Optimally adapted indexing trees for medical image databases. - Xiaoning Qian; Hemant D. Tagare (ISBI, 2002)

Shape based retrieval in NHANES II. - Hemant D. Tagare; Xiaoning Qian; Robert K. Fulbright; L. Rodney Long; Sameer K. Antani (ACM Multimedia, 2004)

Optimal Embedding for Shape Indexing in Medical Image Databases. - Xiaoning Qian; Hemant D. Tagare (MICCAI (2), 2005)

Segmentation of Rat Cardiac Ultrasound Images with Large Dropout Regions. - Xiaoning Qian; Hemant D. Tagare; Zhong Tao 001 (CVPR Workshops, 2006)

Overcoming dropout while segmenting cardiac ultrasound images. - Xiaoning Qian; Hemant D. Tagare (ISBI, 2006)

Detection of Complex Vascular Structures using Polar Neighborhood Intensity Profile. - Xiaoning Qian; Matthew P. Brennan; Donald P. Dione; Lawrence W. Dobrucki (ICCV, 2007)

Effect of Function Perturbation on the Steady-State Distribution of Genetic Regulatory Networks: Optimal Structural Intervention. - Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2008)

Effective visualization of complex vascular structures using a non-parametric vessel detection method. - Alark Joshi; Xiaoning Qian; Donald P. Dione; Ketan R. Bulsara; Christopher K. Breuer; Albert J. Sinusas; Xenophon Papademetris (IEEE Trans. Vis. Comput. Graph., 2008)

Control-compatible state reduction for Boolean networks. - Xiaoning Qian; Edward R. Dougherty (GENSiPS, 2009)

Intervention in gene regulatory networks via greedy control policies based on long-run behavior. - Xiaoning Qian; Ivan Ivanov 001; Noushin Ghaffari; Edward R. Dougherty (BMC Syst. Biol., 2009)

Querying Pathways in Protein Interaction Networks Based on Hidden Markov Models. - Xiaoning Qian; Sing-Hoi Sze; Byung-Jun Yoon (J. Comput. Biol., 2009)

A non-parametric vessel detection method for complex vascular structures. - Xiaoning Qian; Matthew P. Brennan; Donald P. Dione; Wawrzyniec L. Dobrucki; Marcel Jackowski; Christopher K. Breuer; Albert J. Sinusas; Xenophon Papademetris (Medical Image Anal., 2009)

A comparative study on sensitivities of Boolean networks. - Xiaoning Qian; Edward R. Dougherty (GENSiPS, 2010)

Shape matching based on graph alignment using hidden Markov models. - Xiaoning Qian; Byung-Jun Yoon (ICASSP, 2010)

Serial nonrigid vascular registration using weighted normalized mutual information. - Jung W. Suh; Dustin Scheinost; Xiaoning Qian; Albert J. Sinusas; Christopher K. Breuer; Xenophon Papademetris (ISBI, 2010)

A CoD-based reduction algorithm for designing stationary control policies on Boolean networks. - Noushin Ghaffari; Ivan Ivanov 001; Xiaoning Qian; Edward R. Dougherty (Bioinform., 2010)

State reduction for network intervention in probabilistic Boolean networks. - Xiaoning Qian; Noushin Ghaffari; Ivan Ivanov 001; Edward R. Dougherty (Bioinform., 2010)

Adapting indexing trees to data distribution in feature spaces. - Xiaoning Qian; Hemant D. Tagare (Comput. Vis. Image Underst., 2010)

Stationary and structural control in gene regulatory networks: basic concepts. - Edward R. Dougherty; Ranadip Pal; Xiaoning Qian; Michael L. Bittner; Aniruddha Datta (Int. J. Syst. Sci., 2010)

Optimal embedding for shape indexing in medical image databases. - Xiaoning Qian; Hemant D. Tagare; Robert K. Fulbright; L. Rodney Long; Sameer K. Antani (Medical Image Anal., 2010)

Selection policy-induced reduction mappings for Boolean networks. - Ivan Ivanov 001; Plamen Simeonov; Noushin Ghaffari; Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2010)

Session TA8a1: Signal processing methods for representation, analysis, and control of biological systems. - Byung-Jun Yoon; Xiaoning Qian (ACSCC, 2011)

Uncertainty-based essentiality in gene regulatory networks. - Xiaoning Qian; Byung-Jun Yoon; Edward R. Dougherty (GENSiPS, 2011)

Contour-based hidden Markov model to segment 2D ultrasound images. - Xiaoning Qian; Byung-Jun Yoon (ICASSP, 2011)

A CoD-based stationary control policy for intervening in large gene regulatory networks. - Noushin Ghaffari; Ivan Ivanov 001; Xiaoning Qian; Edward R. Dougherty (BMC Bioinform., 2011)

Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores. - Xiaoning Qian; Sayed Mohammad Ebrahim Sahraeian; Byung-Jun Yoon (BMC Bioinform., 2011)

Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. - Xiaoning Qian; Byung-Jun Yoon (BMC Bioinform., 2011)

Supervised logistic principal component analysis for pathway based genome-wide association studies. - Meng Lu; Jianhua Z. Huang; Xiaoning Qian (BCB, 2012)

Functional module identification by block modeling using simulated annealing with path relinking. - Yijie Wang 003; Xiaoning Qian (BCB, 2012)

A new phenotypically constrained control policy in boolean networks based on basins of attraction. - Xiaoning Qian (GENSiPS, 2012)

