HR job title
- Professor
- Contact Info
- 1 979 862 6441
- Websites
Braga Neto, Ulisses Professor
Positions
My research interests focus on statistical signal processing and control, and pattern recognition and machine learning, with applications in bioinformatics, materials informatics, and epidemiological models.
Research Areas
- Overview
- Publications
- Research
- Teaching
- Works By Students
- Background
- Contact
- Other
- View All
Overview
Publications
selected publications
-
academic article
-
Ghane, P., Zarnaghinaghsh, N., & Braga-Neto, U.
(2021).
Comparison of Classification Algorithms Towards Subject-Specific and Subject-Independent BCI. 00, 1-6.
-
Tan, Y., Cator III, D., Ndeffo-Mbah, M., & Braga-Neto, U.
(2021).
A stochastic metapopulation state-space approach to modeling and estimating COVID-19 spread. Math Biosci Eng.
18(6), 7685-7710.
-
Tan, Y., Lima Neto, F., & Braga-Neto, U.
(2020).
PALLAS: Penalized mAximum LikeLihood and pArticle Swarms for Inference of Gene Regulatory Networks from Time Series Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
PP(99), 1-1.
-
McClenny, L., & Braga-Neto, U.
(2020).
Self-Adaptive Physics-Informed Neural Networks using a Soft Attention Mechanism
-
Davi, C., & Braga-Neto, U.
(2020).
A Semi-Supervised Generative Adversarial Network for Prediction of Genetic Disease Outcomes
-
Bahadorinejad, A., Imani, M., & Braga-Neto, U. M.
(2020).
Adaptive Particle Filtering for Fault Detection in Partially-Observed Boolean Dynamical Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
17(4), 1105-1114.
-
McClenny, L., Haile, M., Attari, V., Sadler, B., Braga-Neto, U., & Arroyave, R.
(2020).
Deep Multimodal Transfer-Learned Regression in Data-Poor Domains
-
Kunselman, C., Attari, V., McClenny, L., Braga-Neto, U., & Arroyave, R.
(2020).
Semi-supervised learning approaches to class assignment in ambiguous microstructures. ACTA MATERIALIA.
188, 49-62.
-
Imani, M., Dougherty, E. R., & Braga-Neto, U.
(2020).
Boolean Kalman filter and smoother under model uncertainty. Automatica.
111, 108609-108609.
-
Davi, C., Pastor, A., Oliveira, T., Neto, F., Braga-Neto, U., Bigham, A. W., ... Acioli-Santos, B.
(2019).
Severe Dengue Prognosis Using Human Genome Data and Machine Learning. IEEE Transactions on Biomedical Engineering.
66(10), 2861-2868.
-
Imani, M., & Braga-Neto, U. M.
(2019).
Control of Gene Regulatory Networks Using Bayesian Inverse Reinforcement Learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
16(4), 1250-1261.
-
Hajiramezanali, E., Imani, M., Braga-Neto, U., Qian, X., & Dougherty, E. R.
(2019).
Scalable optimal Bayesian classification of single-cell trajectories under regulatory model uncertainty. BMC GENOMICS.
20(Suppl 6), 435.
-
Imani, M., & Braga-Neto, U. M.
(2019).
Point-Based Methodology to Monitor and Control Gene Regulatory Networks via Noisy Measurements. IEEE Transactions on Control Systems Technology.
27(3), 1023-1035.
-
Karbalayghareh, A., Braga-Neto, U., & Dougherty, E. R.
(2019).
Classification of Single-Cell Gene Expression Trajectories from Incomplete and Noisy Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
16(1), 193-207.
-
Xie, S., & Braga-Neto, U. M.
(2019).
On the Bias of Precision Estimation Under Separate Sampling. Cancer Informatics.
18, 1176935119860822-117693511986082.
-
Imani, M., & Braga-Neto, U.
(2018).
Gene regulatory network state estimation from arbitrary correlated measurements. EURASIP Journal on Advances in Signal Processing.
2018(1), 22.
-
Imani, M., & Braga-Neto, U. M.
(2018).
Control of Gene Regulatory Networks With Noisy Measurements and Uncertain Inputs. IEEE Transactions on Control of Network Systems.
5(2), 760-769.
-
Karbalayghareh, A., Braga-Neto, U., & Dougherty, E. R.
(2018).
Intrinsically Bayesian robust classifier for single-cell gene expression trajectories in gene regulatory networks. BMC Syst Biol.
12(Suppl 3), 23.
-
Bahadorinejad, A., & Braga-Neto, U. M.
(2018).
Optimal Fault Detection and Diagnosis in Transcriptional Circuits Using Next-Generation Sequencing. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
15(2), 516-525.
