 MIC Prediction and Feature Selection using XGBoost for
Neural Networks,
Cory KromerEdwards, Mariana Castanheira, and Suely Oliveira,
Journal submission.
 An empirical analysis of swarmbased heuristic optimization
methods,
Jamil Gafur, Cory KromerEdwards, Suely Oliveira, and David
Stewart
Journal submission.
 A Kmedoids Approach to
Exploring Districting Plans,
Jared Grove, Suely Oliveira, Anthony Pizzimenti, and
David Stewart,
Journal
submission.
 A Smoothing Algorithm for L1 Support Vector Machines,
Jeff Hajewski, Ibrahim Emirahmetoglu, Suely Oliveira and David
Stewart,
Journal submission.
 Cancer
Cells are Highly Susceptible
to Accumulation of Templete Insertions linked to MMBIR
Beth Osia, Thamer Alsulaiman,
Tyler Jackson, Juraj Kramara, Suely Oliveira, and Anna
Malkova,
Nucleic Acids Research, 2021, gkab685. https://doi.org/10.1093/nar/gkab685
 Estimation
of Multidimensional Item Response Theory Models with
Correlated Latent Variables using variational autoencoders,
Geoffrey Converse, Mariana Curi, Suely Oliveira, Jonathan
Templin,
Machine Learning 110, 1463–1480 (2021). https://doi.org/10.1007/s10994021060057
 Distributed
Evolution of Deep Autoencoders
Hajewski J., Oliveira S., Xing X . In: Arai K. (eds) Intelligent
Computing. Lecture Notes in Networks and Systems, vol 283.
Springer, ChamComputing Conference, London, UK, July 2021
https://doi.org/10.1007/9783030801199_6.
See also https://arxiv.org/pdf/2004.07607.pdf
 Incorporating
item response theory into knowledge tracing.
Geoffrey Converse, Suely Oliveira, and Shi Pu
In Ido Roll, Danielle McNamara, Sergey Sosnovsky, Rose Luckin,
and Vania Dimitrova, editors, Artificial Intelligence in
Education, pages 114–118. Springer International Publishing,
2021.
https://doi.org/10.1007/9783030782702
 Exploring
Tradeoffs in Parallel BeamACO,
Jeff Hajewski, Suely Oliveira, David Stewart and Laura Weiler,
11th Annual Computing and Communication Workshop and Conference,
IEEE CCWC 2021  Virtual, USA, January 2021, pp. 15251534.
https://ieeexplore.ieee.org/document/9376177
 Efficient
Evolution of Variational Autoenconders,
Jeff Hajewski and Suely Oliveira,
11th Annual Computing and Communication Workshop and Conference,
IEEE CCWC 2021  Virtual, USA, January 2021, pp. 15411550.
https://ieeexplore.ieee.org/document/9376167
 Year,
Location and Species Information In Predicting MIC Values
with BetaLacatamase Genes,
Cory KramerEdwards, Mariana Castanheira, Suely Oliveira,
Data mining from genomic
variants and its application to genomewide analysis,
IEEE International Conference on Bioinformatics and Biomedicine
(BIBM) workshop, Dec. 2020, pp. 13831390.
https://www.computer.org/csdl/proceedingsarticle/bibm/2020/09313331/1qmg2YfK5Pi
 gBeamACO:
a greedy and faster variant of BeamACO,
Jeff Hajewski, Suely Oliveira, David Stewart and Laura Weiler,
SWINGA workshop at GECCO (Genetic
and Evolutionary Computation), pages
1434–1440, July 2020.
https://dl.acm.org/doi/10.1145/3377929.3398081
(https://arxiv.org/abs/2004.11137)
 Evolving
Deep Autoenconders
Jeff Hajewski, Suely Oliveira, X. Xing
GECCO'20 (Genetic and Evolutionary Computation)
Proceedings, pages 123124, July 2020
https://dl.acm.org/doi/10.1145/3377929.3390011
 An
Evolutionary Approach to Variational Autoencoders
Jeff Hajewski and Suely Oliveira,
10th Annual Computing and Communication Workshop
and Conference,
IEEE CCWC 2020  Las Vegas, USA, January 2020

A
Scalable System for Neural Architecture Search
Jeff
Hajewski and Suely Oliveira,
10th Annual Computing and Communication Workshop and
Conference,
IEEE CCWC 2020  Las Vegas, USA , January 2020