Network-based methods to identify highly discriminating subsets of biomarkers. - Seyed Javad Sajjadi; Xiaoning Qian; Bo Zeng 001 (GENSiPS, 2012)

Structural intervention of gene regulatory networks by general rank-k matrix perturbation. - Xiaoning Qian; Byung-Jun Yoon; Edward R. Dougherty (ICASSP, 2012)

How Influential Are You: Detecting Influential Bloggers in a Blogging Community. - Md. Imrul Kayes; Xiaoning Qian; John Skvoretz; Adriana Iamnitchi (SocInfo, 2012)

Comparative Analysis of Biological Networks: Hidden Markov model and Markov chain-based approach. - Byung-Jun Yoon; Xiaoning Qian; Sayed Mohammad Ebrahim Sahraeian (IEEE Signal Process. Mag., 2012)

Intervention in Gene Regulatory Networks via Phenotypically Constrained Control Policies Based on Long-Run Behavior. - Xiaoning Qian; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Blockmodel module identification in protein interaction networks through Markov random walk. - Yijie Wang 003; Xiaoning Qian (EUSIPCO, 2013)

Phenotypically constrained Boolean network inference with prescribed steady states. - Xiaoning Qian; Edward R. Dougherty (GENSiPS, 2013)

Identifying overlapping functional modules in biological networks by Markov random walk. - Yijie Wang 003; Xiaoning Qian (GlobalSIP, 2013)

Functional analysis of grasping motion. - Wei Dai; Yu Sun 004; Xiaoning Qian (IROS, 2013)

Simultaneous Tracking, 3D Reconstruction and Deforming Point Detection for Stereoscope Guided Surgery. - Bingxiong Lin; Adrian S. Johnson; Xiaoning Qian; Jaime Sánchez 003; Yu Sun 004 (AE-CAI, 2013)

Thin plate spline feature point matching for organ surfaces in minimally invasive surgery imaging. - Bingxiong Lin; Yu Sun 004; Xiaoning Qian (Image-Guided Procedures, 2013)

Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints. - Shaogang Ren; Bo Zeng 001; Xiaoning Qian (BMC Bioinform., 2013)

A novel subgradient-based optimization algorithm for blockmodel functional module identification. - Yijie Wang 003; Xiaoning Qian (BMC Bioinform., 2013)

Feature ranking based on synergy networks to identify prognostic markers in DPT-1. - Amin Ahmadi Adl; Xiaoning Qian; Ping Xu; Kendra Vehik; Jeffrey P. Krischer (EURASIP J. Bioinform. Syst. Biol., 2013)

Dense Surface Reconstruction With Shadows in MIS. - Bingxiong Lin; Yu Sun 004; Xiaoning Qian (IEEE Trans. Biomed. Eng., 2013)

Quantifying the Objective Cost of Uncertainty in Complex Dynamical Systems. - Byung-Jun Yoon; Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2013)

Network-regularized bi-clique finding for tumor stratification. - Amin Ahmadi Adl; Xiaoning Qian (BCB, 2014)

Biological network clustering by robust NMF. - Yijie Wang 003; Xiaoning Qian (BCB, 2014)

Stochastic coordinate descent Frank-Wolfe algorithm for large-scale biological network alignment. - Yijie Wang 003; Xiaoning Qian (GlobalSIP, 2014)

Structured sparse PCA to identify miRNA co-regulatory modules. - Shaogang Ren; Xiaoning Qian (ICASSP, 2014)

Joint clustering of protein interaction networks by block modeling. - Yijie Wang 003; Xiaoning Qian (ICASSP, 2014)

Vesselness based feature extraction for endoscopic image analysis. - Bingxiong Lin; Yu Sun 004; Jaime Sánchez 003; Xiaoning Qian (ISBI, 2014)

Functional module identification in protein interaction networks by interaction patterns. - Yijie Wang 003; Xiaoning Qian (Bioinform., 2014)

Supervised categorical principal component analysis for genome-wide association analyses. - Meng Lu; Hye-Seung Lee; David Hadley; Jianhua Z. Huang; Xiaoning Qian (BMC Genom., 2014)

Joint clustering of protein interaction networks through Markov random walk. - Yijie Wang 003; Xiaoning Qian (BMC Syst. Biol., 2014)

Selected Articles from the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2012). - Yufei Huang 001; Yidong Chen 002; Xiaoning Qian (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Logistic Principal Component Analysis for Rare Variants in Gene-Environment Interaction Analysis. - Meng Lu; Hye-Seung Lee; David Hadley; Jianhua Z. Huang; Xiaoning Qian (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Network-Based Methods to Identify Highly Discriminating Subsets of Biomarkers. - Seyed Javad Sajjadi; Xiaoning Qian; Bo Zeng 001; Amin Ahmadi Adl (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

A Scalable Algorithm for Structured Kernel Feature Selection. - Shaogang Ren; Shuai Huang 001; John A. Onofrey; Xenios Papademetris; Xiaoning Qian (AISTATS, 2015)

A computationally efficient solution strategy for optimal gene knockouts for targeted overproduction. - Meltem Apaydin; Bo Zeng 001; Shaogang Ren; Xiaoning Qian (BCB, 2015)

A computational framework for finding functional modules across multiple biological networks. - Yijie Wang 003; Xiaoning Qian (BCB, 2015)