-
Atashpaz-Gargari, E., Reis, M. S., Braga-Neto, U. M., Barrera, J., & Dougherty, E. R.
(2018).
A fast Branch-and-Bound algorithm for U-curve feature selection. Pattern Recognition.
73, 172-188.
-
Nagaraja, K., & Braga-Neto, U.
(2018).
Bayesian Classification of Proteomics Biomarkers from Selected Reaction Monitoring Data using an Approximate Bayesian Computation-Markov Chain Monte Carlo Approach. Cancer Informatics.
17, 1176935118786927-117693511878692.
-
Karbalayghareh, A., Braga-Neto, U., Hua, J., & Dougherty, E. R.
(2018).
Classification of State Trajectories in Gene Regulatory Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
15(1), 68-82.
-
Imani, M., & Braga-Neto, U. M.
(2018).
Particle filters for partially-observed Boolean dynamical systems. Automatica.
87, 238-250.
-
Imani, M., Dehghannasiri, R., Braga-Neto, U. M., & Dougherty, E. R.
(2018).
Sequential Experimental Design for Optimal Structural Intervention in Gene Regulatory Networks Based on the Mean Objective Cost of Uncertainty. Cancer Informatics.
17, 1176935118790247-117693511879024.
-
Mcclenny, L. D., Imani, M., & Braga-Neto, U. M.
(2017).
BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems. BMC Bioinformatics.
18(1), 519.
-
Oliveira, R., Cordeiro, M. T., Moura, P., Baptista Filho, P., Braga-Neto, U., Marques, E., & Gil, L.
(2017).
Serum cytokine/chemokine profiles in patients with dengue fever (DF) and dengue hemorrhagic fever (FHD) by using protein array. J Clin Virol.
89, 39-45.
-
Imani, M., & Braga-Neto, U. M.
(2017).
Maximum-Likelihood Adaptive Filter for Partially Observed Boolean Dynamical Systems. IEEE Transactions on Signal Processing.
65(2), 359-371.
-
Chen, T., & Braga-Neto, U. M.
(2016).
Bayesian estimation of the discrete coefficient of determination. EURASIP Journal on Bioinformatics and Systems Biology.
2016(1), 1-19.
-
Chen, T., & Braga-Neto, U. M.
(2015).
Statistical Detection of Intrinsically Multivariate Predictive Genes. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
12(4), 951-963.
-
Banerjee, U., & Braga-Neto, U. M.
(2015).
Bayesian ABC-MCMC Classification of Liquid Chromatography-Mass Spectrometry Data. Cancer Informatics.
14(Suppl 5), 175-182.
-
Braga-Neto, U. M., Zollanvari, A., & Dougherty, E. R.
(2014).
Cross-validation under separate sampling: strong bias and how to correct it. Bioinformatics.
30(23), 3349-3355.
-
Atashpaz-Gargari, E., Braga-Neto, U. M., & Dougherty, E. R.
(2014).
Modeling and systematic analysis of biomarker validation using selected reaction monitoring. EURASIP Journal on Bioinformatics and Systems Biology.
2014(1), 17-12.
-
Vu, T., Sima, C., Braga-Neto, U. M., & Dougherty, E. R.
(2014).
Unbiased bootstrap error estimation for linear discriminant analysis. EURASIP Journal on Bioinformatics and Systems Biology.
2014(1), 15-14.
-
Afsari, B., Braga-Neto, U. M., & Geman, D.
(2014).
Rank discriminants for predicting phenotypes from RNA expression. Ann Appl Stat.
8(3), 1469-1491.
-
Pastor, A. F., Rodrigues Moura, L., Neto, J., Nascimento, E., Calzavara-Silva, C. E., Gomes, A., ... Acioli-Santos, B.
(2013).
Complement factor H gene (CFH) polymorphisms C-257T, G257A and haplotypes are associated with protection against severe dengue phenotype, possible related with high CFH expression. Human Immunology.
74(9), 1225-1230.
-
Chen, T., & Braga-Neto, U. M.
(2013).
Statistical detection of boolean regulatory relationships. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
10(5), 1310-1321.
-
Chen, T., & Braga-Neto, U. M.
(2013).
Maximum-Likelihood Estimation of the Discrete Coefficient of Determination in Stochastic Boolean Systems. IEEE Transactions on Signal Processing.
61(15), 3880-3894.
-
Xavier Eurico de Alencar, L., de Mendona Braga-Neto, U., Jos Moura do Nascimento, E., Tenrio Cordeiro, M., Maria Silva, A., Alexandre Antunes de Brito, C., ... Marques, E.
(2013).
HLA-B44 Is Associated with Dengue Severity Caused by DENV-3 in a Brazilian Population. Journal of Tropical Medicine.
