Refereed Publications

  1. Efficient Basis Pursuit DeNoising via Active Sets and Homotopy
    Suely Oliveira and David Stewart,
    4th Intenational Conference on Fuzzy Systems and Data Mining, FSDM 2018.

  2. Smoothed Hinge loss L1 Support Vector Machines,
    Jeff Hajewski, Suely Oliveira, and David Stewart,
    Optimization Based Techniques for emerging Data Mining Problems
    Workshop Proceedings, IEEE Computer Society Press, ICDM 2018.

  3. A Comparison of Canny Edge Detection Implementations with Hadoop,
    Josiah Smalley, and Suely Oliveira,   FICC Proceedings,
    Advances in Intelligent Systems and Computing Series, Springer, 2018.

  4.  Community Detection Algorithm for Big Social Networks using Hybrid Architecture,
    Rahil Sharma and Suely Oliveira,
    Big Data Research, vol 10, pp. 44-52, 2017. (pdf)


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

  6. High Quality Multi-core Multi-level Algorithm for Community Detection,
    S. Oliveira and Rahil Sharma,
    Int. J. Computational Science and Engineering. 
    Vol. 15 No. 3-4, pp 311-321, 2017 (pdf)

  7.  Parallel Landscape Driven Data Reduction Technique and Spatial Interpolation for Massive LiDAR Data Processing,
    Rahil Sharma, Zewei Xu, Ramanathan Sugumaran and Suely Oliveira,
    ISPRS International Journal of Geo-Information
    , Vol. 5, No. 6, pp. 97, 2016 (pdf) 
  8.  Identification and Prediction of Functional Protein Modules using Community Detection Algorithms,
    S. Oliveira and Rahil Sharma,
    International Journal of Bioinformatics Research and Applications,  Vol. 12, No. 2, pp. 129 - 148, 2016, (pdf)

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

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

  11. Physically accurate gramular flow simulation,
    Suely Oliveira and David E. Stewart
    International Conference on Computational Science, ICCS 2012
    Procedia Computer Science, 2012 Vol 9 pp. 286-291 (pdf)

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

  13. GAmization: An improved anonymization technique using Genetic algorithm
    Murshed Manzoor and Suely Oliveira
    Annual International Conference on Software Engineering and Applications, 2011

  14. Analysis of nonlinear dynamics of vocal folds using high-speed video observation and biomechanical modeling,
    Alan P. Pinheiro, David E. Stewart, Carlos D. Maciel, Jose C. Pereira and Suely Oliveira,
    Digital Signal Processing, , Vol. 22, No. 2, pp. 304-313, 2011.

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

  16.  Problems with Nonparametric Entropy Estimation of Voice Signals,

    P. Scalassara, C. D. Maciel, J. C. Pereira, S. P. Oliveira, D. E. Stewart,

    International Congress of Mechanical Engineering, COBEM, 
    Gramado
    , Rio Grande do Sul, Nov. 15-10,  2009. (COB09-1677)

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

  18.  A Spectral Clustering Algorithm for Manufacturing Cell Formation,
    S. Oliveira, J. F. F. Ribeiro and S. C. Seok,
    Computer and Industrial Engineering, 2009, Vol. 57, pp. 1008-1014.

  19.  A Mathematical Model for Load Balancing,
    S. Oliveira and T. Soma,
    Proceedings of The Sixth (6th) International Conference of Numerical Analysis and Applied Mathematics.

    Kos, Greece, September 2008.

  20.  A Comparative Study of Similarity Measures forManufacturing Cell Formation,
    S. Oliveira, J. F. F. Ribeiro and S. C. Seok,
    Journal of Manufacturing Systems,  2008, Vol. 27, pp. 19–25. 

  21.  H-matrices preconditioners for symmetric saddle-point systems from meshfree discretizations,
    S. Le Borne, S. Oliveira, and F. Yang,
    Numerical Linear Algebra and its Applications, 2008, Vol. 15, No. 10, pp. 911–924.