Domain-Knowledge Driven Cognitive Degradation Modeling for Alzheimer's Disease. - Ying Lin; Kaibo Liu; Eunshin Byon; Xiaoning Qian; Shuai Huang 001 (SDM, 2015)

Tumor stratification by a novel graph-regularized bi-clique finding algorithm. - Amin Ahmadi Adl; Xiaoning Qian (Comput. Biol. Chem., 2015)

Efficient Vessel Feature Detection for Endoscopic Image Analysis. - Bingxiong Lin; Yu Sun 004; Jaime E. Sánchez; Xiaoning Qian (IEEE Trans. Biomed. Eng., 2015)

Inference of gene regulatory networks: validation and uncertainty. - Xiaoning Qian; Byung-Jun Yoon; Edward R. Dougherty (Big Data over Networks, 2016)

A reliable alternative of OptKnock for desirable mutant microbial strains. - Meltem Apaydin; Bo Zeng 001; Xiaoning Qian (BHI, 2016)

Optimal experimental design in canonical expansions with applications to signal compression. - Roozbeh Dehghannasiri; Xiaoning Qian; Edward R. Dougherty (GlobalSIP, 2016)

Pairwise interaction analysis of logistic regression models. - Easton Li Xu; Xiaoning Qian; Tie Liu 002; Shuguang Cui (GlobalSIP, 2016)

Co-segmentation of multiple images through random walk on graphs. - Yijie Wang 003; Byung-Jun Yoon; Xiaoning Qian (ICASSP, 2016)

Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. - Hyundoo Jeong; Xiaoning Qian; Byung-Jun Yoon (BMC Bioinform., 2016)

Bayesian module identification from multiple noisy networks. - Siamak Zamani Dadaneh; Xiaoning Qian (EURASIP J. Bioinform. Syst. Biol., 2016)

Stochastic block coordinate Frank-Wolfe algorithm for large-scale biological network alignment. - Yijie Wang 003; Xiaoning Qian (EURASIP J. Bioinform. Syst. Biol., 2016)

Sparse exponential family Principal Component Analysis. - Meng Lu; Jianhua Z. Huang; Xiaoning Qian (Pattern Recognit., 2016)

Bayesian Regression With Network Prior: Optimal Bayesian Filtering Perspective. - Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2016)

Bayesian Kalman filtering in the presence of unknown noise statistics using factor graphs. - Roozbeh Dehghannasiri; Mohammad Shahrokh Esfahani; Xiaoning Qian; Edward R. Dougherty (ACSSC, 2017)

An objective-based experimental design framework for signal processing in the context of canonical expansions. - Roozbeh Dehghannasiri; Xiaoning Qian; Edward R. Dougherty (ACSSC, 2017)

Feature Selection with Interactions in Logistic Regression Models using Multivariate Synergies for a GWAS Application. - Easton Li Xu; Xiaoning Qian; Qilian Yu; Han Zhang 006; Shuguang Cui (BCB, 2017)

CNB-MAC'17: The Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control. - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci (BCB, 2017)

Image co-saliency detection via locally adaptive saliency map fusion. - Chung-Chi Tsai; Xiaoning Qian; Yen-Yu Lin (ICASSP, 2017)

Noise-tolerant deep learning for histopathological image segmentation. - Weizhi Li; Xiaoning Qian; Jim Jing-Yan Ji (ICIP, 2017)

Segmentation guided local proposal fusion for co-saliency detection. - Chung-Chi Tsai; Xiaoning Qian; Yen-Yu Lin (ICME, 2017)

Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors. - Shahin Boluki; Mohammad Shahrokh Esfahani; Xiaoning Qian; Edward R. Dougherty (BMC Bioinform., 2017)

Effective computational detection of piRNAs using n-gram models and support vector machine. - Chun-Chi Chen; Xiaoning Qian; Byung-Jun Yoon (BMC Bioinform., 2017)

CUFID-query: accurate network querying through random walk based network flow estimation. - Hyundoo Jeong; Xiaoning Qian; Byung-Jun Yoon (BMC Bioinform., 2017)

Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci (BMC Bioinform., 2017)

Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction. - Yijie Wang 003; Xiaoning Qian (BMC Syst. Biol., 2017)

Optimal hybrid sequencing and assembly: Feasibility conditions for accurate genome reconstruction and cost minimization strategy. - Chun-Chi Chen; Noushin Ghaffari; Xiaoning Qian; Byung-Jun Yoon (Comput. Biol. Chem., 2017)

Optimal experimental design in the context of canonical expansions. - Roozbeh Dehghannasiri; Xiaoning Qian; Edward R. Dougherty (IET Signal Process., 2017)

CHI: A contemporaneous health index for degenerative disease monitoring using longitudinal measurements. - Yijun Huang; Qiang Meng; Heather L. Evans; William B. Lober; Yu Cheng 001; Xiaoning Qian; Ji Liu 002; Shuai Huang 001 (J. Biomed. Informatics, 2017)

Prognostics of surgical site infections using dynamic health data. - Chuyang Ke; Yan Jin; Heather L. Evans; Bill Lober; Xiaoning Qian; Ji Liu 002; Shuai Huang 001 (J. Biomed. Informatics, 2017)

Detecting Pairwise Interactive Effects of Continuous Random Variables for Biomarker Identification with Small Sample Size. - Amin Ahmadi Adl; Hye-Seung Lee; Xiaoning Qian (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Detection of Cooperative Interactions in Logistic Regression Models. - Easton Li Xu; Xiaoning Qian; Tie Liu 002; Shuguang Cui (IEEE Trans. Signal Process., 2017)