2013, 648475-11.
-
Atashpaz-Gargari, E., Sima, C., Braga-Neto, U. M., & Dougherty, E. R.
(2013).
Relationship between the accuracy of classifier error estimation and complexity of decision boundary. Pattern Recognition.
46(5), 1315-1322.
-
Martins, D. C., de Oliveira, E. A., Braga-Neto, U. M., Hashimoto, R. F., & Cesar, R. M.
(2013).
Signal propagation in Bayesian networks and its relationship with intrinsically multivariate predictive variables. Information Sciences.
225, 18-34.
-
de Melo, A. B., Nascimento, E., Braga-Neto, U., Dhalia, R., Silva, A. M., Oelke, M., ... Marques, E.
(2013).
T-cell memory responses elicited by yellow fever vaccine are targeted to overlapping epitopes containing multiple HLA-I and -II binding motifs. PLoS Neglected Tropical Diseases.
7(1), e1938-e1938.
-
Sun, Y., Braga-Neto, U., & Dougherty, E. R.
(2012).
A systematic model of the LC-MS proteomics pipeline. BMC GENOMICS.
13 Suppl 6(S6), S2.
-
Allen, C. C., Alves, B., Li, X., Tedeschi, L. O., Zhou, H., Paschal, J. C., ... Amstalden, M.
(2012).
Gene expression in the arcuate nucleus of heifers is affected by controlled intake of high- and low-concentrate diets. J Anim Sci.
90(7), 2222-2232.
-
Sun, Y., Zhang, J., Braga-Neto, U., & Dougherty, E. R.
(2012).
BPDA2d--a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry. Bioinformatics.
28(4), 564-572.
-
Zollanvari, A., Braga-Neto, U., & Dougherty, E. R.
(2012).
Exact representation of the second-order moments for resubstitution and leave-one-out error estimation for linear discriminant analysis in the univariate heteroskedastic Gaussian model. Pattern Recognition.
45(2), 908-917.
-
Braga-Neto, U., Kuang, R., Lhdesmki, H., Vikalo, H., & Yoon, B.
(2011).
Genomic Signal Processing. EURASIP Journal on Advances in Signal Processing.
2010(1), 137263.
-
Sima, C., Braga-Neto, U. M., & Dougherty, E. R.
(2011).
High-dimensional bolstered error estimation. Bioinformatics.
27(21), 3056-3064.
-
de Melo, A. B., da Silva, M., Magalhes, M., Gonzales Gil, L., Freese de Carvalho, E. M., Braga-Neto, U. M., ... Cordeiro, M. T.
(2011).
Description of a prospective 17DD yellow fever vaccine cohort in Recife, Brazil. AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE.
85(4), 739-747.
-
Wang, Y., Ghaffari, N., Johnson, C. D., Braga-Neto, U. M., Wang, H., Chen, R., & Zhou, H.
(2011).
Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens. BMC Bioinformatics.
12 Suppl 10(S10), S5.
-
Wren, J. D., Kupfer, D. M., Perkins, E. J., Bridges, S., Winters-Hilt, S., Dozmorov, M. G., & Braga-Neto, U.
(2011).
Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction. BMC Bioinformatics.
12 Suppl 10(S10), S1.
-
Zollanvari, A., Braga-Neto, U. M., & Dougherty, E. R.
(2011).
Analytic Study of Performance of Error Estimators for Linear Discriminant Analysis. IEEE Transactions on Signal Processing.
59(9), 4238-4255.
-
Dougherty, E. R., Zollanvari, A., & Braga-Neto, U. M.
(2011).
The illusion of distribution-free small-sample classification in genomics. Curr Genomics.
12(5), 333-341.
-
Chen, T., & Braga-Neto, U.
(2010).
Exact Performance of CoD Estimators in Discrete Prediction. EURASIP Journal on Advances in Signal Processing.
2010(1), 487893.
-
Vu, T. T., & Braga-Neto, U. M.
(2010).
Small-Sample Error Estimation for Bagged Classification Rules. EURASIP Journal on Advances in Signal Processing.
2010(1), 548906.
-
Banon, G., Braga-Neto, U., & Cesar, R. M.
(2010).
ISMM 2007 Special Issue. Image and Vision Computing.
28(10), 1427-1428.
-
Sun, Y., Zhang, J., Braga-Neto, U., & Dougherty, E. R.
(2010).
BPDA - a Bayesian peptide detection algorithm for mass spectrometry. BMC Bioinformatics.
11(1), 490.
-
Braga-Neto, U. M., & Dougherty, E. R.
(2010).
Exact correlation between actual and estimated errors in discrete classification. Pattern Recognition Letters.
31(5), 407-412.
