Edward R. Dougherty

Publication Activity (10 Years)

Years Active: 1988-2024
Publications (10 Years): 73

Top Venues

IEEE Trans. Signal Process.

IEEE ACM Trans. Comput. Biol. Bioinform.

CoRR

EURASIP J. Bioinform. Syst. Biol.

Publications

Xihaier Luo, Seyednami Niyakan, Patrick R. Johnstone, Sean McCorkle, Gilchan Park, Vanessa López-Marrero, Shinjae Yoo, Edward R. Dougherty, Xiaoning Qian, Francis J. Alexander, Shantenu Jha, Byung-Jun Yoon
Pathway-based analyses of gene expression profiles at low doses of ionizing radiation. Frontiers Bioinform. 4 (2024)
Shahin Boluki, Siamak Zamani Dadaneh, Edward R. Dougherty, Xiaoning Qian
Bayesian Proper Orthogonal Decomposition for Learnable Reduced-Order Models With Uncertainty Quantification. IEEE Trans. Artif. Intell. 5 (3) (2024)
Samira Reihanian, Edward R. Dougherty, Amin Zollanvari
Optimal Bayesian Regression With Vector Autoregressive Data Dependency. IEEE Trans. Signal Process. 72 (2024)
Xihaier Luo, Sean McCorkle, Gilchan Park, Vanessa López-Marrero, Shinjae Yoo, Edward R. Dougherty, Xiaoning Qian, Francis J. Alexander, Byung-Jun Yoon
Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response. CoRR (2023)
Puhua Niu, Maria J. Soto, Shuai Huang, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian Blaby, Xiaoning Qian
Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction. J. Comput. Biol. 30 (7) (2023)
Hyun-Myung Woo, Xiaoning Qian, Li Tan, Shantenu Jha, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
Optimal decision-making in high-throughput virtual screening pipelines. Patterns 4 (11) (2023)
Xiaoning Qian, Byung-Jun Yoon, Raymundo Arróyave, Xiaofeng Qian, Edward R. Dougherty
Knowledge-driven learning, optimization, and experimental design under uncertainty for materials discovery. Patterns 4 (11) (2023)
Xihaier Luo, Sean McCorkle, Gilchan Park, Vanessa López-Marrero, Shinjae Yoo, Edward R. Dougherty, Xiaoning Qian, Francis J. Alexander, Byung-Jun Yoon
Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response. BIBM (2022)
Omar Maddouri, Xiaoning Qian, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
Robust importance sampling for error estimation in the context of optimal Bayesian transfer learning. Patterns 3 (3) (2022)
Eunji Kim, Ivan Ivanov, Edward R. Dougherty
Network Classification Based on Reducibility With Respect to the Stability of Canalizing Power of Genes in a Gene Regulatory Network - A Boolean Network Modeling Perspective. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
Mingzhou Fan, Byung-Jun Yoon, Francis J. Alexander, Edward R. Dougherty, Xiaoning Qian
Adaptive Group Testing with Mismatched Models. ICASSP (2022)
Shahin Boluki, Xiaoning Qian, Edward R. Dougherty
Optimal Bayesian supervised domain adaptation for RNA sequencing data. Bioinform. 37 (19) (2021)
Omar Maddouri, Xiaoning Qian, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
Robust Importance Sampling for Error Estimation in the Context of Optimal Bayesian Transfer Learning. CoRR (2021)
Guang Zhao, Edward R. Dougherty, Byung-Jun Yoon, Francis J. Alexander, Xiaoning Qian
Efficient Active Learning for Gaussian Process Classification by Error Reduction. NeurIPS (2021)
Guang Zhao, Edward R. Dougherty, Byung-Jun Yoon, Francis J. Alexander, Xiaoning Qian
Bayesian Active Learning by Soft Mean Objective Cost of Uncertainty. AISTATS (2021)
Byung-Jun Yoon, Xiaoning Qian, Edward R. Dougherty
Quantifying the Multi-Objective Cost of Uncertainty. IEEE Access 9 (2021)
Hyun-Myung Woo, Xiaoning Qian, Li Tan, Shantenu Jha, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
