Ulisses M. Braga-Neto

121 papers A* 2C 5Misc 7Journal 74Unranked 32
YearRankTypeTitle / Venue / Authors
2025 J jnl
A State-Space Approach to Nonstationary Discriminant Analysis.
CoRR
Shuilian Xie, Mahdi Imani, Edward R. Dougherty, Ulisses M. Braga-Neto
2023 J jnl
Self-adaptive physics-informed neural networks.
J. Comput. Phys.
Levi D. McClenny, Ulisses M. Braga-Neto
2022 J jnl
PALLAS: Penalized mAximum LikeLihood and pArticle Swarms for Inference of Gene Regulatory Networks From Time Series Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yukun Tan, Fernando B. Lima Neto, Ulisses M. Braga-Neto
2022 J jnl
PSO-PINN: Physics-Informed Neural Networks Trained with Particle Swarm Optimization.
CoRR
Caio Davi, Ulisses M. Braga-Neto
2021 — conf
A Semi-Supervised Generative Adversarial Network for Prediction of Genetic Disease Outcomes.
MLSP
Caio Davi, Ulisses M. Braga-Neto
2021 J jnl
A stochastic metapopulation state-space approach to modeling and estimating Covid-19 spread.
CoRR
Yukun Tan, Durward Cator III, Martial L. Ndeffo Mbah, Ulisses M. Braga-Neto
2021 — conf
Comparison of Classification Algorithms Towards Subject-Specific and Subject-Independent BCI.
BCI
Parisa Ghane, Narges Zarnaghinaghsh, Ulisses M. Braga-Neto
2021 J jnl
Generalized Resubstitution for Classification Error Estimation.
CoRR
Parisa Ghane, Ulisses M. Braga-Neto
2021 — conf
Self-Adaptive Physics-Informed Neural Networks using a Soft Attention Mechanism.
AAAI Spring Symposium: MLPS
Levi D. McClenny, Ulisses M. Braga-Neto
2021 J jnl
TensorDiffEq: Scalable Multi-GPU Forward and Inverse Solvers for Physics Informed Neural Networks.
CoRR
Levi D. McClenny, Mulugeta A. Haile, Ulisses M. Braga-Neto
2020 J jnl
A Semi-Supervised Generative Adversarial Network for Prediction of Genetic Disease Outcomes.
CoRR
Caio Davi, Ulisses M. Braga-Neto
2020 J jnl
Adaptive Particle Filtering for Fault Detection in Partially-Observed Boolean Dynamical Systems.
IEEE ACM Trans. Comput. Biol. Bioinform.
Arghavan Bahadorinejad, Mahdi Imani, Ulisses M. Braga-Neto
2020 J jnl
Boolean Kalman filter and smoother under model uncertainty.
Autom.
Mahdi Imani, Edward R. Dougherty, Ulisses M. Braga-Neto
2020 J jnl
Comparison of Classification Algorithms Towards Subject-Specific and Subject-Independent BCI.
CoRR
Parisa Ghane, Ulisses M. Braga-Neto
2020 J jnl
Deep Multimodal Transfer-Learned Regression in Data-Poor Domains.
CoRR
Levi D. McClenny, Mulugeta A. Haile, Vahid Attari, Brian M. Sadler, Ulisses M. Braga-Neto, Raymundo Arróyave
2020 — book
Fundamentals of Pattern Recognition and Machine Learning
Ulisses M. Braga-Neto
2020 — conf
Inference of Protein-Protein Interaction Networks from Liquid-Chromatography Mass-Spectrometry Data by Approximate Bayesian Computation-Sequential Monte Carlo Sampling.
MLSP
Yukun Tan, Fernando B. Lima Neto, Ulisses M. Braga-Neto
2020 J jnl
Machine Learning Requires Probability and Statistics [Perspectives].
IEEE Signal Process. Mag.
Ulisses M. Braga-Neto, Edward R. Dougherty
2020 J jnl
Self-Adaptive Physics-Informed Neural Networks using a Soft Attention Mechanism.