  22.  A Matrix-based Multilevel Approach to Identify Functional Protein Modules,
    S. Oliveira and S.C. Seok, 
    Int. J. Bioinformatics Research and Applications, 2008, Vol. 4, No. 1, pp.11–27. (pdf)

  23. Joint Domain-Decomposition H-LU preconditioners for saddle-point Problems
    S. Le Borne and S. Oliveira,
    Electronic Transactions on Numerical Analysis,  2007, Vol. 26, pp. 285-298. (pdf)

  24.   Multilevel approaches for large scale proteomic networks,
    S. Oliveira and S.C. Seok,
    International Journal of Computer Mathematics, 84(5) (2007), pp. 683-695. (pdf)

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

  26. An Algebraic Approach for H-Matrices Preconditioners
    S. Oliveira and F. Yang,
    Computing, 2007, Vol. 80, pp. 169-188.  (pdf) 

  27. Hierarchical Preconditioners for Parabolic Optimal Control Problems,
    S. Oliveira and F.Yang,
    ICCS Proceedings, Lectures Notes in Computer Science 4487, Springer 2007, pp. 221-228. (pdf)

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

  29.  Triangular clique based multilevel approaches to identify protein functional modules,
    S. Oliveira and S.C. Seok,
    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)

  30.  A multilevel approach to identify functional modules in a Yeast Protein-Protein interaction network,
    S. Oliveira and S.C. Seok,
    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)

  31.  Parallel support set searches for meshfree methods ,
     C. Cartwright, S. Oliveira and D. Stewart,
    SIAM Journal on Scientific Computing,  28(4) (2006),  pp. 1318-1334.  (pdf)

  32.  Spectral document clustering algorithms with different data structures,
    S. Oliveira, and S.C. Seok,
    Proceedings of The 2005 International Conference on Scientific Computing - CSC'05,  pp. 223-229.

  33. A multilevel approach for document clustering,
    S. Oliveira and S.C. Seok,
    5th International Conference on Computational Science - ICCS 2005,
    Lecture Notes in Computer Science 3514,  Springer 2005, pp. 204-211.  (pdf)

  34. Algebraic multigrid (AMG) for saddle point systems from meshfree discretizations,
    K. H. Leem, S. Oliveira and D. Stewart,
    Numerical Linear Algebra and Applications, 11(3) (2004),  pp. 293-308.  (pdf)

  35. Semidefinite programming for graph partitioning with preference in data distribution,
    S. Oliveira, T. Soma and D. Stewart,
    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)


  36. A subspace semidefinite programming for spectral graph partitioning,
    S. Oliveira, T. Soma and D. Stewart,
    International Conference on Computational Science - ICCS 2002 Part I, 
    Lecture Notes in Computer Science
    2329,  Springer,  pp. 1058--1067. (pdf)

  37. Exact prediction of QR fill-in by row-merge trees,
    S. Oliveira,
    SIAM Journal on Scientific Computing, 2001,
    Vol. 22, No. 6, pp. 1962-1973  (pdf)

  38. A New efficient parallel algorithm for computing eigenvalues of symmetric tridiagonal matrices,
    D.K. Friesen, S. Oliveira and J. Zhang
    Proceedings of the Tenth SIAM Conference on Parallel Processing for Scientific Computing,
    Portsmouth, Virginia, March 2001.

  39.  A parallel quadtree algorithm for efficient assembly of stifness matrices in meshfree Galerkin methods,
    C. Cartwright, S. Oliveira and D.Stewart,
    Proceedings of Irregular 2001, International Parallel and Distributed Processing Symposium, April 2001.
    Published by IEEE Computer Society.