Optimal Decision Making in High-Throughput Virtual Screening Pipelines. CoRR (2021)
Alireza Karbalayghareh, Xiaoning Qian, Edward R. Dougherty
Optimal Bayesian Transfer Learning for Count Data. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (2) (2021)
Guang Zhao, Edward R. Dougherty, Byung-Jun Yoon, Francis J. Alexander, Xiaoning Qian
Uncertainty-aware Active Learning for Optimal Bayesian Classifier. ICLR (2021)
Byung-Jun Yoon, Xiaoning Qian, Edward R. Dougherty
Quantifying the multi-objective cost of uncertainty. CoRR (2020)
Guang Zhao, Xiaoning Qian, Byung-Jun Yoon, Francis J. Alexander, Edward R. Dougherty
Model-Based Robust Filtering and Experimental Design for Stochastic Differential Equation Systems. IEEE Trans. Signal Process. 68 (2020)
Mahdi Imani, Edward R. Dougherty, Ulisses M. Braga-Neto
Boolean Kalman filter and smoother under model uncertainty. Autom. 111 (2020)
Ulisses M. Braga-Neto, Edward R. Dougherty
Machine Learning Requires Probability and Statistics [Perspectives]. IEEE Signal Process. Mag. 37 (4) (2020)
Shahin Boluki, Siamak Zamani Dadaneh, Xiaoning Qian, Edward R. Dougherty
Optimal clustering with missing values. BMC Bioinform. (12) (2019)
Shahin Boluki, Xiaoning Qian, Edward R. Dougherty
Experimental Design via Generalized Mean Objective Cost of Uncertainty. IEEE Access 7 (2019)
Amin Zollanvari, Edward R. Dougherty
Optimal Bayesian Classification With Vector Autoregressive Data Dependency. IEEE Trans. Signal Process. 67 (12) (2019)
Shahin Boluki, Mohammad Shahrokh Esfahani, Xiaoning Qian, Edward R. Dougherty
Constructing Pathway-Based Priors within a Gaussian Mixture Model for Bayesian Regression and Classification. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (2) (2019)
Alireza Karbalayghareh, Ulisses M. Braga-Neto, Edward R. Dougherty
Classification of Single-Cell Gene Expression Trajectories from Incomplete and Noisy Data. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (1) (2019)
Eunji Kim, Ivan Ivanov, Edward R. Dougherty
Quantifying the notions of canalizing and master genes in a gene regulatory network - a Boolean network modeling perspective. Bioinform. 35 (4) (2019)
Shahin Boluki, Siamak Zamani Dadaneh, Xiaoning Qian, Edward R. Dougherty
Optimal Clustering with Missing Values. CoRR (2019)
Esmaeil Atashpaz-Gargari, Marcelo da Silva Reis, Ulisses M. Braga-Neto, Junior Barrera, Edward R. Dougherty
A fast Branch-and-Bound algorithm for U-curve feature selection. Pattern Recognit. 73 (2018)
Jason M. Knight, Ivan Ivanov, Karen Triff, Robert S. Chapkin, Edward R. Dougherty
Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (2) (2018)
Ehsan Hajiramezanali, Mahdi Imani, Ulisses M. Braga-Neto, Xiaoning Qian, Edward R. Dougherty
Scalable Optimal Bayesian Classification of Single-Cell Trajectories under Regulatory Model Uncertainty. BCB (2018)
Shahin Boluki, Siamak Zamani Dadaneh, Xiaoning Qian, Edward R. Dougherty
Optimal Clustering with Missing Values. BCB (2018)
Mahdi Imani, Roozbeh Dehghannasiri, Ulisses M. Braga-Neto, Edward R. Dougherty
Sequential Experimental Design for Optimal Structural Intervention in Gene Regulatory Networks Based on the Mean Objective Cost of Uncertainty. CoRR (2018)
Wasiu Opeyemi Oduola, Xiangfang Li, Chang Duan, Lijun Qian, Edward R. Dougherty
Sequential Therapeutic Response Modeling for Tumor Treatment Using Computational Hybrid Control Systems Approach. IEEE Trans. Biomed. Eng. 65 (4) (2018)
Siamak Zamani Dadaneh, Edward R. Dougherty, Xiaoning Qian
Optimal Bayesian Classification With Missing Values. IEEE Trans. Signal Process. 66 (16) (2018)
Roozbeh Dehghannasiri, Mohammad Shahrokh Esfahani, Xiaoning Qian, Edward R. Dougherty