Identifying
BetaLactamase Resistance with Neural Network,
Cory
KromerEdwards, Jace Neubaum, Suely Oliveira, Caitlin Smith,
Evan WalserKuntz, and Andrew West,
IEEE International Conference on Bioinformatics and
Biomedicine Proceedings 2019, San Diego, USA. (published in
February 2020)
 Variational
Autoenconders for Baseball Player Evaluation,
Geoffrey Converse, Brooke Arnold, Mariana Curi, and Suely
Oliveira,
5th International Conference on Fuzzy Systems and Data Mining,
FSDM 2019, Kitakyushu, Japan
 Two
Simple Tricks for Fast CacheAware Parallel Particle Swarm
Optimization,
Jeff Hajewski and Suely Oliveira,
CEC 2019, IEEE Congress on Evolutionary Computation 2019,
Wellington, New Zealand.
 Autoencoders
for Educational Assessment,
Geoffrey Converse, Mariana Curi, and Suely Oliveira,
AIED 2019 Proceedings The 20th International Conference on
Artificial Intelligence in Education 2019, Chicago, USA.
 Parallelizing
Basis Pursuit Denoising,
Cory KromerEdwards, Suely Oliveira and David
Stewart,
IJCNN International Joint Conference on Neural
Networks 2019, Budapest, Hungary.
 Interpretable
Variational Autoenconders for Cognitive Models,
Mariana Curi, Geoffrey Converse, Jeff Hajewski
and Suely Oliveira,
IJCNN International Joint Conference on Neural Networks 2019,
Budapest, Hungary.
 Distributed
SmSVM Ensemble Learning,
Jeff Hajewski and Suely Oliveira,
INNS International Neural Network Society, Big Data and
Deep Learning,
SpringerVerlag Proceedings, 2019, Sest Levanti, Italy.
 Efficient
Basis Pursuit DeNoising via Active Sets and Homotopy,
Suely P. Oliveira and David E. Stewart,
4th International Conference on Fuzzy Systems and Data Mining,
FSDM 2018, Bangkok, Thailand.
 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.
 A
Comparison of Canny Edge Detection Implementations with
Hadoop,
Josiah Smalley, and Suely
Oliveira, Future of Information and
Communications Proceedings,
Advances in Intelligent Systems and Computing Series, Springer,
2018.
 Community
Detection Algorithm for Big Social Networks using Hybrid
Architecture,
Rahil Sharma and Suely Oliveira,
Big Data Research, vol 10, pp. 4452, 2017. (pdf)
 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)
 High
Quality Multicore Multilevel Algorithm for Community
Detection,
S. Oliveira and
Rahil Sharma,
Int. J. Computational Science and Engineering. Vol. 15 No. 34, pp 311321, 2017
(pdf)
 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 GeoInformation,
Vol. 5, No. 6, pp. 97, 2016 (pdf)

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)
 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. 357376 ISBN: 9781118345788, 2013.
 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. 111123, 2012.
 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. 286291 (pdf)
 Clustering for Bioinformatics
via Matrix Optimization,
S. Oliveira and D. E. Stewart,
2nd ACMBCB'11 Conference on Bioinformatics, Computational
Biology and Biomedicine,
Chicago, IL, USA, 2011, pp.
559563. (pdf)
 GAmization:
An improved anonymization technique using Genetic algorithm,
Murshed Manzoor and Suely Oliveira,
Annual International Conference on Software Engineering and
Applications, 2011.

Analysis
of nonlinear dynamics of vocal folds using highspeed
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. 304313,
2011.

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 16 2009.

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. 1510, 2009.
(COB091677)

