multi-level Algorithm for Community Detection.  to appear in  Int. J. Computational Science and Engineering. 2017. http://www.inderscience.com/info/ingeneral/forthcoming.php?jcode=ijcse

  5. Rahil Sharma, Zewei Xu, Ramanathan Sugumaran and Suely Oliveira, Parallel Landscape Driven Data Reduction Technique and Spatial Interpolation for Massive LiDAR Data Processing, ISPRS International Journal of Geo-Information, 2016, Vol. 5, No. 6, pp. 97. http://www.mdpi.com/2220-9964/5/6/97
  6. S. Oliveira and Rahil Sharma, “Identification and Prediction of Functional Protein Modules using Community Detection Algorithms”, International Journal of Bioinformatics Research and Applications, 2016, Vol. 12, No. 2, pp. 129 - 148. http://www.inderscienceonline.com/doi/abs/10.1504/IJBRA.2016.077124

  7. S. Oliveira, Network Algorithms for Protein Interactions, book chapter Network Algorithms for Protein Interactions pp. 357-376 in Algorithmic and AI Methods for Protein Bioinformatics, ed. Yio Pan, Jianxin Wang and Min Li, Wiley, Fall 2013. ISBN: 978-1-118-34578-8

  8. LyX Document Marcelo O. Silva, Roseli A. F. Romero, Suely P. Oliveira and David E. Stewart, Improving the Stability of Algorithms for Path Planning Based on Boundary Value Problems, Far East Journal of Applied Mathematics,  2012, Vol. 69, No. 2, pp. 111–123.

  9. S. Oliveira and D. E. Stewart, Clustering for Bioinformatics via Matrix Optimization, 2nd ACM-BCB'11 Conference on Bioinformatics, Computational Biology and Biomedicine, Chicago, IL, USA, 2011, pp. 559-563.

  10. (doi: 10.1016/j.dsp.2010.11.002) Alan P. Pinheiro, David E. Stewart, Carlos D. Maciel, Jose C. Pereira and Suely Oliveira, Analysis of nonlinear dynamics of vocal folds using high-speed video observation and biomechanical modeling, Digital Signal Processing, 2011, Vol. 22, No. 2, pp. 304-313.

  11. (Ebook link)  D. Espanhol, C. D. Maciel, S. P. Oliveira, J.C. Pereira, Natural Clustering with Python, 9th International Symposium on Mathematical and Computational Biology, Brasilia, Distrito Federal, August 1-6 2009.

  12. P. Scalassara, C. D. Maciel, J. C. Pereira, S. P. Oliveira, D. E. Stewart,  Problems with Nonparametric Entropy Estimation of Voice Signals, International Congress of Mechanical Engineering, COBEM,  Gramado, Rio Grande do Sul, Nov. 15-10,  2009. (COB09-1677, http://www.abcm.org.br/anais/cobem/2009/papers.htm and search for "Scalassara")

  13. S. Oliveira and D Stewart, A Product Arnoldi Algorithm for Long Product of Matrices, 8th Brazilian conference on dynamics, control and applications, DINCON'09, Bauru, Sao Paulo, May 18--22, 2009.

  14. (doi: 10.1016/j.cie.2009.04.008) S. OLIVEIRA, J. F. F. RIBEIRO and S. C. SEOK, A Spectral Clustering Algorithm for Manufacturing Cell Formation, Computer and Industrial Engineering, 2009, Vol. 57, pp. 1008-1014.    

  15. S. OLIVEIRA and T. SOMA, A Mathematical Model for Load Balancing. Proceedings of The Sixth (6th) International Conference of Numerical Analysis and Applied Mathematics. Kos, Greece, September 2008.

  16. (doi: 10.1016/j.jmsy.2008.07.002) S. OLIVEIRA, J. F. F. RIBEIRO and S. C. SEOK, A Comparative Study of Similarity Measures forManufacturing Cell Formation, Journal of Manufacturing Systems,  2008, Vol. 27, pp. 19–25.    

  17. (doi: 10.1002/nla.599) S. LE BORNE, S. OLIVEIRA, AND F. YANG, H-matrices preconditioners for symmetric saddle-point systems from meshfree discretizations, Numerical Linear Algebra and its Applications, 2008, Vol. 15, No. 10, pp. 911–924.  