Optimal Bayesian Kalman Filtering With Prior Update. IEEE Trans. Signal Process. 66 (8) (2018)
Alireza Karbalayghareh, Xiaoning Qian, Edward R. Dougherty
Optimal Bayesian Transfer Regression. IEEE Signal Process. Lett. 25 (11) (2018)
Roozbeh Dehghannasiri, Xiaoning Qian, Edward R. Dougherty
A Bayesian robust Kalman smoothing framework for state-space models with uncertain noise statistics. EURASIP J. Adv. Signal Process. 2018 (2018)
Alireza Karbalayghareh, Xiaoning Qian, Edward R. Dougherty
Optimal Bayesian Transfer Learning. CoRR (2018)
Roozbeh Dehghannasiri, Xiaoning Qian, Edward R. Dougherty
Intrinsically Bayesian robust Karhunen-Loève compression. Signal Process. 144 (2018)
Roozbeh Dehghannasiri, Xiaoning Qian, Edward R. Dougherty
Robust Smoothing for State-Space Models with Unknown Noise Statistics. ACSSC (2018)
Lori A. Dalton, Marco E. Benalcázar, Edward R. Dougherty
Optimal Clustering under Uncertainty. CoRR (2018)
Alireza Karbalayghareh, Xiaoning Qian, Edward R. Dougherty
Optimal Bayesian Transfer Learning. IEEE Trans. Signal Process. 66 (14) (2018)
Daniel N. Mohsenizadeh, Roozbeh Dehghannasiri, Edward R. Dougherty
Optimal Objective-Based Experimental Design for Uncertain Dynamical Gene Networks with Experimental Error. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (1) (2018)
Alireza Karbalayghareh, Ulisses M. Braga-Neto, Edward R. Dougherty
Classification of Gaussian trajectories with missing data in Boolean gene regulatory networks. ICASSP (2017)
Shuilian Xie, Mahdi Imani, Edward R. Dougherty, Ulisses M. Braga-Neto
Nonstationary linear discriminant analysis. ACSSC (2017)
Roozbeh Dehghannasiri, Xiaoning Qian, Edward R. Dougherty
Optimal experimental design in the context of canonical expansions. IET Signal Process. 11 (8) (2017)
Shahin Boluki, Mohammad Shahrokh Esfahani, Xiaoning Qian, Edward R. Dougherty
Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors. BMC Bioinform. 18 (14) (2017)
Xiangfang Li, Oluwaseyi Omotere, Lijun Qian, Edward R. Dougherty
Review of stochastic hybrid systems with applications in biological systems modeling and analysis. EURASIP J. Bioinform. Syst. Biol. 2017 (2017)
Roozbeh Dehghannasiri, Xiaoning Qian, Edward R. Dougherty
An objective-based experimental design framework for signal processing in the context of canonical expansions. ACSSC (2017)
Alireza Karbalayghareh, Ulisses M. Braga-Neto, Edward R. Dougherty
Intrinsically Bayesian Robust Classifier for Single-Cell Gene Expression Time Series in Gene Regulatory Networks. BCB (2017)
Roozbeh Dehghannasiri, Mohammad Shahrokh Esfahani, Xiaoning Qian, Edward R. Dougherty
Bayesian Kalman filtering in the presence of unknown noise statistics using factor graphs. ACSSC (2017)
Artyom M. Grigoryan, Edward R. Dougherty, Sos S. Agaian
Optimal Wiener and homomorphic filtration: Review. Signal Process. 121 (2016)
Roozbeh Dehghannasiri, Xiaoning Qian, Edward R. Dougherty
Optimal experimental design in canonical expansions with applications to signal compression. GlobalSIP (2016)
Amin Zollanvari, Edward R. Dougherty
Incorporating prior knowledge induced from stochastic differential equations in the classification of stochastic observations. EURASIP J. Bioinform. Syst. Biol. 2016 (2016)
Xiaoning Qian, Edward R. Dougherty
Bayesian Regression With Network Prior: Optimal Bayesian Filtering Perspective. IEEE Trans. Signal Process. 64 (23) (2016)
Daniel N. Mohsenizadeh, Roozbeh Dehghannasiri, Edward R. Dougherty
Optimal dynamics uncertainty reduction in gene networks in the presence of experimental error. BHI (2016)
Eunji Kim, Ivan Ivanov, Jianping Hua, Robert S. Chapkin, Edward R. Dougherty