Robust Smoothing for State-Space Models with Unknown Noise Statistics. - Roozbeh Dehghannasiri; Xiaoning Qian; Edward R. Dougherty (ACSSC, 2018)

Scalable Optimal Bayesian Classification of Single-Cell Trajectories under Regulatory Model Uncertainty. - Ehsan Hajiramezanali; Mahdi Imani; Ulisses M. Braga-Neto; Xiaoning Qian; Edward R. Dougherty (BCB, 2018)

Unsupervised CNN-Based Co-saliency Detection with Graphical Optimization. - Kuang-Jui Hsu; Chung-Chi Tsai; Yen-Yu Lin; Xiaoning Qian; Yung-Yu Chuang (ECCV (5), 2018)

Recursive Structure Similarity: A Novel Algorithm for Graph Clustering. - Yixin Fang; Ruoming Jin; Wei Xiong; Xiaoning Qian; Dejing Dou; Hai Phan 001 (ICTAI, 2018)

Bayesian multi-domain learning for cancer subtype discovery from next-generation sequencing count data. - Ehsan Hajiramezanali; Siamak Zamani Dadaneh; Alireza Karbalayghareh; Mingyuan Zhou; Xiaoning Qian (NeurIPS, 2018)

Covariate-dependent negative binomial factor analysis of RNA sequencing data. - Siamak Zamani Dadaneh; Mingyuan Zhou; Xiaoning Qian (Bioinform., 2018)

Bayesian negative binomial regression for differential expression with confounding factors. - Siamak Zamani Dadaneh; Mingyuan Zhou; Xiaoning Qian (Bioinform., 2018)

Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci; Ranadip Pal (BMC Bioinform., 2018)

Safe Active Feature Selection for Sparse Learning. - Shaogang Ren; Jianhua Z. Huang; Shuai Huang 001; Xiaoning Qian (CoRR, 2018)

Fast Exact Computation of Expected HyperVolume Improvement. - Guang Zhao; Raymundo Arróyave; Xiaoning Qian (CoRR, 2018)

A Bayesian robust Kalman smoothing framework for state-space models with uncertain noise statistics. - Roozbeh Dehghannasiri; Xiaoning Qian; Edward R. Dougherty (EURASIP J. Adv. Signal Process., 2018)

Switching-State Dynamical Modeling of Daily Behavioral Data. - Randy Ardywibowo; Shuai Huang 001; Shupeng Gui; Cao Xiao; Yu Cheng 001; Ji Liu 002; Xiaoning Qian (J. Heal. Informatics Res., 2018)

Safe Feature Screening for Generalized LASSO. - Shaogang Ren; Shuai Huang 001; Jieping Ye; Xiaoning Qian (IEEE Trans. Pattern Anal. Mach. Intell., 2018)

Convex clustering with metric learning. - Xiaopeng Lucia Sui; Li Xu; Xiaoning Qian; Tie Liu 002 (Pattern Recognit., 2018)

Intrinsically Bayesian robust Karhunen-Loève compression. - Roozbeh Dehghannasiri; Xiaoning Qian; Edward R. Dougherty (Signal Process., 2018)

Optimal Bayesian Transfer Regression. - Alireza Karbalayghareh; Xiaoning Qian; Edward R. Dougherty (IEEE Signal Process. Lett., 2018)

A Collaborative Learning Framework for Estimating Many Individualized Regression Models in a Heterogeneous Population. - Ying Lin; Kaibo Liu; Eunshin Byon; Xiaoning Qian; Shan Liu; Shuai Huang 001 (IEEE Trans. Reliab., 2018)

Optimal Bayesian Classification With Missing Values. - Siamak Zamani Dadaneh; Edward R. Dougherty; Xiaoning Qian (IEEE Trans. Signal Process., 2018)

Optimal Bayesian Kalman Filtering With Prior Update. - Roozbeh Dehghannasiri; Mohammad Shahrokh Esfahani; Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2018)

Optimal Bayesian Transfer Learning. - Alireza Karbalayghareh; Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2018)

Adaptive Activity Monitoring with Uncertainty Quantification in Switching Gaussian Process Models. - Randy Ardywibowo; Guang Zhao; Zhangyang Wang; Bobak Mortazavi; Shuai Huang 001; Xiaoning Qian (AISTATS, 2019)

Collaborative Global-Local Networks for Memory-Efficient Segmentation of Ultra-High Resolution Images. - Wuyang Chen 001; Ziyu Jiang; Zhangyang Wang; Kexin Cui; Xiaoning Qian (CVPR, 2019)

Cone-Beam Computed Tomography (CBCT) Segmentation by Adversarial Learning Domain Adaptation. - Xiaoqian Jia; Sicheng Wang 003; Xiao Liang; Anjali Balagopal; Dan Nguyen; Ming Yang 008; Zhangyang Wang; Jim Xiuquan Ji; Xiaoning Qian; Steve B. Jiang (MICCAI (6), 2019)

Variational Graph Recurrent Neural Networks. - Ehsan Hajiramezanali; Arman Hasanzadeh; Krishna R. Narayanan; Nick Duffield; Mingyuan Zhou; Xiaoning Qian (NeurIPS, 2019)