-
Dougherty, E., Sima, C., Hua, .., Hanczar, B., & Braga-Neto, U.
(2010).
Performance of Error Estimators for Classification. Current Bioinformatics.
5(1), 53-67.
-
Zollanvari, A., Braga-Neto, U. M., & Dougherty, E. R.
(2010).
Joint Sampling Distribution Between Actual and Estimated Classification Errors for Linear Discriminant Analysis. 2011 IEEE INTERNATIONAL SYMPOSIUM ON INFORMATION THEORY PROCEEDINGS (ISIT).
56(2), 784-804.
-
Braga-Neto, U. M.
(2009).
Classification and error estimation for discrete data. Curr Genomics.
10(7), 446-462.
-
Nascimento, E., Braga-Neto, U., Calzavara-Silva, C. E., Gomes, A., Abath, F., Brito, C., ... Marques, E.
(2009).
Gene expression profiling during early acute febrile stage of dengue infection can predict the disease outcome. PLoS One.
4(11), e7892-e7892.
-
Zollanvari, A., Braga-Neto, U. M., & Dougherty, E. R.
(2009).
On the sampling distribution of resubstitution and leave-one-out error estimators for linear classifiers. Pattern Recognition.
42(11), 2705-2723.
-
Zollanvari, A., Cunningham, M. J., Braga-Neto, U., & Dougherty, E. R.
(2009).
Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes. BMC Bioinformatics.
10(SUPPL. 11),
-
Zollanvari, A., Cunningham, M. J., Braga-Neto, U., & Dougherty, E. R.
(2009).
Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes. BMC Bioinformatics.
10 Suppl 11(S11), S10.
-
Wren, J. D., Gusev, Y., Isokpehi, R. D., Berleant, D., Braga-Neto, U., Wilkins, D., & Bridges, S.
(2009).
Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics.
10(SUPPL. 11),
-
Wren, J. D., Gusev, Y., Isokpehi, R. D., Berleant, D., Braga-Neto, U., Wilkins, D., & Bridges, S.
(2009).
Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction. BMC Bioinformatics.
10 Suppl 11(S11), S1.
-
Nascimento, E., Silva, A. M., Cordeiro, M. T., Brito, C. A., Gil, L., Braga-Neto, U., & Marques, E.
(2009).
Alternative complement pathway deregulation is correlated with dengue severity. PLoS One.
4(8), e6782-e6782.
-
Serpedin, E., Garcia-Frias, J., Huang, Y., & Braga-Neto, U.
(2009).
Applications of signal processing techniques to bioinformatics, genomics, and proteomics. EURASIP Journal on Bioinformatics and Systems Biology.
2009(1), 250306-250306.
-
Vu, T. T., & Braga-Neto, U. M.
(2009).
Is bagging effective in the classification of small-sample genomic and proteomic data?. EURASIP Journal on Bioinformatics and Systems Biology.
2009(1), 158368-158368.
-
Cordeiro, M. T., Braga-Neto, U., Nogueira, R., & Marques, E.
(2009).
Reliable classifier to differentiate primary and secondary acute dengue infection based on IgG ELISA. PLoS One.
4(4), e4945-e4945.
-
Sun, Y., Braga-Neto, U., & Dougherty, E. R.
(2009).
Impact of missing value imputation on classification for DNA microarray gene expression data--a model-based study. 2009(1), 504069-504069.
-
Martins, D. C., Braga-Neto, U. M., Hashimoto, R. F., Bittner, M. L., & Dougherty, E. R.
(2008).
Intrinsically Multivariate Predictive Genes. IEEE Journal of Selected Topics in Signal Processing.
2(3), 424-439.
-
Acioli-Santos, B., Segat, L., Dhalia, R., Brito, C., Braga-Neto, U. M., Marques, E., & Crovella, S.
(2008).
MBL2 gene polymorphisms protect against development of thrombocytopenia associated with severe dengue phenotype. Human Immunology.
69(2), 122-128.
-
Braga-Neto, U.
(2007).
Fads and fallacies in the name of small-sample microarray classification - A highlight of misunderstanding and erroneous usage in the applications of genomic signal processing. IEEE: Signal Processing Magazine.
24(1), 91-99.
-
Xu, Q., Hua, J., Braga-Neto, U., Xiong, Z., Suh, E., & Dougherty, E. R.
(2006).
Confidence intervals for the true classification error conditioned on the estimated error. Technol Cancer Res Treat.
5(6), 579-589.
-
Braga-Neto, U. M., & Marques, E.
(2006).
From functional genomics to functional immunomics: new challenges, old problems, big rewards. PLoS Computational Biology.
2(7), e81-e81.
-
DOUGHERTY, E. R., & BRAGA-NETO, U.