  18. (doi: 10.1504/IJBRA.2008.017161) S. OLIVEIRA AND S.C. SEOK,   A Matrix-based Multilevel Approach to Identify Functional Protein Modules, Int. J. Bioinformatics Research and Applications, 2008, Vol. 4, No. 1, pp.11–27. (pdf)  

  19. S. Le BORNE AND S. OLIVEIRA,   Joint Domain-Decomposition H-LU preconditioners for saddle-point Problems ,  Electronic Transactions on Numerical Analysis,  2007, Vol. 26, pp. 285-298. (pdf)

  20. (doi: 10.1080/00207160701332382) S. OLIVEIRA AND S.C. SEOK,   Multilevel approaches for large scale proteomic networks,  International Journal of Computer Mathematics, 84(5) (2007), pp. 683-695. (postscript) and (pdf)  

  21. S. OLIVEIRA AND F. YANG,  H-matrix preconditioners for Invariant Probability Distribution in Dynamical Systems, Proceedings of the International Conference on Computational and Mathematical Methods in Science and Engineering, CMMSE 2007, Chicago 20-23, June 2007, pp. 333-340.

  22. (doi: 10.1007/s00607-007-0224-4) S. OLIVEIRA AND F. YANG,    An Algebraic Approach for H-Matrices Preconditioners,  Computing, 2007, Vol. 80, pp. 169-188. (postscript) and (pdf)  

  23. (doi: 10.1007/978-3-540-72584-8_29) S. OLIVEIRA AND F. YANG,    Hierarchical Preconditioners for Parabolic Optimal Control Problems,  ICCS Proceedings, Lectures Notes in Computer Science 4487, Springer 2007, pp. 221-228. (pdf)  

  24. S. OLIVEIRA AND F. YANG,    H-matrix preconditioners for saddle-point systems from meshfree discretization, 14th International Conference on Computational & Experimental Engineering and Sciences - ICCES07, Minisymposium on Meshfree Methods and Applications Proceedings. (pdf)

  25. (doi: 10.1007/978-3-540-71351-7_43) S. OLIVEIRA AND S.C. SEOK,    Triangular clique based multilevel approaches to identify protein functional modules, 7th International Conference High Performance Computing for Computational Science - VECPAR 2006, Selected Papers and Invited Talks. Lecture Notes in Computer Science 4395, Springer 2006, pp. 556-565. (pdf)  

  26. (doi: 10.1007/11758525_98) S. OLIVEIRA AND S.C. SEOKA multilevel approach to identify functional modules in a Yeast Protein-Protein interaction network, 2nd International Workshop on Bioinformatics Research and Applications - 6th International Conference Computational Science - ICCS 2006, Lecture Notes in Computer Science  3992, Springer 2006,  pp.  726--733. (pdf)  

  27. (doi: 10.1137/S1064827502414321) C. CARTWRIGHT, S. OLIVEIRA AND D. STEWART, Parallel support set searches for meshfree methods , SIAM Journal on Scientific Computing,  28(4) (2006),  pp. 1318-1334.  (pdf) or (postscript) 

  28. S. OLIVEIRA, ANDS.C. SEOK, Spectral document clustering algorithms with different data structures, Proceedings of The 2005 International Conference on Scientific Computing - CSC'05,  pp. 223-229.

  29. (doi: 10.1007/11428831_26) S. OLIVEIRA AND S.C. SEOK, A multilevel approach for document clustering, 5th International Conference on Computational Science - ICCS 2005, Lecture Notes in Computer Science 3514,  Springer 2005, pp. 204-211.  (pdf) or (postscript)  

  30. (doi: 10.1002/nla.383) K. H. LEEM, S. OLIVEIRA ANDD. STEWART, Algebraic multigrid (AMG) for saddle point systems from meshfree discretizations,  Numerical Linear Algebra and Applications, 11(3) (2004),  pp. 293-308.  (pdf) or (postscript)

  31. (doi: 10.1007/3-540-36569-9_48) S. OLIVEIRA, T. SOMA AND D. STEWART, Semidefinite programming for graph partitioning with preference in data distribution, 5th International Conference High Performance Computing for Computational Science - VECPAR 2002, Selected Papers and Invited Talks.    Lecture Notes in Computer Science 2565,  Springer-Verlag Heidelberg,  2003 , pp.307-321. (pdf)  

  32. (doi: 10.1007/3-540-46043-8_107)    S. OLIVEIRA, T. SOMA AND D. STEWART, A subspace semidefinite programming for spectral graph partitioning, International Conference on Computational Science - ICCS 2002 Part I,  Lecture Notes in Computer Science 2329,  Springer,  pp. 1058--1067. (pdf) 

  33. (doi: 10.1137/S1064827599333965)  S. OLIVEIRA,   Exact prediction of QR fill-in by row-merge trees. SIAM Journal on Scientific Computing, 2001, Vol. 22, No. 6, pp. 1962-1973  (pdf)   or (postscript)  

  34. D.K. FRIESEN,   S. OlIVEIRA, AND J. ZHANG, A New efficient parallel algorithm for computing eigenvalues of symmetric tridiagonal  matrices,  Proceedings of the Tenth SIAM Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, March 2001.