CoRR
Levi D. McClenny, Ulisses M. Braga-Neto
2019 J jnl
Classification of Single-Cell Gene Expression Trajectories from Incomplete and Noisy Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Alireza Karbalayghareh, Ulisses M. Braga-Neto, Edward R. Dougherty
2019 J jnl
Control of Gene Regulatory Networks Using Bayesian Inverse Reinforcement Learning.
IEEE ACM Trans. Comput. Biol. Bioinform.
Mahdi Imani, Ulisses M. Braga-Neto
2019 A* conf
MFBO-SSM: Multi-Fidelity Bayesian Optimization for Fast Inference in State-Space Models.
AAAI
Mahdi Imani, Seyede Fatemeh Ghoreishi, Douglas L. Allaire, Ulisses M. Braga-Neto
2019 J jnl
Point-Based Methodology to Monitor and Control Gene Regulatory Networks via Noisy Measurements.
IEEE Trans. Control. Syst. Technol.
Mahdi Imani, Ulisses M. Braga-Neto
2019 J jnl
Severe Dengue Prognosis Using Human Genome Data and Machine Learning.
IEEE Trans. Biomed. Eng.
Caio Davi, André Pastor, Thiego Oliveira, Fernando Buarque de Lima Neto, Ulisses M. Braga-Neto, Abigail W. Bigham, Michael Bamshad, Ernesto T. A. Marques Jr., Bartolomeu Acioli-Santos
2018 J jnl
A fast Branch-and-Bound algorithm for U-curve feature selection.
Pattern Recognit.
Esmaeil Atashpaz-Gargari, Marcelo da Silva Reis, Ulisses M. Braga-Neto, Junior Barrera, Edward R. Dougherty
2018 A* conf
Bayesian Control of Large MDPs with Unknown Dynamics in Data-Poor Environments.
NeurIPS
Mahdi Imani, Seyede Fatemeh Ghoreishi, Ulisses M. Braga-Neto
2018 J jnl
Classification of State Trajectories in Gene Regulatory Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Alireza Karbalayghareh, Ulisses M. Braga-Neto, Jianping Hua, Edward Russell Dougherty
2018 J jnl
Control of Gene Regulatory Networks With Noisy Measurements and Uncertain Inputs.
IEEE Trans. Control. Netw. Syst.
Mahdi Imani, Ulisses M. Braga-Neto
2018 J jnl
Finite-horizon LQR controller for partially-observed Boolean dynamical systems.
Autom.
Mahdi Imani, Ulisses M. Braga-Neto
2018 J jnl
Gene regulatory network state estimation from arbitrary correlated measurements.
EURASIP J. Adv. Signal Process.
Mahdi Imani, Ulisses M. Braga-Neto
2018 — conf
Inference of gene regulatory Networks by Maximum-likelihood adaptive filtering and discrete fish School Search.
MLSP
Yukun Tan, Fernando B. Lima Neto, Ulisses M. Braga-Neto
2018 C conf
Optimal Control of Gene Regulatory Networks with Unknown Cost Function.
ACC
Mahdi Imani, Ulisses M. Braga-Neto
2018 J jnl
Optimal Fault Detection and Diagnosis in Transcriptional Circuits Using Next-Generation Sequencing.
IEEE ACM Trans. Comput. Biol. Bioinform.
Arghavan Bahadorinejad, Ulisses M. Braga-Neto
2018 J jnl
Particle filters for partially-observed Boolean dynamical systems.
Autom.
Mahdi Imani, Ulisses M. Braga-Neto
2018 — conf
Scalable Optimal Bayesian Classification of Single-Cell Trajectories under Regulatory Model Uncertainty.
BCB
Ehsan Hajiramezanali, Mahdi Imani, Ulisses M. Braga-Neto, Xiaoning Qian, Edward R. Dougherty
2018 J jnl
Sequential Experimental Design for Optimal Structural Intervention in Gene Regulatory Networks Based on the Mean Objective Cost of Uncertainty.
CoRR
Mahdi Imani, Roozbeh Dehghannasiri, Ulisses M. Braga-Neto, Edward R. Dougherty
2017 Misc conf
A Bayesian approach to Top-Scoring Pairs classification.