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
1822, 2009.
 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.
10081014.
 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.
 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.
 Hmatrices preconditioners for
symmetric saddlepoint 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.
 A Matrixbased 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)
 Joint
DomainDecomposition HLU preconditioners for saddlepoint
Problems ,
S. Le Borne and S. Oliveira,
Electronic Transactions on Numerical Analysis, 2007, Vol.
26, pp. 285298. (pdf)
 Multilevel approaches for large
scale proteomic networks,
S. Oliveira and S.C. Seok,
International Journal of Computer Mathematics, 84(5) (2007), pp.
683695. (pdf)
 Hmatrix
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 2023, June 2007, pp. 333340.
 An
Algebraic Approach for HMatrices Preconditioners,
S. Oliveira and F. Yang,
Computing, 2007, Vol. 80, pp. 169188. (pdf)
 Hierarchical
Preconditioners for Parabolic Optimal Control Problems,
S. Oliveira and F.Yang,
ICCS Proceedings, Lectures Notes in Computer Science 4487,
Springer 2007, pp. 221228. (pdf)
 Hmatrix
preconditioners for saddlepoint 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)
 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.
556565. (pdf)
 A multilevel approach to
identify functional modules in a Yeast ProteinProtein
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. 726733. (pdf)
 Parallel
support set searches for meshfree methods ,
C. Cartwright, S. Oliveira and D. Stewart,
SIAM Journal on Scientific Computing, 28(4) (2006),
pp. 13181334. (pdf)
 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. 223229.
 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.
204211. (pdf)
 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. 293308. (pdf)
 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, SpringerVerlag
Heidelberg, 2003 , pp.307321. (pdf)
 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. 10581067. (pdf)
 Exact
prediction of QR fillin by rowmerge trees,
S. Oliveira,
SIAM Journal on Scientific Computing, 2001, Vol. 22, No. 6,
pp. 19621973 (pdf)
 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.
 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.
 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. 13681383 (pdf)
 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.
175190.
(pdf)
 A
multilevel algorithm for spectral partitioning with
extended eigenmodels,
S. Oliveira and T. Soma
Lecture Notes in Computer Science 1800, Springer, May
2000, pp. 477484.
 Analysis
of different partitioning schemes for parallel
GramSchmidt algorithms,
S. Oliveira, L. Borges, M. Holzrichter, and T. Soma,
Parallel Algorithms and Applications. 14(4) (2000), pp.
293320. (pdf)
 On
the convergence rate of a preconditioned subspace
eigensolver,
S. Oliveira,
Computing, 63 (1999), pp. 219231. (pdf)
 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. 225246. (pdf)
 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. 978985.
 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. 763770.
 A
parallel Davidsontype algorithm for several eigenvalues,
L. Borges and
S. Oliveira,
Journal of Computational Physics, 144 (1998), pp.
727748. (pdf)
 Analysis
of a multigrid method for a transport equation by
numerical fourier analysis,
S. Oliveira,
Computers and Mathematics with Applications, 35
(1998), pp. 712. (pdf)
 A
new parallel chasing algorithm for transforming arrowhead
matrices to tridiagonal form,
S.
Oliveira,
Mathematics of Computation, 67 (1998), pp. 221235. (pdf)
 Preconditioned
Krylov subspace for transport equations,
S. Oliveira
and Y. Deng,
Progress in Nuclear Energy, 33 (1998), pp. 155174. (pdf)
 New
partitioning schemes for parallel modified GramSchmidt
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. 233239.
 An efficient parallel chasing
algorithm,
Z. Chen, Y.
Deng and S. Oliveira,
SIAM Conference on Parallel Processing for Scientific
Computing Proceedings, March 1997.
CDROM publication (6 pages).
 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. 316325.
 Parallel
multigrid methods for transport equations: The anisotropic
case,
S. Oliveira,
Parallel Computing, 22 (1996), pp. 513537. (pdf)
 A preconditioned multigrid subspace
algorithms for computing eigenvalues and eigenvectors,
S. Oliveira,
Proceedings of Algebraic Multilevel Iterative Methods
with Applications,
Nijmegen, June 1996, pp. 229232.
 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. 637648.
 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.
601635. (pdf)
 Krylov subspace methods for
transport equations,
S. Oliveira,
10^{th} ENFIR Meeting on Reactor
Physics, August 1995, pp. 522527.
 A parallel multilevel algorithm for
anisotropic transport equations,
S. Oliveira,
Computational Techniques and Applications Conference
Canberra, Australia (CTAC93), July 1994, pp. 388396.
 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.
474493. (pdf)
 FFTs
and threedimensional Poisson solvers for hypercubes,
R. A. Sweet,
W. L. Briggs, S. Oliveira, J. L. Porsche and T. Turnbull,
Parallel Computing, 17 (1991), pp. 121131.
Additional
Publications
 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. 679692.
 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. 3342.
 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. 391398.
 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)
 L. BORGES AND
S. OLIVEIRA, Highly indefinite
multigrid for eigenvalue problems, Copper Mountain
Conference on Iterative Methods Proceedings, April 1996.
(7 pages)