(2006).
EPISTEMOLOGY OF COMPUTATIONAL BIOLOGY: MATHEMATICAL MODELS AND EXPERIMENTAL PREDICTION AS THE BASIS OF THEIR VALIDITY. Journal of Biological System.
14(01), 65-90.
-
Braga-Neto, U., & Dougherty, E. R.
(2005).
Classification. Eurasip Book Series on Signal Processing and Communications.
2, 93-128.
-
Braga-Neto, U., & Dougherty, E.
(2005).
Exact performance of error estimators for discrete classifiers. Pattern Recognition.
38(11), 1799-1814.
-
Braga-Neto, U., & Goutsias, J.
(2005).
Constructing multiscale connectivities. Computer Vision and Image Understanding.
99(1), 126-150.
-
Braga-Neto, U., & Goutsias, J.
(2005).
Object-based image analysis using multiscale connectivity. IEEE Trans Pattern Anal Mach Intell.
27(6), 892-907.
-
Braga-Neto, U.
(2005).
Multiscale Connected Operators. Journal of Mathematical Imaging and Vision.
22(2-3), 199-216.
-
Sima, C., Braga-Neto, U., & Dougherty, E. R.
(2005).
Superior feature-set ranking for small samples using bolstered error estimation. Bioinformatics.
21(7), 1046-1054.
-
Braga-Neto, U., & Goutsias, J.
(2004).
Grayscale level connectivity: theory and applications. IEEE Trans Image Process.
13(12), 1567-1580.
-
Choudhary, M.
(2004).
Automatic target detection and tracking in forward-looking infrared image sequences using morphological connected operators. Journal of Electronic Imaging.
13(4), 802-802.
-
Braga-Neto, U., & Dougherty, E.
(2004).
Bolstered error estimation. Pattern Recognition.
37(6), 1267-1281.
-
Braga-Neto, U. M., & Dougherty, E. R.
(2004).
Is cross-validation valid for small-sample microarray classification?. Bioinformatics.
20(3), 374-380.
-
Braga-Neto, U., Hashimoto, R., Dougherty, E. R., Nguyen, D. V., & Carroll, R. J.
(2004).
Is cross-validation better than resubstitution for ranking genes?. Bioinformatics.
20(2), 253-258.
-
Braga-Neto, U., & Goutsias, J.
(2004).
Supremal Multiscale Signal Analysis. SIAM Journal on Mathematical Analysis.
36(1), 94-120.
-
Braga-Neto, U., & Goutsias, J.
(2003).
A Theoretical Tour of Connectivity in Image Processing and Analysis. Journal of Mathematical Imaging and Vision.
19(1), 5-31.
-
Braga-Neto, U., & Goutsias, J.
(2003).
A multiscale approach to connectivity. Computer Vision and Image Understanding.
89(1), 70-107.
-
Han, X., Xu, C., Braga-Neto, U., & Prince, J. L.
(2002).
Topology correction in brain cortex segmentation using a multiscale, graph-based algorithm. IEEE Transactions on Medical Imaging.
21(2), 109-121.
-
Braga-Neto, U., & Goutsias, J.
(2002).
Connectivity on Complete Lattices: New Results. Computer Vision and Image Understanding.
85(1), 22-53.
-
Candas, A. J., Braga Neto, U., & Carvalho Filho, E.
(1997).
A Mathematical Morphology Approach to the Star/Galaxy Characterization. Journal of the Brazilian Computer Society.
3(3),
-
Ghane, P., Zarnaghinaghsh, N., & Braga-Neto, U.
(2021).
Comparison of Classification Algorithms Towards Subject-Specific and Subject-Independent BCI. 00, 1-6.
-
book
-
Braga-Neto, U. M., & Dougherty, E. R.
(2015).
Error Estimation for Pattern Recognition. John Wiley & Sons, Inc..
-
Braga-Neto, U. M., & Dougherty, E. R.
(2015).
Error Estimation for Pattern Recognition. John Wiley & Sons, Inc..
-
chapter
-
Braga Neto, U., & Dougherty, E. R.
(2005).
Classification. Dougherty, E., Shmulevich, I., Chen, J., & Wang, Z. J. (Eds.),
Genomic Signal Processing and Statistics.
(pp. 93-128).
Hindawi Publishing Corporation.
-
Braga Neto, U., & Dougherty, E. R.
(2005).
Classification. Dougherty, E., Shmulevich, I., Chen, J., & Wang, Z. J. (Eds.),
Genomic Signal Processing and Statistics.
(pp. 93-128).
Hindawi Publishing Corporation.
-
conference paper
-
Imani, M., Ghoreishi, S. F., & Braga-Neto, U. M.