Semi-Implicit Graph Variational Auto-Encoders. - Arman Hasanzadeh; Ehsan Hajiramezanali; Krishna R. Narayanan; Nick Duffield; Mingyuan Zhou; Xiaoning Qian (NeurIPS, 2019)

Experimental Design via Generalized Mean Objective Cost of Uncertainty. - Shahin Boluki; Xiaoning Qian; Edward R. Dougherty (IEEE Access, 2019)

TOPAS: network-based structural alignment of RNA sequences. - Chun-Chi Chen; Hyundoo Jeong; Xiaoning Qian; Byung-Jun Yoon (Bioinform., 2019)

RNAdetect: efficient computational detection of novel non-coding RNAs. - Chun-Chi Chen; Xiaoning Qian; Byung-Jun Yoon (Bioinform., 2019)

Optimal clustering with missing values. - Shahin Boluki; Siamak Zamani Dadaneh; Xiaoning Qian; Edward R. Dougherty (BMC Bioinform., 2019)

Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci; Ranadip Pal (BMC Bioinform., 2019)

Early detection and risk assessment for chronic disease with irregular longitudinal data analysis. - Kai He; Shuai Huang 001; Xiaoning Qian (J. Biomed. Informatics, 2019)

Dynamic Inspection of Latent Variables in State-Space Systems. - Tianshu Feng; Xiaoning Qian; Kaibo Liu; Shuai Huang 001 (IEEE Trans Autom. Sci. Eng., 2019)

Constructing Pathway-Based Priors within a Gaussian Mixture Model for Bayesian Regression and Classification. - Shahin Boluki; Mohammad Shahrokh Esfahani; Xiaoning Qian; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Image Co-Saliency Detection and Co-Segmentation via Progressive Joint Optimization. - Chung-Chi Tsai; Weizhi Li; Kuang-Jui Hsu; Xiaoning Qian; Yen-Yu Lin (IEEE Trans. Image Process., 2019)

Learnable Bernoulli Dropout for Bayesian Deep Learning. - Shahin Boluki; Randy Ardywibowo; Siamak Zamani Dadaneh; Mingyuan Zhou; Xiaoning Qian (AISTATS, 2020)

Uncertainty Quantification for Deep Context-Aware Mobile Activity Recognition and Unknown Context Discovery. - Zepeng Huo; Arash Pakbin; Xiaohan Chen; Nathan C. Hurley; Ye Yuan 012; Xiaoning Qian; Zhangyang Wang; Shuai Huang 001; Bobak Mortazavi (AISTATS, 2020)

Neural Network Quantization with Scale-Adjusted Training. - Qing Jin; Linjie Yang; Zhenyu Liao; Xiaoning Qian (BMVC, 2020)

Arsm Gradient Estimator for Supervised Learning to Rank. - Siamak Zamani Dadaneh; Shahin Boluki; Mingyuan Zhou; Xiaoning Qian (ICASSP, 2020)

Semi-Implicit Stochastic Recurrent Neural Networks. - Ehsan Hajiramezanali; Arman Hasanzadeh; Nick Duffield; Krishna Narayanan 001; Mingyuan Zhou; Xiaoning Qian (ICASSP, 2020)

NADS: Neural Architecture Distribution Search for Uncertainty Awareness. - Randy Ardywibowo; Shahin Boluki; Xinyu Gong; Zhangyang Wang; Xiaoning Qian (ICML, 2020)

Bayesian Graph Neural Networks with Adaptive Connection Sampling. - Arman Hasanzadeh; Ehsan Hajiramezanali; Shahin Boluki; Mingyuan Zhou; Nick Duffield; Krishna Narayanan 001; Xiaoning Qian (ICML, 2020)

GPSRL: Learning Semi-Parametric Bayesian Survival Rule Lists from Heterogeneous Patient Data. - Ameer Hamza Shakur; Xiaoning Qian; Zhangyang Wang; Bobak Mortazavi; Shuai Huang 001 (ICPR, 2020)

BayReL: Bayesian Relational Learning for Multi-omics Data Integration. - Ehsan Hajiramezanali; Arman Hasanzadeh; Nick Duffield; Krishna Narayanan 001; Xiaoning Qian (NeurIPS, 2020)

Pairwise Supervised Hashing with Bernoulli Variational Auto-Encoder and Self-Control Gradient Estimator. - Siamak Zamani Dadaneh; Shahin Boluki; Mingzhang Yin; Mingyuan Zhou; Xiaoning Qian (UAI, 2020)

ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks. - Yijie Wang 003; Hyundoo Jeong; Byung-Jun Yoon; Xiaoning Qian (BMC Genom., 2020)

Pessimistic optimisation for modelling microbial communities with uncertainty. - Meltem Apaydin; Liang Xu 007; Bo Zeng 001; Xiaoning Qian (Int. J. Comput. Biol. Drug Des., 2020)

Deep Co-Saliency Detection via Stacked Autoencoder-Enabled Fusion and Self-Trained CNNs. - Chung-Chi Tsai; Kuang-Jui Hsu; Yen-Yu Lin; Xiaoning Qian; Yung-Yu Chuang (IEEE Trans. Multim., 2020)

Model-Based Robust Filtering and Experimental Design for Stochastic Differential Equation Systems. - Guang Zhao; Xiaoning Qian; Byung-Jun Yoon; Francis J. Alexander; Edward R. Dougherty (IEEE Trans. Signal Process., 2020)

