HR job title
- Professor
- Contact Info
- 1 979 845 7441
- Websites
- ORCiD
- 0000-0002-4347-2476
Qian, Xiaoning Associate Professor
Positions
- Associate Professor, Electrical and Computer Engineering, College of Engineering
Xiaoning Qian's research interests include machine learning and Bayesian experimental design as well as their applications in computational network biology, genomic signal processing, and biomedical signal and image analysis. He is affiliated with the Center for Bioinformatics and Genomic Systems Engineering and the Center for Translational Environmental Health Research at Texas A&M.
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Overview
Publications
selected publications
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academic article
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Qian, X., Yoon, B., Arryave, R., Qian, X., & Dougherty, E. R.
(2023).
Knowledge-driven learning, optimization, and experimental design under uncertainty for materials discovery. 4(11), 100863-100863.
-
Maddouri, O., Qian, X., & Yoon, B.
(2023).
Geometric Affinity Propagation for Clustering With Network Knowledge. 35(11), 11419-11436.
-
Zadeh, S. H., Behbahanian, A., Broucek, J., Fan, M., Vazquez, G., Noroozi, M., ... Arroyave, R.
(2023).
An Interpretable Boosting-Based Predictive Model for Transformation Temperatures of Shape Memory Alloys. 226, 112225-112225.
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Erbeli, F., He, K., Cheek, C., Rice, M., & Qian, X.
(2023).
Exploring the Machine Learning Paradigm in Determining Risk for Reading Disability. Scientific Studies of Reading.
27(1), 5-20.
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Boluki, S., Dadaneh, S. Z., Dougherty, E. R., & Qian, X.
(2023).
Bayesian Proper Orthogonal Decomposition for Learnable Reduced-Order Models with Uncertainty Quantification. IEEE Transactions on Artificial Intelligence.
PP(99), 1-13.
-
Lin, F., Qian, X., Mortazavi, B., Wang, Z., Huang, S., & Chen, C.
(2023).
Modeling user choice behavior under data corruption: Robust learning of the latent decision threshold model. IISE TRANSACTIONS.
ahead-of-print(ahead-of-print), 1-14.
-
Wilson, N., Willhelm, D., Qian, X., Arroyave, R., & Qian, X.
(2022).
Batch active learning for accelerating the development of interatomic potentials. COMPUTATIONAL MATERIALS SCIENCE.
208, 111330-111330.
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Maddouri, O., Qian, X., Alexander, F. J., Dougherty, E. R., & Yoon, B.
(2022).
Robust importance sampling for error estimation in the context of optimal Bayesian transfer learning. 3(3), 100428-100428.
-
Shakur, A. H., Huang, S., Qian, X., & Chang, X.
(2021).
SURVFIT: Doubly sparse rule learning for survival data. 117, 103691-103691.
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Karbalayghareh, A., Qian, X., & Dougherty, E. R.
(2021).
Optimal Bayesian Transfer Learning for Count Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
18(2), 644-655.
-
Nagashima, Y., He, K., Singh, J., Metrani, R., Crosby, K. M., Jifon, J., ... Koiwa, H.
(2021).
Transition of aromatic volatile and transcriptome profiles during melon fruit ripening. Plant Science.
304, 110809-110809.
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Lei, B., Kirk, T. Q., Bhattacharya, A., Pati, D., Qian, X., Arroyave, R., & Mallick, B. K.
(2021).
Bayesian optimization with adaptive surrogate models for automated experimental design. npj Computational Materials.
7(1), 194.
-
Yoon, B., Qian, X., & Dougherty, E. R.
(2021).
Quantifying the Multi-Objective Cost of Uncertainty. 9, 80351-80359.
-
Tsai, C., Hsu, K., Lin, Y., Qian, X., & Chuang, Y.
(2020).
Deep Co-Saliency Detection via Stacked Autoencoder-Enabled Fusion and Self-Trained CNNs. IEEE Transactions on Multimedia.
22(4), 1016-1031.
-
Nagashima, Y., Ma, Z., Liu, X., Qian, X., Zhang, X., von Schaewen, A., & Koiwa, H.
(2020).
Multiple Quality Control Mechanisms in the ER and TGN Determine Subcellular Dynamics and Salt-Stress Tolerance Function of KORRIGAN1. The Plant Cell.
32(2), 470-485.
-
Zhao, G., Qian, X., Yoon, B., Alexander, F. J., & Dougherty, E. R.
(2020).