  35. C. CARTWRIGHT, S. OLIVEIRA AND D. STEWART, A parallel quadtree algorithm for efficient assembly of stifness matrices in meshfree Galerkin methods,  Proceedings of Irregular 2001, International Parallel and Distributed Processing Symposium, April 2001. Published by IEEE Computer Society.

  36. (doi: 10.1137/S0097539799359361) X. HAN, S. OLIVEIRA AND D. STEWART, Finding sets covering a point with applications to meshfree Galerkin methods, SIAM Journal on Computing, 30(4) (2000), pp. 1368-1383 (pdf) or (postscript)  

  37. (doi: 10.1016/S0024-3795(99)00273-6) S. OLIVEIRA AND D. STEWART, Exponential splittings of  product of  matrices and accurately computing singular values of long products, Linear Algebra and Its Applications, 310 (2000), pp. 175-190.  (pdf) or (postscript)      

  38. (doi: 10.1007/3-540-45591-4_64) S. OLIVEIRA AND  T.  SOMA, A multilevel algorithm for spectral partitioning with extended eigen-models, In  Lecture Notes in Computer Science1800, Springer,  May 2000,  pp. 477--484.  

  39. (doi: 10.1080/10637199808947392) S. OLIVEIRA, L. BORGES, M. HOLZRICHTER, AND T. SOMA, Analysis of different partitioning schemes for parallel Gram-Schmidt algorithms, Parallel Algorithms and Applications. 14(4)  (2000), pp. 293-320. (pdf) or (postscript)  

  40. (doi: 10.1007/s006070050032) S. OLIVEIRA, On the convergence rate of a preconditioned subspace eigensolver, Computing, 63 (1999), pp. 219-231. (pdf) or (postscript)  

  41. (doi: 10.1142/S0129054199000162) M. HOLZRICHTER AND S. OLIVEIRA, A graph based Davidson algorithm for the graph partitioning problem, International Journal of Foundations of Computer Science, 10 (1999), pp. 225-246. (pdf) or (postscript)  

  42. (doi: 10.1007/BFb0097982) M. HOLZRICHTER AND S. OLIVEIRA, A graph based method for generating the Fiedler vector of irregular problems, in Parallel and Distributed Processing, Lecture Notes in Computer Science 1586, Springer, April 1999, pp. 978-985.  

  43. (doi: 10.1007/BFb0057834) L. BORGES AND S. OLIVEIRA, A parallel solver for extreme eigenvalues, in Proceedings of Europar 98, Lecture Notes in Computer Science 1470, Springer, September 1998, pp. 763-770.

  44. (doi: 10.1006/jcph.1998.6003) L. BORGES AND S. OLIVEIRA, A parallel Davidson-type algorithm for several eigenvalues, Journal of Computational Physics,  144 (1998), pp. 727-748. (pdf) or (postscript)   

  45. (doi: 10.1016/S0898-1221(98)00092-3) S. OLIVEIRA, Analysis of a multigrid method for a transport equation by numerical fourier analysis, Computers and Mathematics with Applications, 35 (1998), pp. 7-12. (pdf) or (postscript)    

  46. (doi: 10.1090/S0025-5718-98-00895-3) S. OLIVEIRA, A new parallel chasing algorithm for transforming arrowhead matrices to tridiagonal form, Mathematics of Computation, 67 (1998), pp. 221-235. (pdf) or (postscript)  

  47. (doi: 10.1016/S0149-1970(97)00099-1) S. OLIVEIRA AND Y. DENG, Preconditioned Krylov subspace for transport equations, Progress in Nuclear Energy, 33 (1998), pp. 155-174. (pdf) or (postscript)    

  48. (doi:10.1109/ISPAN.1997.645102) S. OLIVEIRA AND T. SOMA, New partitioning schemes for parallel modified Gram-Schmidt orthogonalization, in Proceedings of the 1997 International Symposium on Parallel Architectures, Algorithms and Networks - ISPAN97, F. Lai, B. Maggs, and F. Hsu, eds., IEEE Computer Society, December 1997, pp. 233-239.

  49. Z. CHEN, Y. DENG AND S. OLIVEIRA, An efficient parallel chasing algorithm, in SIAM Conference on Parallel Processing for Scientific Computing Proceedings, March 1997.  CD-ROM publication (6 pages).