Physics-constrained Automatic Feature Engineering for Predictive Modeling in Materials Science. - Ziyu Xiang; Mingzhou Fan; Guillermo Vázquez Tovar; William Trehern; Byung-Jun Yoon; Xiaofeng Qian; Raymundo Arróyave; Xiaoning Qian (AAAI, 2021)

Bayesian Active Learning by Soft Mean Objective Cost of Uncertainty. - Guang Zhao; Edward R. Dougherty; Byung-Jun Yoon; Francis J. Alexander; Xiaoning Qian (AISTATS, 2021)

Sparse Gated Mixture-of-Experts to Separate and Interpret Patient Heterogeneity in EHR data. - Zepeng Huo; Lida Zhang; Rohan Khera; Shuai Huang 001; Xiaoning Qian; Zhangyang Wang; Bobak J. Mortazavi (BHI, 2021)

Contextual Dropout: An Efficient Sample-Dependent Dropout Module. - Xinjie Fan; Shujian Zhang; Korawat Tanwisuth; Xiaoning Qian; Mingyuan Zhou (ICLR, 2021)

Uncertainty-aware Active Learning for Optimal Bayesian Classifier. - Guang Zhao; Edward R. Dougherty; Byung-Jun Yoon; Francis J. Alexander; Xiaoning Qian (ICLR, 2021)

Efficient Active Learning for Gaussian Process Classification by Error Reduction. - Guang Zhao; Edward R. Dougherty; Byung-Jun Yoon; Francis J. Alexander; Xiaoning Qian (NeurIPS, 2021)

Quantifying the Multi-Objective Cost of Uncertainty. - Byung-Jun Yoon; Xiaoning Qian; Edward R. Dougherty (IEEE Access, 2021)

Optimal Bayesian supervised domain adaptation for RNA sequencing data. - Shahin Boluki; Xiaoning Qian; Edward R. Dougherty (Bioinform., 2021)

COVID-Datathon: Biomarker identification for COVID-19 severity based on BALF scRNA-seq data. - Seyednami Niyakan; Xiaoning Qian (CoRR, 2021)

SURVFIT: Doubly sparse rule learning for survival data. - Ameer Hamza Shakur; Shuai Huang 001; Xiaoning Qian; Xiangyu Chang (J. Biomed. Informatics, 2021)

Risk Factor Identification in Heterogeneous Disease Progression with L1-Regularized Multi-state Models. - Xuan Dang; Shuai Huang 001; Xiaoning Qian (J. Heal. Informatics Res., 2021)

Penalized Cox's proportional hazards model for high-dimensional survival data with grouped predictors. - Xuan Dang; Shuai Huang 001; Xiaoning Qian (Stat. Comput., 2021)

Optimal Bayesian Transfer Learning for Count Data. - Alireza Karbalayghareh; Xiaoning Qian; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

VFDS: Variational Foresight Dynamic Selection in Bayesian Neural Networks for Efficient Human Activity Recognition. - Randy Ardywibowo; Shahin Boluki; Zhangyang Wang; Bobak J. Mortazavi; Shuai Huang 001; Xiaoning Qian (AISTATS, 2022)

Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response. - Xihaier Luo; Sean McCorkle; Gilchan Park; Vanessa López-Marrero; Shinjae Yoo; Edward R. Dougherty; Xiaoning Qian; Francis J. Alexander; Byung-Jun Yoon (BIBM, 2022)

Adaptive Group Testing with Mismatched Models. - Mingzhou Fan; Byung-Jun Yoon; Francis J. Alexander; Edward R. Dougherty; Xiaoning Qian (ICASSP, 2022)

Dynimp: Dynamic Imputation for Wearable Sensing Data through Sensory and Temporal Relatedness. - Zepeng Huo; Taowei Ji; Yifei Liang; Shuai Huang 001; Zhangyang Wang; Xiaoning Qian; Bobak Mortazavi (ICASSP, 2022)

MoReL: Multi-omics Relational Learning. - Arman Hasanzadeh; Ehsan Hajiramezanali; Nick Duffield; Xiaoning Qian (ICLR, 2022)

VariGrow: Variational Architecture Growing for Task-Agnostic Continual Learning based on Bayesian Novelty. - Randy Ardywibowo; Zepeng Huo; Zhangyang Wang; Bobak J. Mortazavi; Shuai Huang 001; Xiaoning Qian (ICML, 2022)

Density-Aware Personalized Training for Risk Prediction in Imbalanced Medical Data. - Zepeng Huo; Xiaoning Qian; Shuai Huang 001; Zhangyang Wang; Bobak J. Mortazavi (MLHC, 2022)

Attention-Based Deep Bayesian Counting For AI-Augmented Agriculture. - Yucheng Wang; Mengmeng Gu; Mingyuan Zhou; Xiaoning Qian (SenSys, 2022)

Deep graph representations embed network information for robust disease marker identification. - Omar Maddouri; Xiaoning Qian; Byung-Jun Yoon (Bioinform., 2022)

Robust importance sampling for error estimation in the context of optimal Bayesian transfer learning. - Omar Maddouri; Xiaoning Qian; Francis J. Alexander; Edward R. Dougherty; Byung-Jun Yoon (Patterns, 2022)

Uncertainty-aware Unsupervised Video Hashing. - Yucheng Wang; Mingyuan Zhou; Yu Sun 004; Xiaoning Qian (AISTATS, 2023)