ICASSP
Emre Arslan, Ulisses M. Braga-Neto
2017 Misc conf
Bayesian top scoring pairs for feature selection.
ACSSC
Emre Arslan, Ulisses M. Braga-Neto
2017 J jnl
BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems.
BMC Bioinform.
Levi D. McClenny, Mahdi Imani, Ulisses M. Braga-Neto
2017 Misc conf
Boolean Kalman Filter with correlated observation noise.
ICASSP
Levi D. McClenny, Mahdi Imani, Ulisses M. Braga-Neto
2017 Misc conf
Classification of Gaussian trajectories with missing data in Boolean gene regulatory networks.
ICASSP
Alireza Karbalayghareh, Ulisses M. Braga-Neto, Edward R. Dougherty
2017 J jnl
Control of Gene Regulatory Networks with Noisy Measurements and Uncertain Inputs.
CoRR
Mahdi Imani, Ulisses M. Braga-Neto
2017 — conf
Intrinsically Bayesian Robust Classifier for Single-Cell Gene Expression Time Series in Gene Regulatory Networks.
BCB
Alireza Karbalayghareh, Ulisses M. Braga-Neto, Edward R. Dougherty
2017 J jnl
Maximum-Likelihood Adaptive Filter for Partially Observed Boolean Dynamical Systems.
IEEE Trans. Signal Process.
Mahdi Imani, Ulisses M. Braga-Neto
2017 C conf
Multiple Model Adaptive controller for Partially-Observed Boolean Dynamical Systems.
ACC
Mahdi Imani, Ulisses M. Braga-Neto
2017 Misc conf
Nonstationary linear discriminant analysis.
ACSSC
Shuilian Xie, Mahdi Imani, Edward R. Dougherty, Ulisses M. Braga-Neto
2017 Misc conf
Optimal finite-horizon sensor selection for Boolean Kalman Filter.
ACSSC
Mahdi Imani, Ulisses M. Braga-Neto
2016 J jnl
Bayesian estimation of the discrete coefficient of determination.
EURASIP J. Bioinform. Syst. Biol.
Ting Chen, Ulisses M. Braga-Neto
2016 — conf
Point-based value iteration for partially-observed Boolean dynamical systems with finite observation space.
CDC
Mahdi Imani, Ulisses M. Braga-Neto
2016 C conf
State-feedback control of Partially-Observed Boolean Dynamical Systems using RNA-seq time series data.
ACC
Mahdi Imani, Ulisses M. Braga-Neto
2015 Misc conf
Optimal gene regulatory network inference using the Boolean Kalman filter and multiple model adaptive estimation.
ACSSC
Mahdi Imani, Ulisses M. Braga-Neto
2015 — conf
Optimal state estimation for boolean dynamical systems using a boolean Kalman smoother.
GlobalSIP
Mahdi Imani, Ulisses M. Braga-Neto
2015 J jnl
Statistical Detection of Intrinsically Multivariate Predictive Genes.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ting Chen, Ulisses M. Braga-Neto
2014 — conf
A Naive-Bayes approach to Bolstered error estimation in high-dimensional spaces.
GlobalSIP
Xingde Jiang, Ulisses M. Braga-Neto
2014 J jnl
Cross-validation under separate sampling: strong bias and how to correct it.
Bioinform.
Ulisses M. Braga-Neto, Amin Zollanvari, Edward R. Dougherty
2014 J jnl
Modeling and systematic analysis of biomarker validation using selected reaction monitoring.
EURASIP J. Bioinform. Syst. Biol.
Esmaeil Atashpaz-Gargari, Ulisses M. Braga-Neto, Edward R. Dougherty
2014 — conf
Optimal fault detection in stochastic Boolean regulatory networks.
GlobalSIP
Arghavan Bahadorinejad, Ulisses M. Braga-Neto
2014 J jnl
Unbiased bootstrap error estimation for linear discriminant analysis.
EURASIP J. Bioinform. Syst. Biol.