Model-Based Robust Filtering and Experimental Design for Stochastic Differential Equation Systems. 68, 3849-3859.
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Choobdar, S., Ahsen, M. E., Crawford, J., Tomasoni, M., Fang, T., Lamparter, D., ... Marbach, D.
(2019).
Assessment of network module identification across complex diseases. Nature Methods.
16(9), 843-852.
-
Chen, C., Jeong, H., Qian, X., & Yoon, B.
(2019).
TOPAS: network-based structural alignment of RNA sequences. 35(17), 2941-2948.
-
He, K., Huang, S., & Qian, X.
(2019).
Early detection and risk assessment for chronic disease with irregular longitudinal data analysis. 96, 103231-103231.
-
Fong, T., Qian, X., Li, K., & Huang, S.
(2019).
Dynamic Inspection of Latent Variables in State-Space Systems. IEEE Transactions on Automation Science and Engineering.
16(3), 1232-1243.
-
Yoon, B., Qian, X., Kahveci, T., & Pal, R.
(2019).
Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). 20(Suppl 12), 316.
-
Boluki, S., Zamani Dadaneh, S., Qian, X., & Dougherty, E. R.
(2019).
Optimal clustering with missing values. BMC Bioinformatics.
20(Suppl 12), 321.
-
Chen, C., Qian, X., & Yoon, B.
(2019).
RNAdetect: efficient computational detection of novel non-coding RNAs. Bioinformatics.
35(7), 1133-1141.
-
Boluki, S., Esfahani, M. S., Qian, X., & Dougherty, E. R.
(2019).
Constructing Pathway-Based Priors within a Gaussian Mixture Model for Bayesian Regression and Classification. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
16(2), 524-537.
-
Talapatra, A., Boluki, S., Honarmandi, P., Solomou, A., Zhao, G., Ghoreishi, S. F., ... Arroyave, R.
(2019).
Experiment Design Frameworks for Accelerated Discovery of Targeted Materials Across Scales. Frontiers in Materials.
6, 82.
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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.
-
Boluki, S., Qian, X., & Dougherty, E. R.
(2019).
Experimental Design via Generalized Mean Objective Cost of Uncertainty. IEEE Access.
7, 2223-2230.
-
Tsai, C., Li, W., Hsu, K., Qian, X., & Lin, Y.
(2019).
Image Co-Saliency Detection and Co-Segmentation via Progressive Joint Optimization. IEEE Transactions on Image Processing.
28(1), 56-71.
-
Dehghannasiri, R., Qian, X., & Dougherty, E. R.
(2018).
A Bayesian robust Kalman smoothing framework for state-space models with uncertain noise statistics. EURASIP Journal on Advances in Signal Processing.
2018(1), 55.
-
Ren, S., Huang, S., Ye, J., & Qian, X.
(2018).
Safe Feature Screening for Generalized LASSO. 40(12), 2992-3006.
-
Talapatra, A., Boluki, S., Duong, T., Qian, X., Dougherty, E., & Arroyave, R.
(2018).
Autonomous efficient experiment design for materials discovery with Bayesian model averaging. Physical Review Materials.
2(11), 113803.
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Karbalayghareh, A., Qian, X., & Dougherty, E. R.
(2018).
Optimal Bayesian Transfer Regression. IEEE Signal Processing Letters.
25(11), 1655-1659.
-
Dadaneh, S. Z., Zhou, M., & Qian, X.
(2018).
Bayesian negative binomial regression for differential expression with confounding factors. Bioinformatics.
34(19), 3349-3356.
-
Dadaneh, S. Z., Dougherty, E. R., & Qian, X.
(2018).
Optimal Bayesian Classification With Missing Values. IEEE Transactions on Signal Processing.
66(16), 4182-4192.
-
Karbalayghareh, A., Qian, X., & Dougherty, E. R.
(2018).
Optimal Bayesian Transfer Learning. IEEE Transactions on Signal Processing.
66(14), 3724-3739.
-
Ren, S., Huang, J. Z., Huang, S., & Qian, X.
(2018).
Safe Active Feature Selection for Sparse Learning
-
Dehghannasiri, R., Esfahani, M. S., Qian, X., & Dougherty, E. R.
(2018).
Optimal Bayesian Kalman Filtering With Prior Update. IEEE Transactions on Signal Processing.
66(8), 1982-1996.
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Yoon, B., Qian, X., Kahveci, T., & Pal, R.
(2018).
Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). 19(Suppl 3), 69.