Model-based study of the Effectiveness of Reporting Lists of Small Feature Sets using RNA-Seq Data. BCB (2016)
Wasiu Opeyemi Oduola, Xiangfang Li, Chang Duan, Lijun Qian, Fen Wu, Edward R. Dougherty
Analysis and control of genetic regulatory systems with switched drug inputs. BHI (2016)
Roozbeh Dehghannasiri, Mohammad Shahrokh Esfahani, Edward R. Dougherty
Inference of Nonlinear ODE-Based Gene Regulatory Networks via Intrinsically Bayesian Robust Kalman Filtering. BCB (2016)
Roozbeh Dehghannasiri, Mohammad Shahrokh Esfahani, Edward R. Dougherty
A Bayesian framework for robust Kalman filtering under uncertain noise statistics. ACSSC (2016)
Lori A. Dalton, Marco Benalcázar, Marcel Brun, Edward R. Dougherty
Analytic Representation of Bayes Labeling and Bayes Clustering Operators for Random Labeled Point Processes. IEEE Trans. Signal Process. 63 (6) (2015)
Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (4) (2015)
Ariana Broumand, Mohammad Shahrokh Esfahani, Byung-Jun Yoon, Edward R. Dougherty
Discrete optimal Bayesian classification with error-conditioned sequential sampling. Pattern Recognit. 48 (11) (2015)
Edward R. Dougherty, Lori A. Dalton, Francis J. Alexander
Small data is the problem. ACSSC (2015)
Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC Bioinform. 16 (2015)
Daniel N. Mohsenizadeh, Jianping Hua, Michael L. Bittner, Edward R. Dougherty
Dynamical modeling of uncertain interaction-based genomic networks. BMC Bioinform. 16 (S13) (2015)
Mohammad Shahrokh Esfahani, Edward R. Dougherty
An Optimization-Based Framework for the Transformation of Incomplete Biological Knowledge into a Probabilistic Structure and Its Application to the Utilization of Gene/Protein Signaling Pathways in Discrete Phenotype Classification. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (6) (2015)
Daniel N. Mohsenizadeh, Roozbeh Dehghannasiri, Edward R. Dougherty
An experimental design to reduce dynamics uncertainty in genomic networks. BCB (2015)
Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC Bioinform. 16 (S13) (2015)
Amin Zollanvari, Edward R. Dougherty
Generalized Consistent Error Estimator of Linear Discriminant Analysis. IEEE Trans. Signal Process. 63 (11) (2015)
Hongjia Ouyang, Jie Fang, Liangzhong Shen, Edward R. Dougherty, Wenbin Liu
Learning restricted Boolean network model by time-series data. EURASIP J. Bioinform. Syst. Biol. 2014 (2014)
Thang T. Vu, Chao Sima, Ulisses M. Braga-Neto, Edward R. Dougherty
Unbiased bootstrap error estimation for linear discriminant analysis. EURASIP J. Bioinform. Syst. Biol. 2014 (2014)
Mohammadmahdi R. Yousefi, Edward R. Dougherty
A comparison study of optimal and suboptimal intervention policies for gene regulatory networks in the presence of uncertainty. EURASIP J. Bioinform. Syst. Biol. 2014 (2014)
Amin Zollanvari, Edward R. Dougherty
Moments and root-mean-square error of the Bayesian MMSE estimator of classification error in the Gaussian model. Pattern Recognit. 47 (6) (2014)
Mohammad Shahrokh Esfahani, Edward R. Dougherty
Effect of separate sampling on classification accuracy. Bioinform. 30 (2) (2014)
Xiangfang Lindsey Li, Sunday Ogedengbe, Lijun Qian, Edward R. Dougherty
Sensitivity analysis for drug effect study: An NF-κB pathway example. GlobalSIP (2014)
Lori A. Dalton, Edward R. Dougherty
Intrinsically Optimal Bayesian Robust Filtering. IEEE Trans. Signal Process. 62 (3) (2014)
Jason M. Knight, Ivan Ivanov, Edward R. Dougherty
MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification. BMC Bioinform. 15 (2014)
Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