Thang T. Vu, Chao Sima, Ulisses M. Braga-Neto, Edward R. Dougherty
2013 — conf
Effect of mixing probabilities on the bias of cross-validation under separate sampling.
GENSiPS
Amin Zollanvari, Ulisses M. Braga-Neto, Edward R. Dougherty
2013 — conf
Improved branch-and-bound algorithm for U-curve optimization.
GENSiPS
Esmaeil Atashpaz-Gargari, Ulisses M. Braga-Neto, Edward R. Dougherty
2013 J jnl
Maximum-Likelihood Estimation of the Discrete Coefficient of Determination in Stochastic Boolean Systems.
IEEE Trans. Signal Process.
Ting Chen, Ulisses M. Braga-Neto
2013 — conf
Optimal Bayesian MMSE estimation of the coefficient of determination for discrete prediction.
GENSiPS
Ting Chen, Ulisses M. Braga-Neto
2013 — conf
Particle filtering approach to state estimation in Boolean dynamical systems.
GlobalSIP
Ulisses M. Braga-Neto
2013 J jnl
Relationship between the accuracy of classifier error estimation and complexity of decision boundary.
Pattern Recognit.
Esmaeil Atashpaz-Gargari, Chao Sima, Ulisses M. Braga-Neto, Edward R. Dougherty
2013 J jnl
Signal propagation in Bayesian networks and its relationship with intrinsically multivariate predictive variables.
Inf. Sci.
David Correa Martins Jr., Evaldo Araújo de Oliveira, Ulisses M. Braga-Neto, Ronaldo Fumio Hashimoto, Roberto Marcondes Cesar Jr.
2012 — conf
A statistical test for intrinsically multivariate predictive genes.
GENSiPS
Ting Chen, Ulisses M. Braga-Neto
2012 J jnl
BPDA2d - a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry.
Bioinform.
Youting Sun, Jianqiu Zhang, Ulisses M. Braga-Neto, Edward R. Dougherty
2012 J jnl
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 Recognit.
Amin Zollanvari, Ulisses M. Braga-Neto, Edward R. Dougherty
2012 — conf
Joint state and parameter estimation for Boolean dynamical systems.
SSP
Ulisses M. Braga-Neto
2011 — conf
A parallel programming framework with Markovian messaging for LC-MS peptide detection.
BIBM Workshops
Zhenghao Zhang, Youting Sun, Ulisses M. Braga-Neto, Edward R. Dougherty, Jianqiu Zhang
2011 J jnl
Analytic Study of Performance of Error Estimators for Linear Discriminant Analysis.
IEEE Trans. Signal Process.
Amin Zollanvari, Ulisses M. Braga-Neto, Edward R. Dougherty
2011 J jnl
Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens.
BMC Bioinform.
Ying Wang, Noushin Ghaffari, Charles D. Johnson, Ulisses M. Braga-Neto, Hui Wang, Rui Chen, Huaijun Zhou
2011 J jnl
High-dimensional bolstered error estimation.
Bioinform.
Chao Sima, Ulisses M. Braga-Neto, Edward R. Dougherty
2011 — conf
Maximum likelihood estimation of the binary Coefficient of Determination.
ACSCC
Ting Chen, Ulisses M. Braga-Neto
2011 — conf
Modeling and systematic analysis of LC-MS proteomics pipeline.
GENSiPS
Youting Sun, Ulisses M. Braga-Neto, Edward R. Dougherty
2011 — conf
Multiple reaction monitoring: Modeling and systematic analysis.
GENSiPS
Esmaeil Atashpaz-Gargari, Ulisses M. Braga-Neto, Edward R. Dougherty
2011 — conf
Optimal state estimation for Boolean dynamical systems.
ACSCC
Ulisses M. Braga-Neto
2011 J jnl
Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.
BMC Bioinform.
Jonathan D. Wren, Doris M. Kupfer, Edward J. Perkins, Susan Bridges, Stephen Winters-Hilt, Mikhail G. Dozmorov, Ulisses M. Braga-Neto
2011 — conf
Relationship between the accuracy of classifier error estimation and distribution complexity.