Enhancing Cryo-EM Particle Picking Through Consistency Model-based Latent Space Denoiser. - Alif Bin Abdul Qayyum; Xiaoning Qian; Byung-Jun Yoon (BCB, 2023)

Efficient Approximations of Complete Interatomic Potentials for Crystal Property Prediction. - Yuchao Lin; Keqiang Yan; Youzhi Luo; Yi Liu 059; Xiaoning Qian; Shuiwang Ji (ICML, 2023)

Efficient and Equivariant Graph Networks for Predicting Quantum Hamiltonian. - Haiyang Yu 005; Zhao Xu 005; Xiaofeng Qian; Xiaoning Qian; Shuiwang Ji (ICML, 2023)

A Latent Diffusion Model for Protein Structure Generation. - Cong Fu 003; Keqiang Yan; Limei Wang; Wing Yee Au 002; Michael McThrow; Tao Komikado; Koji Maruhashi; Kanji Uchino; Xiaoning Qian; Shuiwang Ji (LoG, 2023)

QH9: A Quantum Hamiltonian Prediction Benchmark for QM9 Molecules. - Haiyang Yu 005; Meng Liu 015; Youzhi Luo; Alex Strasser; Xiaofeng Qian; Xiaoning Qian; Shuiwang Ji (NeurIPS, 2023)

Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction. - Puhua Niu; Maria J. Soto; Shuai Huang 001; Byung-Jun Yoon; Edward R. Dougherty; Francis J. Alexander; Ian Blaby; Xiaoning Qian (J. Comput. Biol., 2023)

Accelerating scientific discoveries through data-driven innovations. - Francis J. Alexander; Meifeng Lin; Xiaoning Qian; Byung-Jun Yoon (Patterns, 2023)

Knowledge-driven learning, optimization, and experimental design under uncertainty for materials discovery. - Xiaoning Qian; Byung-Jun Yoon; Raymundo Arróyave; Xiaofeng Qian; Edward R. Dougherty (Patterns, 2023)

Optimal decision-making in high-throughput virtual screening pipelines. - Hyun-Myung Woo; Xiaoning Qian; Li Tan; Shantenu Jha; Francis J. Alexander; Edward R. Dougherty; Byung-Jun Yoon (Patterns, 2023)

Geometric Affinity Propagation for Clustering With Network Knowledge. - Omar Maddouri; Xiaoning Qian; Byung-Jun Yoon (IEEE Trans. Knowl. Data Eng., 2023)

Uncertainty-aware Continuous Implicit Neural Representations for Remote Sensing Object Counting. - Siyuan Xu; Yucheng Wang; Mingzhou Fan; Byung-Jun Yoon; Xiaoning Qian (AISTATS, 2024)

Calibration of Compartmental Epidemiological Models via Graybox Bayesian Optimization. - Puhua Niu; Byung-Jun Yoon; Xiaoning Qian (BHI, 2024)

Learning Active Subspaces for Effective and Scalable Uncertainty Quantification in Deep Neural Networks. - Sanket R. Jantre; Nathan M. Urban; Xiaoning Qian; Byung-Jun Yoon (ICASSP, 2024)

Complete and Efficient Graph Transformers for Crystal Material Property Prediction. - Keqiang Yan; Cong Fu 003; Xiaofeng Qian; Xiaoning Qian; Shuiwang Ji (ICLR, 2024)

Path-Guided Particle-based Sampling. - Mingzhou Fan; Ruida Zhou; Chao Tian 002; Xiaoning Qian (ICML, 2024)

Hierarchical Neural Operator Transformer with Learnable Frequency-aware Loss Prior for Arbitrary-scale Super-resolution. - Xihaier Luo; Xiaoning Qian; Byung-Jun Yoon (ICML, 2024)

GFlowNet Training by Policy Gradients. - Puhua Niu; Shili Wu; Mingzhou Fan; Xiaoning Qian (ICML, 2024)

A Space Group Symmetry Informed Network for O(3) Equivariant Crystal Tensor Prediction. - Keqiang Yan; Alexandra Saxton; Xiaofeng Qian; Xiaoning Qian; Shuiwang Ji (ICML, 2024)

When Uncertainty-Based Active Learning May Fail? - Amir Hossein Rahmati; Mingzhou Fan; Ruida Zhou; Nathan M. Urban; Byung-Jun Yoon; Xiaoning Qian (ICPR (1), 2024)

Learning Flexible Time-windowed Granger Causality Integrating Heterogeneous Interventional Time Series Data. - Ziyi Zhang; Shaogang Ren; Xiaoning Qian; Nick Duffield (KDD, 2024)

Implicit Neural Representations for Simultaneous Reduction and Continuous Reconstruction of Multi-Altitude Climate Data. - Alif Bin Abdul Qayyum; Xihaier Luo; Nathan M. Urban; Xiaoning Qian; Byung-Jun Yoon (MLSP, 2024)

Invariant Tokenization of Crystalline Materials for Language Model Enabled Generation. - Keqiang Yan; Xiner Li; Hongyi Ling; Kenna Ashen; Carl Edwards; Raymundo Arróyave; Marinka Zitnik; Heng Ji 001; Xiaofeng Qian; Xiaoning Qian; Shuiwang Ji (NeurIPS, 2024)