  50. S. OLIVEIRA, A convergence proof of an iterative subspace method for eigenvalues problem, in Foundations of Computational Mathematics Selected Papers, F. Cucker and M. Shub, eds., Springer, January 1997, pp. 316-325.  

  51. (doi: 10.1016/0167-8191(96)00012-9) S. OLIVEIRA, Parallel multigrid methods for transport equations: The anisotropic case, Parallel Computing, 22 (1996), pp. 513-537. (pdf) or (postscript)    

  52. S. OLIVEIRA, A preconditioned multigrid subspace algorithms for computing eigenvalues and eigenvectors, in Proceedings of Algebraic Multilevel Iterative Methods with Applications, Nijmegen, June 1996, pp. 229-232.

  53. S. OLIVEIRA, Multigrid and Krylov subspace methods for transport equations: Absorption case, in Proceedings of the 7th Copper Mountain Conference on Multigrid Methods, NASA Conference Publications, September 1996, pp. 637-648.

  54. (doi: 10.1137/0916038) T. MANTEUFFEL, S. MCCORMICK, J. MOREL, S. OLIVEIRA, AND G. YANG, Fast multigrid solver for transport problems I: Pure scattering, SIAM Journal on Scientific Computing, 16 (1995), pp. 601-635. (pdf) or (postscript)  

  55. S. OLIVEIRA, Krylov subspace methods for transport equations, in 10th ENFIR Meeting on Reactor Physics, August 1995, pp. 522-527.

  56. S. OLIVEIRA, A parallel multilevel algorithm for anisotropic transport equations, in Computational Techniques and Applications Conference (CTAC93), July 1994, pp. 388-396.

  57. (doi: 10.1137/0915032) T. MANTEUFFEL, S. MCCORMICK, J. MOREL, S. OLIVEIRA, AND G. YANG, A parallel version of a multigrid algorithm for isotropic transport equations, SIAM Journal on Scientific Computing, 15 (1994), pp. 474-493. (pdf) or (postscript)  

  58. (doi: 10.1016/S0167-8191(05)80100-0) R. A. SWEET, W. L. BRIGGS, S. OLIVEIRA, J. L. PORSCHE AND T. TURNBULL, FFTs and three-dimensional Poisson solvers for hypercubes, Parallel Computing, 17 (1991), pp. 121-131.  

    Other Publications


       
  59. S. OLIVEIRA, T. SOMA,  AND  D. STEWART, Semidefinite programming for graph partitioning with Preferences, in Proceedings 5th International Meeting on High  Performance Computing for Computational Science - VECPAR 2002,  Part III, 2002,  pp.  679--692.
     
  60. S. OLIVEIRA, Using graph theory to improve some algorithms in scientific computing, in NEMACOM: New Methods in Applied and Computational Mathematics, R.V.N. Melnik, S.Oliveira, and D.E. Stewart, eds., Canberra, 2000, Centre for Mathematics and its Applications, Australian National University, pp. 33--42.

  61. M. HOLZRICHTER AND S. OLIVEIRA, Adapting Davidson algorithms for graph partitioning, Iterative Methods in Scientific Computation IV, IMACS Series in Computational and Applied Mathematics vol. 5, October 1999, pp. 391-398.

  62. S. OLIVEIRA, D. STEWART AND W. WU, Multigrid methods for solving variational inequalities by a penalty method, Copper Mountain Conference on Iterative Methods Proceedings, April 1996.  (7 pages)

  63. L. BORGES AND S. OLIVEIRA, Highly indefinite multigrid for eigenvalue problems, Copper Mountain Conference on Iterative Methods Proceedings, April 1996.  (7 pages)

       Extended Abstracts

  1. S. OLIVEIRA AND S.C. SEOK, Matrix-based algorithms for document clustering, Second International Workshop on Combinatorial Scientific Computing (CSC05), June 21-23, 2005 at CERFACS, Toulouse, France.

  2. S. OLIVEIRA AND S.C. SEOK, A Fast and accurate multilevel approach for document clustering, 2005 SIAM Annual Meeting, July 11-15, 2005 New Orleans.

  3. S. OLIVEIRA AND F. YANG,  High performance computing with hierarchical or H-matrices. Midwest Numerical Analysis Conference, p. 42, Ed. W. Han, May 2005.

  4. S. OLIVEIRA AND S.C. SEOK, A fast and accurate multi-level approach for document clustering, Midwest Numerical Analysis Conference, p. 42, Ed. W. Han, May 2005.