GENSiPS
Esmaeil Atashpaz-Gargari, Chao Sima, Ulisses M. Braga-Neto, Edward R. Dougherty
2011 — conf
Sample-based estimators for the instrinsically multivariate prediction score.
GENSiPS
Ting Chen, Ulisses M. Braga-Neto
2011 — conf
Session TA1b: Biosignal estimation and classification.
ACSCC
Ulisses M. Braga-Neto, Antonia Papandreou-Suppappola
2011 — conf
Studying the possibility of peaking phenomenon in linear support vector machines with non-separable data.
GENSiPS
Sardar Afra, Ulisses M. Braga-Neto
2010 — conf
Approximate expressions for the variances of non-randomized error estimators and CoD estimators for the discrete histogram rule.
GENSiPS
Ting Chen, Ulisses M. Braga-Neto
2010 J jnl
BPDA - A Bayesian peptide detection algorithm for mass spectrometry.
BMC Bioinform.
Youting Sun, Jianqiu Zhang, Ulisses M. Braga-Neto, Edward R. Dougherty
2010 J jnl
Exact Performance of CoD Estimators in Discrete Prediction.
EURASIP J. Adv. Signal Process.
Ting Chen, Ulisses M. Braga-Neto
2010 J jnl
Exact correlation between actual and estimated errors in discrete classification.
Pattern Recognit. Lett.
Ulisses M. Braga-Neto, Edward R. Dougherty
2010 J jnl
ISMM 2007 Special Issue.
Image Vis. Comput.
Gerald Jean Francis Banon, Ulisses M. Braga-Neto, Roberto Marcondes Cesar Jr.
2010 J jnl
Joint sampling distribution between actual and estimated classification errors for linear discriminant analysis.
IEEE Trans. Inf. Theory
Amin Zollanvari, Ulisses M. Braga-Neto, Edward R. Dougherty
2010 — conf
RMS bounds and sample size considerations for error estimation in linear discriminant analysis.
GENSiPS
Amin Zollanvari, Ulisses M. Braga-Neto, Edward R. Dougherty
2010 J jnl
Small-Sample Error Estimation for Bagged Classification Rules.
EURASIP J. Adv. Signal Process.
Thang T. Vu, Ulisses M. Braga-Neto
2009 J jnl
Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes.
BMC Bioinform.
Amin Zollanvari, Mary Jane Cunningham, Ulisses M. Braga-Neto, Edward R. Dougherty
2009 J jnl
Applications of Signal Processing Techniques to Bioinformatics, Genomics, and Proteomics.
EURASIP J. Bioinform. Syst. Biol.
Erchin Serpedin, Javier Garcia-Frías, Yufei Huang, Ulisses M. Braga-Neto
2009 — conf
Bagging degrades the performance of linear discriminant classifiers.
GENSiPS
Thang T. Vu, Ulisses M. Braga-Neto, Edward R. Dougherty
2009 — conf
Bolstered error estimator with feature selection.
GENSiPS
Chao Sima, Thang T. Vu, Ulisses M. Braga-Neto, Edward R. Dougherty
2009 J jnl
Impact of Missing Value Imputation on Classification for DNA Microarray Gene Expression Data - A Model-Based Study.
EURASIP J. Bioinform. Syst. Biol.
Youting Sun, Ulisses M. Braga-Neto, Edward R. Dougherty
2009 J jnl
Is Bagging Effective in the Classification of Small-Sample Genomic and Proteomic Data?
EURASIP J. Bioinform. Syst. Biol.
Thang T. Vu, Ulisses M. Braga-Neto
2009 J jnl
On the sampling distribution of resubstitution and leave-one-out error estimators for linear classifiers.
Pattern Recognit.
Amin Zollanvari, Ulisses M. Braga-Neto, Edward R. Dougherty
2009 J jnl
Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.
BMC Bioinform.
Jonathan D. Wren, Yuriy Gusev, Raphael D. Isokpehi, Daniel Berleant, Ulisses M. Braga-Neto, Dawn Wilkins, Susan Bridges
2009 — conf
Sample size calculation from specified RMS of the resubstitution error for linear classifiers.