Computationally efficient experimental design strategy for reducing gene network uncertainty. GlobalSIP (2014)
Jie Fang, Hongjia Ouyang, Liangzhong Shen, Edward R. Dougherty, Wenbin Liu
Using the minimum description length principle to reduce the rate of false positives of best-fit algorithms. EURASIP J. Bioinform. Syst. Biol. 2014 (2014)
Fang Jin, Rupinder Paul Khandpur, Nathan Self, Edward R. Dougherty, Sheng Guo, Feng Chen, B. Aditya Prakash, Naren Ramakrishnan
Modeling mass protest adoption in social network communities using geometric brownian motion. KDD (2014)
Fang Jin, Wei Wang, Liang Zhao, Edward R. Dougherty, Yang Cao, Chang-Tien Lu, Naren Ramakrishnan
Misinformation Propagation in the Age of Twitter. Computer 47 (12) (2014)
Esmaeil Atashpaz-Gargari, Ulisses M. Braga-Neto, Edward R. Dougherty
Modeling and systematic analysis of biomarker validation using selected reaction monitoring. EURASIP J. Bioinform. Syst. Biol. 2014 (2014)
Ulisses M. Braga-Neto, Amin Zollanvari, Edward R. Dougherty
Cross-validation under separate sampling: strong bias and how to correct it. Bioinform. 30 (23) (2014)
Mohammad Shahrokh Esfahani, Edward R. Dougherty
Incorporation of Biological PathwayKnowledge in the Construction of Priorsfor Optimal Bayesian Classification. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (1) (2014)
Mohammad Shahrokh Esfahani, Jason M. Knight, Amin Zollanvari, Byung-Jun Yoon, Edward R. Dougherty
Classifier design given an uncertainty class of feature distributions via regularized maximum likelihood and the incorporation of biological pathway knowledge in steady-state phenotype classification. Pattern Recognit. 46 (10) (2013)
Mohammad Shahrokh Esfahani, Edward R. Dougherty
Effect of separate sampling on classification and the minimax criterion. GENSiPS (2013)
Fang-Han Hsu, Edward R. Dougherty, Yidong Chen, Erchin Serpedin
Estimating Conditional Probabilities for the Detection of Unfavorable Copy Number Alterations in a Targeted Therapy. IEEE Trans. Biomed. Eng. 60 (10) (2013)
Edward R. Dougherty
On the impoverishment of scientific education. EURASIP J. Bioinform. Syst. Biol. 2013 (2013)
Mohammadmahdi R. Yousefi, Aniruddha Datta, Edward R. Dougherty
Optimal Intervention in Markovian Gene Regulatory Networks With Random-Length Therapeutic Response to Antitumor Drug. IEEE Trans. Biomed. Eng. 60 (12) (2013)
Noushin Ghaffari, Mohammadmahdi R. Yousefi, Charles D. Johnson, Ivan Ivanov, Edward R. Dougherty
Modeling the Next Generation Sequencing sample processing pipeline for the purposes of classification. BMC Bioinform. 14 (2013)
Mohammadmahdi R. Yousefi, Edward R. Dougherty
Bayesian optimal control of Markovian genetic regulatory networks. ACSSC (2013)
Fang Jin, Edward R. Dougherty, Parang Saraf, Yang Cao, Naren Ramakrishnan
Epidemiological modeling of news and rumors on Twitter. SNAKDD (2013)
Xiaoning Qian, Edward R. Dougherty
Phenotypically constrained Boolean network inference with prescribed steady states. GENSiPS (2013)
Xiangfang Li, Lijun Qian, Michael L. Bittner, Edward R. Dougherty
Drug effect study on proliferation and survival pathways on cell line-based platform: A stochastic hybrid systems approach. GENSiPS (2013)
Edward R. Dougherty, Lori A. Dalton
Scientific knowledge is possible with small-sample classification. EURASIP J. Bioinform. Syst. Biol. 2013 (2013)
Lijun Qian, Xiangfang Li, Edward R. Dougherty
Robust identification of molecularly targeted drug effect coefficient using H∞ filter. GlobalSIP (2013)

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Publication Activity (10 Years)

Top Topics

Top Venues

Edward R. Dougherty