Multi-fidelity Bayesian Optimization with Multiple Information Sources of Input-dependent Fidelity. - Mingzhou Fan; Byung-Jun Yoon; Edward R. Dougherty; Nathan M. Urban; Francis J. Alexander; Raymundo Arróyave; Xiaoning Qian (UAI, 2024)

Towards Invariant Time Series Forecasting in Smart Cities. - Ziyi Zhang; Shaogang Ren; Xiaoning Qian; Nick Duffield (WWW (Companion Volume), 2024)

Multi-modal Representation Learning for Cross-modal Prediction of Continuous Weather Patterns from Discrete Low-Dimensional Data. - Alif Bin Abdul Qayyum; Xihaier Luo; Nathan M. Urban; Xiaoning Qian; Byung-Jun Yoon (CoRR, 2024)

Causal Bayesian Optimization via Exogenous Distribution Learning. - Shaogang Ren; Xiaoning Qian (CoRR, 2024)

Dynamic Incremental Optimization for Best Subset Selection. - Shaogang Ren; Xiaoning Qian (CoRR, 2024)

Understanding Uncertainty-based Active Learning Under Model Mismatch. - Amir Hossein Rahmati; Mingzhou Fan; Ruida Zhou; Nathan M. Urban; Byung-Jun Yoon; Xiaoning Qian (CoRR, 2024)

LoRA-BERT: a Natural Language Processing Model for Robust and Accurate Prediction of long non-coding RNAs. - Nicholas Jeon; Xiaoning Qian; Lamin SaidyKhan; Paul de Figueiredo; Byung-Jun Yoon (CoRR, 2024)

Hyperparameter Tuning Through Pessimistic Bilevel Optimization. - Meltem Apaydin Ustun; Liang Xu 007; Bo Zeng 001; Xiaoning Qian (CoRR, 2024)

Epidemiological Model Calibration via Graybox Bayesian Optimization. - Puhua Niu; Byung-Jun Yoon; Xiaoning Qian (CoRR, 2024)

Pathway-based analyses of gene expression profiles at low doses of ionizing radiation. - 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 (Frontiers Bioinform., 2024)

MUSTANG: Multi-sample spatial transcriptomics data analysis with cross-sample transcriptional similarity guidance. - Seyednami Niyakan; Jianting Sheng; Yuliang Cao; Xiang Zhang; Zhan Xu; Ling Wu; Stephen T. C. Wong; Xiaoning Qian (Patterns, 2024)

Hashing with Uncertainty Quantification via Sampling-based Hypothesis Testing. - Yucheng Wang; Mingyuan Zhou; Xiaoning Qian (Trans. Mach. Learn. Res., 2024)

Bayesian Proper Orthogonal Decomposition for Learnable Reduced-Order Models With Uncertainty Quantification. - Shahin Boluki; Siamak Zamani Dadaneh; Edward R. Dougherty; Xiaoning Qian (IEEE Trans. Artif. Intell., 2024)

Scale-Invariant Implicit Neural Representations For Object Counting. - Siyuan Xu; Yucheng Wang; Xihaier Luo; Byung-Jun Yoon; Xiaoning Qian (CVPR Workshops, 2025)

Pareto Prompt Optimization. - Guang Zhao; Byung-Jun Yoon; Gilchan Park; Shantenu Jha; Shinjae Yoo; Xiaoning Qian (ICLR, 2025)

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems. - Xuan Zhang; Limei Wang; Jacob Helwig; Youzhi Luo; Cong Fu 003; Yaochen Xie; Meng Liu 015; Yuchao Lin; Zhao Xu 005; Keqiang Yan; Keir Adams; Maurice Weiler; et al. (Found. Trends Mach. Learn., 2025)

Rare Event Detection by Acquisition-Guided Sampling. - Huiling Liao; Xiaoning Qian; Jianhua Z. Huang; Peng Li 001 (IEEE Trans Autom. Sci. Eng., 2025)

Uncertainty-Aware Adaptation of Large Language Models for Protein-Protein Interaction Analysis. - Sanket R. Jantre; Tianle Wang 001; Gilchan Park; Kriti Chopra; Nicholas Jeon; Xiaoning Qian; Nathan M. Urban; Byung-Jun Yoon (CoRR, 2025)

A Materials Foundation Model via Hybrid Invariant-Equivariant Architectures. - Keqiang Yan; Montgomery Bohde; Andrii Kryvenko; Ziyu Xiang; Kaiji Zhao; Siya Zhu; Saagar Kolachina; Doguhan Saritürk; Jianwen Xie; Raymundo Arróyave; Xiaoning Qian; Xiaofeng Qian; et al. (CoRR, 2025)

C-LoRA: Contextual Low-Rank Adaptation for Uncertainty Estimation in Large Language Models. - Amir Hossein Rahmati; Sanket R. Jantre; Weifeng Zhang; Yucheng Wang; Byung-Jun Yoon; Nathan M. Urban; Xiaoning Qian (CoRR, 2025)

Toward Greater Autonomy in Materials Discovery Agents: Unifying Planning, Physics, and Scientists. - Lianhao Zhou; Hongyi Ling; Keqiang Yan; Kaiji Zhao; Xiaoning Qian; Raymundo Arróyave; Xiaofeng Qian; Shuiwang Ji (CoRR, 2025)

Cost-effective Reduced-Order Modeling via Bayesian Active Learning. - Amir Hossein Rahmati; Nathan M. Urban; Byung-Jun Yoon; Xiaoning Qian (CoRR, 2025)