  5. C. CARTWRIGHT, S. OLIVEIRA AND D. STEWART A  parallel quadtree algorithms for efficient assembly of stiffness matrices in meshfree Galerkin methods, Proceedings of the Tenth SIAM Conference on Parallel Processing  for Scientific Computing (CD-ROM), Juan Meza and Chuck Koelbel, editors, SIAM Publ, March 2001.

  6. S. OLIVEIRA, New convergence results for a subspace preconditioning algorithm and its applications to the the graph partitioning problem, Foundations of Computational Mathematics book of Abstracts, University of Oxford, UK, pp. 164-165, July 1999.

  7. S. OLIVEIRA, The Davidson algorithm, convergence theory, graph partitioning. Enumath99 Book of Abstracts, University of Jyvaskyla, Finland, pp. 121-123, July 1999.

  8. S. OLIVEIRA, Graphical approach to design a parallel matrix transformation algorithm, Abstract Book of International Workshop on Accurate Solution of Eigenvalue Problems, July 1998.

  9. S. OLIVEIRA AND M. HOLZRICHTER, New spectral graph partitioning algorithms, Proceedings of Fourth IMACS International Symposium on Iterative Methods in Scientific Computation, October 1998.

  10.  S. OLIVEIRA AND M. HOLZRICHTER, Multilevel graph partitioning algorithms, Proceedings of SIAM Annual Meeting, July 1998.

  11. S. OLIVEIRA, Convergence and parallelization of a preconditioned algorithm for eigenvalues, Proceedings of the Copper Mountain Conference on Iterative Methods, April 1998.

  12. S. OLIVEIRA AND L. BORGES, A parallel algorithm for a multiple eigenvalue iterative method, Proceedings of Third IMACS International Symposium on Iterative Methods in Scientific Computation, July 1997.

  13. S. OLIVEIRA, Convergence and parallelization of a preconditioned preconditioned Krylov subspace methods for transport equation, Third Mexico-United States Workshop on Numerical Particle Transport Proceedings, May 1995.

  14. Y. DENG AND S. OLIVEIRA, Krylov subspace methods for transport equations, Annual SIAM Conference Proceedings, July 1996.

  15. T. MANTEUFFEL, S. MCCORMICK, J. MOREL, S. OLIVEIRA AND G. YANG, Multigrid algorithms for transport equations on the connection machine, Copper Mountain Conference on Iterative Methods, April 1992.


  16. Technical Reports

  17. S. OLIVEIRAAND F. YANG An algebraic approach for H-matrix preconditioners, University of Iowa, Reports on Computational Mathematics, TR-168, September 2006.

  18. S. OLIVEIRAAND F. YANG H-Matrix preconditioners for saddle point systems from meshfree discretizations,  University of Iowa, Reports on Computational Mathematics, TR-169, September 2006.

  19. K. H. LEEM, S. OLIVEIRA AND D. STEWART, Some numerical results from meshless linear systems,  University of Iowa, Reports on Computational Mathematics, TR-140, September 2001.

  20. D.K. FRIESEN,  S. OlIVEIRA AND J. ZHANG.  The modified splitting strategy for the parallel multisection algorithm, The University of Iowa, Reports on Computational Mathematics, TR-139, July 2001.

  21. D. CHIEN, K. H. LEEM AND S. OLIVEIRA, A fast parallel Krylov subspace method for the radiosity equation. The University of Iowa, Reports on Computational Mathematics, TR-128, January 2000.

  22. X. HAN, S. OLIVEIRA AND D. STEWART, New matrix assembly techniques for meshless methods. The University of Iowa, Reports on Computational Mathematics, TR-128, October 1999.

  23. S. OLIVEIRA, Reprocessing a postprocessed elimination tree to obtain exact sparsity prediction in QR factorization, The Univesity of Iowa, Reports  on Compuational  Mathematics , TR-127, October1999.

  24. S. OLIVEIRA, L. BORGES, M. HOLZRICHTER AND T. SOMA, Analysis of architecture independent parallel Gram-Schmidt algorithms, The University of Iowa Reports on Computational Mathematics, TR-121, December 1998.

  25. M. HOLZRICHTER AND  S. OLIVEIRA, New graph partitioning algorithms, The University of Iowa,  Reports on Computational Mathematics,  TR-120,  December 1998
    .
  26. S. OLIVEIRA, New convergence results for Davidson-type algorithms, The University of Iowa, Reoports on Computational Mathematics, TR-119, December 1998.

  27. Y. DENG AND S. OLIVEIRA, Preconditioned Krylov subspace methods for transport equations, Texas A&M University, Computer Science Department TR-95-051.