-
Lin, Y., Liu, K., Byon, E., Qian, X., Liu, S., & Huang, S.
(2018).
A Collaborative Learning Framework for Estimating Many Individualized Regression Models in a Heterogeneous Population. IEEE Transactions on Reliability.
67(1), 328-341.
-
Hajiramezanali, E., Dadaneh, S. Z., de Figueiredo, P., Sze, S., Zhou, M., & Qian, X.
(2018).
Differential Expression Analysis of Dynamical Sequencing Count Data with a Gamma Markov Chain
-
Xu, E. L., Qian, X., Yu, Q., Zhang, H., & Cui, S.
(2018).
Feature selection with interactions in logistic regression models using multivariate synergies for a GWAS application. BMC GENOMICS.
19(Suppl 4), 170.
-
Dehghannasiri, R., Qian, X., & Dougherty, E. R.
(2018).
Intrinsically Bayesian robust Karhunen-Loeve compression. Signal Processing.
144, 311-322.
-
Sui, X. L., Xu, L. i., Qian, X., & Liu, T.
(2018).
Convex clustering with metric learning. Pattern Recognition.
81, 575-584.
-
Solomou, A., Zhao, G., Boluki, S., Joy, J. K., Qian, X., Karaman, I., Arroyave, R., & Lagoudas, D. C.
(2018).
Multi-objective Bayesian materials discovery: Application on the discovery of precipitation strengthened NiTi shape memory alloys through micromechanical modeling. Materials and Design.
160, 810-827.
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Dadaneh, S. Z., Qian, X., & Zhou, M.
(2018).
BNP-Seq: Bayesian Nonparametric Differential Expression Analysis of Sequencing Count Data. JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION.
113(521), 81-94.
-
Boluki, S., Esfahani, M. S., Qian, X., & Dougherty, E. R.
(2017).
Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors. BMC Bioinformatics.
18(Suppl 14), 552.
-
Adl, A. A., Lee, H., & Qian, X.
(2017).
Detecting Pairwise Interactive Effects of Continuous Random Variables for Biomarker Identification with Small Sample Size. 14(6), 1265-1275.
-
Dehghannasiri, R., Qian, X., & Dougherty, E. R.
(2017).
Optimal experimental design in the context of canonical expansions. IET Signal Processing.
11(8), 942-951.
-
Apaydin, M., Xu, L., Zeng, B. o., & Qian, X.
(2017).
Robust mutant strain design by pessimistic optimization. BMC GENOMICS.
18(Suppl 6), 677.
-
Huang, Y., Meng, Q., Evans, H., Lober, W., Cheng, Y. u., Qian, X., Liu, J. i., & Huang, S.
(2017).
CHI: A contemporaneous health index for degenerative disease monitoring using longitudinal measurements. 73, 115-124.
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Xu, E. L., Qian, X., Liu, T., & Cui, S.
(2017).
Detection of Cooperative Interactions in Logistic Regression Models. IEEE Transactions on Signal Processing.
65(7), 1765-1780.
-
Jeong, H., Qian, X., & Yoon, B.
(2017).
CUFID-query: accurate network querying through random walk based network flow estimation. BMC Bioinformatics.
18(Suppl 14), 500.
-
Chen, C., Qian, X., & Yoon, B.
(2017).
Effective computational detection of piRNAs using n-gram models and support vector machine. BMC Bioinformatics.
18(Suppl 14), 517.
-
Chen, C., Ghaffari, N., Qian, X., & Yoon, B.
(2017).
Optimal hybrid sequencing and assembly: Feasibility conditions for accurate genome reconstruction and cost minimization strategy. Computational Biology and Chemistry.
69, 153-163.
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Ke, C., Jin, Y., Evans, H., Lober, B., Qian, X., Liu, J. i., & Huang, S.
(2017).
Prognostics of surgical site infections using dynamic health data. 65, 22-33.
-
Qian, X., & Dougherty, E. R.
(2016).
Bayesian Regression with Network Prior: Optimal Bayesian Filtering Perspective. 64(23), 6243-6253.
-
Zamani Dadaneh, S., & Qian, X.
(2016).
Bayesian module identification from multiple noisy networks. EURASIP Journal on Bioinformatics and Systems Biology.
2016(1), 5-11.
-
Lu, M., Huang, J. Z., & Qian, X.
(2016).
Sparse Exponential Family Principal Component Analysis. Pattern Recognition.
60, 681-691.