(2018).
Bayesian control of large MDPs with unknown dynamics in data-poor environments. ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS (NEURIPS 2020).
8146-8156.
-
Tan, Y., Lima Neto, F. B., & Braga Neto, U.
(2018).
INFERENCE OF GENE REGULATORY NETWORKS BY MAXIMUM-LIKELIHOOD ADAPTIVE FILTERING AND DISCRETE FISH SCHOOL SEARCH. 2019 IEEE 29TH INTERNATIONAL WORKSHOP ON MACHINE LEARNING FOR SIGNAL PROCESSING (MLSP).
1-6.
-
Imani, M., & Braga-Neto, U.
(2018).
Optimal Control of Gene Regulatory Networks with Unknown Cost Function. 1985 American Control Conference.
3939-3944.
-
Hajiramezanali, E., Imani, M., Braga-Neto, U., Qian, X., & Dougherty, E. R.
(2018).
Scalable Optimal Bayesian Classification of Single-Cell Trajectories under Regulatory Model Uncertainty. 596-597.
-
Karbalayghareh, A., Braga-Neto, U., & Dougherty, E. R.
(2017).
Intrinsically Bayesian Robust Classifier for Single-Cell Gene Expression Time Series in Gene Regulatory Networks. 766-767.
-
Imani, M., & Braga-Neto, U.
(2017).
Multiple Model Adaptive controller for Partially-Observed Boolean Dynamical Systems. 1985 American Control Conference.
1103-1108.
-
Arslan, E., & Braga-Neto, U. M.
(2017).
A Bayesian approach to Top-Scoring Pairs classification. 1999 IEEE International Conference on Acoustics, Speech, and Signal Processing. Proceedings. ICASSP99 (Cat. No.99CH36258).
871-875.
-
McClenny, L. D., Imani, M., & Braga-Neto, U. M.
(2017).
Boolean Kalman Filter with correlated observation noise. 1999 IEEE International Conference on Acoustics, Speech, and Signal Processing. Proceedings. ICASSP99 (Cat. No.99CH36258).
866-870.
-
Karbalayghareh, A., Braga-Neto, U., & Dougherty, E. R.
(2017).
Classification of Gaussian trajectories with missing data in Boolean gene regulatory networks. 1999 IEEE International Conference on Acoustics, Speech, and Signal Processing. Proceedings. ICASSP99 (Cat. No.99CH36258).
1078-1082.
-
Arslan, E., & Braga-Neto, U. M.
(2017).
Bayesian top scoring pairs for feature selection. 387-391.
-
Xie, S., Imani, M., Dougherty, E. R., & Braga-Neto, U. M.
(2017).
Nonstationary linear discriminant analysis. 2006 Fortieth Asilomar Conference on Signals, Systems and Computers.
161-165.
-
Imani, M., & Braga-Neto, U. M.
(2017).
Optimal finite-horizon sensor selection for Boolean Kalman Filter. 1481-1485.
-
Imani, M., & Braga-Neto, U.
(2016).
Point-based value iteration for partially-observed Boolean dynamical systems with finite observation space. 2004 43rd IEEE Conference on Decision and Control (CDC) (IEEE Cat. No.04CH37601).
4208-4213.
-
Imani, M., & Braga-Neto, U.
(2016).
State-feedback control of Partially-Observed Boolean Dynamical Systems using RNA-seq time series data. 1985 American Control Conference.
227-232.
-
Imani, M., & Braga-Neto, U.
(2015).
Optimal state estimation for boolean dynamical systems using a boolean Kalman smoother. 972-976.
-
Imani, M., & Braga-Neto, U.
(2015).
Optimal gene regulatory network inference using the Boolean Kalman filter and multiple model adaptive estimation. 2006 Fortieth Asilomar Conference on Signals, Systems and Computers.
423-427.
-
Jiang, X., & Braga-Neto, U.
(2014).
A Naive-Bayes approach to Bolstered error estimation in high-dimensional spaces. 1398-1401.
-
Bahadorinejad, A., & Braga-Neto, U.
(2014).
Optimal fault detection in stochastic Boolean regulatory networks. 1386-1389.
-
Braga-Neto, U.
(2013).
Particle filtering approach to state estimation in Boolean dynamical systems. 2013 IEEE GLOBAL CONFERENCE ON SIGNAL AND INFORMATION PROCESSING (GLOBALSIP).
81-84.
-
Zollanvari, A., Braga-Neto, U. M., & Dougherty, E. R.
(2013).
Effect of mixing probabilities on the bias of cross-validation under separate sampling. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
98-99.
-
Atashpaz-Gargari, E., Braga-Neto, U. M., & Dougherty, E. R.
(2013).