GENSiPS
Amin Zollanvari, Ulisses M. Braga-Neto, Edward R. Dougherty
2008 J jnl
Intrinsically Multivariate Predictive Genes.
IEEE J. Sel. Top. Signal Process.
David Correa Martins Jr., Ulisses M. Braga-Neto, Ronaldo Fumio Hashimoto, Michael L. Bittner, Edward R. Dougherty
2007 J jnl
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 Process. Mag.
Ulisses M. Braga-Neto
2006 J jnl
From Functional Genomics to Functional Immunomics: New Challenges, Old Problems, Big Rewards.
PLoS Comput. Biol.
Ulisses M. Braga-Neto, Ernesto T. A. Marques Jr.
2005 J jnl
Constructing multiscale connectivities.
Comput. Vis. Image Underst.
Ulisses M. Braga-Neto, John Goutsias
2005 J jnl
Exact performance of error estimators for discrete classifiers.
Pattern Recognit.
Ulisses M. Braga-Neto, Edward R. Dougherty
2005 C conf
Grayscale Level Multiconnectivity.
ISMM
Ulisses M. Braga-Neto
2005 J jnl
Impact of error estimation on feature selection.
Pattern Recognit.
Chao Sima, Sanju Attoor, Ulisses M. Braga-Neto, James Lowey, Edward Suh, Edward R. Dougherty
2005 J jnl
Multiscale Connected Operators.
J. Math. Imaging Vis.
Ulisses M. Braga-Neto
2005 J jnl
Object-Based Image Analysis Using Multiscale Connectivity.
IEEE Trans. Pattern Anal. Mach. Intell.
Ulisses M. Braga-Neto, John Goutsias
2005 J jnl
Superior feature-set ranking for small samples using bolstered error estimation.
Bioinform.
Chao Sima, Ulisses M. Braga-Neto, Edward R. Dougherty
2004 J jnl
Automatic target detection and tracking in forward-looking infrared image sequences using morphological connected operators.
J. Electronic Imaging
Ulisses M. Braga-Neto, Manish Choudhary, John Goutsias
2004 J jnl
Bolstered error estimation.
Pattern Recognit.
Ulisses M. Braga-Neto, Edward R. Dougherty
2004 J jnl
Grayscale level connectivity: theory and applications.
IEEE Trans. Image Process.
Ulisses M. Braga-Neto, John K. Goutsias
2004 J jnl
Is cross-validation better than resubstitution for ranking genes?
Bioinform.
Ulisses M. Braga-Neto, Ronaldo Fumio Hashimoto, Edward R. Dougherty, Danh V. Nguyen, Raymond J. Carroll
2004 J jnl
Is cross-validation valid for small-sample microarray classification?
Bioinform.
Ulisses M. Braga-Neto, Edward R. Dougherty
2004 J jnl
Supremal Multiscale Signal Analysis.
SIAM J. Math. Anal.
Ulisses M. Braga-Neto, John Goutsias
2003 J jnl
A Theoretical Tour of Connectivity in Image Processing and Analysis.
J. Math. Imaging Vis.
Ulisses M. Braga-Neto, John K. Goutsias
2003 J jnl
A multiscale approach to connectivity.
Comput. Vis. Image Underst.
Ulisses M. Braga-Neto, John K. Goutsias
2002 J jnl
Connectivity on Complete Lattices: New Results.
Comput. Vis. Image Underst.
Ulisses M. Braga-Neto, John K. Goutsias
2002 J jnl
Topology Correction in Brain Cortex Segmentation Using a Multi-Scale, Graph-Based Algorithm.
IEEE Trans. Medical Imaging
Xiao Han, Chenyang Xu, Ulisses M. Braga-Neto, Jerry L. Prince
2001 — conf
Graph-Based Topology Correction for Brain Cortex Segmentation.
IPMI
Xiao Han, Chenyang Xu, Ulisses M. Braga-Neto, Jerry L. Prince
2000 C conf
Multiresolution Connectivity: An Axiomatic Approach.
ISMM
Ulisses M. Braga-Neto, John Goutsias