  40. Finding sets covering a point with applications to meshfree Galerkin methods,
    X. Han, S. Oliveira and D. Stewart,
    SIAM Journal on Computing, 30(4) (2000), pp. 1368-1383 (pdf)

  41. Exponential splittings of products of matrices and accurately computing singular values of long products,
    S. Oliveira and D. Stewart,
    Linear Algebra and Its Applications, 310 (2000), pp. 175-190.  (pdf)

  42. A multilevel algorithm for spectral partitioning with extended eigen-models,
    S. Oliveira and T. Soma
    Lecture Notes in Computer Science 1800, Springer,  May 2000,  pp. 477--484. 

  43. Analysis of different partitioning schemes for parallel Gram-Schmidt algorithms,
    S. Oliveira, L. Borges, M. Holzrichter, and T. Soma,
    Parallel Algorithms and Applications. 14(4)  (2000), pp. 293-320. (pdf) 

  44. On the convergence rate of a preconditioned subspace eigensolver,
    S. Oliveira,
    Computing, 63 (1999), pp. 219-231. (pdf)


  45. A graph based Davidson algorithm for the graph partitioning problem,
    M. Holzrichter and S. Oliveira,
    International Journal of Foundations of Computer Science, 10 (1999), pp. 225-246. (pdf)


  46. A graph based method for generating the Fiedler vector of irregular problems,
    M. Holzrichter and S. Oliveira,
    Parallel and Distributed Processing,
    Lecture Notes in Computer Science 1586, Springer, April 1999, pp. 978-985. 


  47. A parallel solver for extreme eigenvalues,
    L. Borges and S. Oliveira,
    Proceedings of Europar 98,
    Lecture Notes in Computer Science 1470, Springer, September 1998, pp. 763-770.


  48. A parallel Davidson-type algorithm for several eigenvalues,
    L. Borges and S. Oliveira,
    Journal of Computational Physics,  144 (1998), pp. 727-748. (pdf) 


  49. Analysis of a multigrid method for a transport equation by numerical fourier analysis,
    S. Oliveira,
    Computers and Mathematics with Applications, 35 (1998), pp. 7-12. (pdf)


  50. A new parallel chasing algorithm for transforming arrowhead matrices to tridiagonal form,
     S. Oliveira,
    Mathematics of Computation, 67 (1998), pp. 221-235. (pdf)


  51. Preconditioned Krylov subspace for transport equations,
    S. Oliveira and Y. Deng,
    Progress in Nuclear Energy, 33 (1998), pp. 155-174. (pdf)


  52. New partitioning schemes for parallel modified Gram-Schmidt orthogonalization,
    Oliveira and T. Soma
    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.


  53.  An efficient parallel chasing algorithm,
    Z. Chen, Y. Deng and S. Oliveira,
    SIAM Conference on Parallel Processing for Scientific Computing Proceedings, March 1997. 
    CD-ROM publication (6 pages).

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

  55.  Parallel multigrid methods for transport equations: The anisotropic case,
    S. Oliveira,
    Parallel Computing, 22 (1996), pp. 513-537. (pdf)


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

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

  58.  Fast multigrid solver for transport problems I: Pure scattering,
    T. Manteuffel, S. McCormick, J. Morel, S. Oliveira, and G. Yang,
    SIAM Journal on Scientific Computing, 16 (1995), pp. 601-635. (pdf)


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

  60. A parallel multilevel algorithm for anisotropic transport equations,
    S. Oliveira,
    Computational Techniques and Applications Conference
    Canberra, Australia (CTAC93), July 1994, pp. 388-396.

  61.  A parallel version of a multigrid algorithm for isotropic transport equations,
    T. Manteuffel, S. McCormick, J. Morel, S. Oliveira, and G. Yang,
    SIAM Journal on Scientific Computing, 15 (1994), pp. 474-493.  (pdf)


  62. FFTs and three-dimensional Poisson solvers for hypercubes,
    R. A. Sweet, W. L. Briggs, S. Oliveira, J. L. Porsche and T. Turnbull,
    Parallel Computing, 17 (1991), pp. 121-131.



    Additional  Publications

       
  63. 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.
     
  64. 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.

  65. 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.

  66. 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)

  67. 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.