Improved branch-and-bound algorithm for U-curve optimization. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
100-101.
-
Chen, T., & Braga-Neto, U.
(2013).
Optimal Bayesian MMSE estimation of the coefficient of determination for discrete prediction. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
66-69.
-
Chen, T., & Braga-Neto, U.
(2012).
A statistical test for intrinsically multivariate predictive genes. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
151-154.
-
Braga-Neto, U.
(2012).
Joint state and parameter estimation for Boolean dynamical systems. 704-707.
-
Sun, Y., Braga-Neto, U., & Dougherty, E. R.
(2011).
Modeling and systematic analysis of LC-MS proteomics pipeline. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
112-116.
-
Atashpaz-Gargari, E., Braga-Neto, U. M., & Dougherty, E. R.
(2011).
Multiple reaction monitoring: Modeling and systematic analysis. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
105-107.
-
Atashpaz-Gargari, E., Sima, C., Braga-Neto, U. M., & Dougherty, E. R.
(2011).
Relationship between the accuracy of classifier error estimation and distribution complexity. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
147-149.
-
Chen, T., & Braga-Neto, U.
(2011).
Sample-based estimators for the instrinsically multivariate prediction score. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
139-142.
-
Afra, S., & Braga-Neto, U.
(2011).
Studying the possibility of peaking phenomenon in linear support vector machines with non-separable data. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
218-221.
-
Zhenghao Zhang, .., Youting Sun, .., Braga-Neto, U., Dougherty, E., & Jianqiu Zhang.
(2011).
A parallel programming framework with Markovian messaging for LC-MS peptide detection. 2008 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE WORKSHOPS, PROCEEDINGS.
1057-1059.
-
Chen, T., & Braga-Neto, U.
(2011).
Maximum likelihood estimation of the binary Coefficient of Determination. 2006 Fortieth Asilomar Conference on Signals, Systems and Computers.
1012-1016.
-
Braga-Neto, U.
(2011).
Optimal state estimation for Boolean dynamical systems. 2006 Fortieth Asilomar Conference on Signals, Systems and Computers.
1050-1054.
-
Ting Chen, .., & Braga-Neto, U.
(2010).
Approximate expressions for the variances of non-randomized error estimators and CoD estimators for the discrete histogram rule. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-4.
-
Zollanvari, A., Braga-Neto, U. M., & Dougherty, E. R.
(2010).
RMS bounds and sample size considerations for error estimation in linear discriminant analysis. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-4.
-
Vu, T. T., Braga-Neto, U. M., & Dougherty, E. R.
(2009).
Bagging degrades the performance of linear discriminant classifiers. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-2.
-
Sima, C., Vu, T., Braga-Neto, U. M., & Dougherty, E. R.
(2009).
Bolstered error estimator with feature selection. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-2.
-
Zollanvari, A., Braga-Neto, U. M., & Dougherty, E. R.
(2009).
Sample size calculation from specified RMS of the resubstitution error for linear classifiers. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-2.
-
Braga-Neto, U.
(2008).
An asymptotically-exact expression for the variance of classification error for the discrete histogram rule. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-3.
-
Martins, D. C., Braga-Neto, U., Bittner, M. L., & Dougherty, E. R.
(2008).
Network properties of intrinsically multivariate predictive genes. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-2.
-
Vu, T. T., Braga-Neto, U., & Dougherty, E. R.
(2008).
Preliminary study on bolstered error estimation in high-dimensional spaces. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-2.
-
Braga-Neto, U.
(2005).
Small-sample error estimation: mythology versus mathematics. 35th European Mask and Lithography Conference (EMLC 2019).
59160v-59160v-11-11.
-
Braga-Neto, U.
(2005).
Grayscale level multiconnectivity. 129-138.
-
Han, X., Xu, C., Braga-Neto, U., & Prince, J. L.
(2001).
Graph-based topology correction for brain cortex segmentation. ADVANCED COMPUTING STRATEGIES FOR ENGINEERING, PT II.
395-401.
-
Braga-Neto, U. M., & Goutsias, J. I.
(1998).
Detecting mines and minelike objects in highly cluttered multispectral aerial images by means of mathematical morphology. 35th European Mask and Lithography Conference (EMLC 2019).
987-999.
-
Imani, M., Ghoreishi, S. F., & Braga-Neto, U. M.
(2018).
Bayesian control of large MDPs with unknown dynamics in data-poor environments. ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS (NEURIPS 2020).
8146-8156.
-
institutional repository document
-
Ghane, P., & Braga-Neto, U.
(2021).
Generalized Resubstitution for Classification Error Estimation
-
Tan, Y., III, D. C., Ndeffo-Mbah, M., & Braga-Neto, U.
(2021).
A stochastic metapopulation state-space approach to modeling and estimating Covid-19 spread
-
McClenny, L. D., Haile, M. A., & Braga-Neto, U. M.
(2021).
TensorDiffEq: Scalable Multi-GPU Forward and Inverse Solvers for Physics Informed Neural Networks
-
Ghane, P., & Braga-Neto, U.
(2021).
Generalized Resubstitution for Classification Error Estimation
Research
principal investigator on
- CIF:Small:Minimum Mean Square Error Estimation and Control of Partially-Observed Boolean Dynamical Systems with Applications in Metagenomics awarded by National Science Foundation - (Arlington, Virginia, United States) 2017 - 2020
- CIF: Small: Optimal Estimation and Network Inference for Boolean Dynamical Systems awarded by National Science Foundation - (Arlington, Virginia, United States) 2013 - 2017
- CAREER: Theory and Application of Small-Sample Error Estimation in Genomic Signal Processing awarded by National Science Foundation - (Arlington, Virginia, United States) 2009 - 2015
investigator on
Teaching
teaching activities
- ECEN214 Elec Circuit Theory Instructor
- ECEN215 Prin Of Electrical Engr Instructor
- ECEN303 Random Signals & Systems Instructor
- ECEN303 Random Signals&systems-germany Instructor
- ECEN314 Signals And Systems Instructor
- ECEN322 Elec & Magnetic Fields-germ Instructor
- ECEN485 Directed Studies Instructor
- ECEN491 Hnr-research Instructor
- ECEN649 Pattern Recognition Instructor
- ECEN684 Professional Internship Instructor
- ECEN684 Professional Internship Instructor
- ECEN685 Directed Studies:uk/germany Instructor
- ECEN689 Sptp: Mtls Informatics Instructor
- ECEN689 Sptp:scientific Machine Learn Instructor
- ECEN691 Research Instructor
- ECEN769 Materials Informatics Instructor
- MSEN660 Materials Informatics Instructor
- MSEN689 Sptp: Mtls Informatics Instructor
Works By Students
chaired theses and dissertations
-
Arslan, Emre (2018-12). A Novel Bayesian Rank-Based Framework for the Classification of High-Dimensional Biological Data.
-
Atashpazgargari, Esmaeil (2014-08). Biomarker Discovery and Validation for Proteomics and Genomics: Modeling And Systematic Analysis.
-
Bahadorinejad, Arghavan (2017-05). Fault Detection and Diagnosis in Gene Regulatory Networks and Optimal Bayesian Classification of Metagenomic Data.
-
Chen, Ting (2013-12). Estimation and Detection of Multivariate Gene Regulatory Relationships.
-
Imani, Mahdi (2019-05). Estimation, Inference and Learning of Partially-Observed Dynamical Systems.
-
Jiang, Xingde (2016-12). Novel Pattern Recognition Approaches to Identification of Gene-Expression Pathways in Banana Cultivars.
-
Koonchanok, Ratanond (2017-12). Computational Tool for Applications of Sparse Canonical Correlation Analysis on Biological Data.
-
Liu, Fan (2018-12). Network Analysis to Reveal Jasmonic Acid Pathway Related Mechanistic Changes for Drought-Tolerant Maize.
-
McClenny, Levi Daniel (2016-08). Optimal State Estimation for Partially Observed Boolean Dynamical Systems in the Presence of Correlated Observation Noise.
-
Nagaraja, Kashyap (2019-05). Bayesian Classification of Proteomics Biomarkers from Selected Reaction Monitoring Data Using an ABC-MCMC Approach.
-
Sun, Youting (2012-05). Model-based Biomarker Detection and Systematic Analysis in Translational Science.
-
Vu, Thang (2011-05). The Bootstrap in Supervised Learning and its Applications in Genomics/Proteomics.
-
Zollanvari, Amin (2010-12). Analytic Study of Performance of Error Estimators for Linear Discriminant Analysis with Applications in Genomics.
Background
education and training
- Ph.D. in Electrical & Computer Engineering, Johns Hopkins University - (Baltimore, Maryland, United States) 2002
- M.S.E. in Electrical & Computer Engineering and Mathematical Sciences, Johns Hopkins University - (Baltimore, Maryland, United States) 1998
- M.S. in Electrical Engineering, State University of Campinas - (Campinas, Brazil) 1994
- B.S. in Electrical Engineering, Federal University of Pernambuco - (Recife, Brazil) 1992
awards and honors
Contact
first name
- Ulisses
has last name
- Braga Neto
mailing address
-
Texas A&M University
Electrical Engineering
3128 TAMU
College Station, TX 77843-3128
USA
Other
In the News
- ulisses@tamu.edu