-
Haghighi, M., Johnson, S. B., Qian, X., Lynch, K. F., Vehik, K., Huang, S., & TEDDY Study Group.
(2016).
A Comparison of Rule-based Analysis with Regression Methods in Understanding the Risk Factors for Study Withdrawal in a Pediatric Study. Scientific Reports.
6(1), 30828.
-
Lin, B., Sun, Y. u., Qian, X., Goldgof, D., Gitlin, R., & You, Y.
(2016).
Video-based 3D reconstruction, laparoscope localization and deformation recovery for abdominal minimally invasive surgery: a survey. International Journal of Medical Robotics and Computer Assisted Surgery.
12(2), 158-178.
-
Jeong, H., Qian, X., & Yoon, B.
(2016).
Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. BMC Bioinformatics.
17(Suppl 13), 395.
-
Lin, B., Sun, Y. u., Sanchez, J. E., & Qian, X.
(2015).
Efficient Vessel Feature Detection for Endoscopic Image Analysis. 62(4), 1141-1150.
-
Huang, Y., Chen, Y., & Qian, X.
(2014).
Selected Articles from the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2012). IEEE/ACM Transactions on Computational Biology and Bioinformatics.
11(6), 981-983.
-
Lu, M., Lee, H., Hadley, D., Huang, J. Z., & Qian, X.
(2014).
Logistic Principal Component Analysis for Rare Variants in Gene-Environment Interaction Analysis. 11(6), 1020-1028.
-
Sajjadi, S. J., Qian, X., Zeng, B. o., & Adl, A. A.
(2014).
Network-Based Methods to Identify Highly Discriminating Subsets of Biomarkers. 11(6), 1029-1037.
-
Staff, T.
(2014).
Correction: A Rule-Based Prognostic Model for Type 1 Diabetes by Identifying and Synthesizing Baseline Profile Patterns. PLoS ONE.
9(9), e109514-e109514.
-
Xu, P., Qian, X., Schatz, D. A., Cuthbertson, D., Krischer, J. P., & DPT-1 Study Group.
(2014).
Distribution of C-peptide and its determinants in North American children at risk for type 1 diabetes. 37(7), 1959-1965.
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Lin, Y., Qian, X., Krischer, J., Vehik, K., Lee, H., & Huang, S.
(2014).
A rule-based prognostic model for type 1 diabetes by identifying and synthesizing baseline profile patterns. PLoS ONE.
9(6), e91095-e91095.
-
Wang, Y., & Qian, X.
(2014).
Joint clustering of protein interaction networks through Markov random walk. BMC Systems Biology.
8 Suppl 1(Suppl 1), S9-S9.
-
Lu, M., Lee, H., Hadley, D., Huang, J. Z., & Qian, X.
(2014).
Supervised categorical principal component analysis for genome-wide association analyses. BMC GENOMICS.
15 Suppl 1(Suppl 1), S10-10.
-
Wang, Y., & Qian, X.
(2014).
Functional module identification in protein interaction networks by interaction patterns. Bioinformatics.
30(1), 81-93.
-
Qian, X.
(2014).
Supervised categorical principal component analysis for genome-wide association analyses. BMC GENOMICS.
15 Suppl 1.
-
Qian, X., & Dougherty, E. R.
(2013).
Validation of gene regulatory network inference based on controllability. Frontiers in Genetics.
4(DEC), 272.
-
Li, J., Bennett, K., Stukalov, A., Fang, B., Zhang, G., Yoshida, T., ... Haura, E. B.
(2013).
Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms. Molecular Systems Biology.
9(1), 705-705.
-
Lin, B., Sun, Y. u., & Qian, X.
(2013).
Dense surface reconstruction with shadows in MIS. 60(9), 2411-2420.
-
Adl, A. A., Qian, X., Xu, P., Vehik, K., & Krischer, J. P.
(2013).
Feature ranking based on synergy networks to identify prognostic markers in DPT-1. EURASIP Journal on Bioinformatics and Systems Biology.
2013(1), 12.
-
Yoon, B., Qian, X., & Dougherty, E. R.
(2013).
Quantifying the Objective Cost of Uncertainty in Complex Dynamical Systems. 61(9), 2256-2266.
-
Wang, Y., & Qian, X.
(2013).
A novel subgradient-based optimization algorithm for blockmodel functional module identification. 14 Suppl 2(Suppl 2), S23.
-
Ren, S., Zeng, B. o., & Qian, X.
(2013).
Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints. 14 Suppl 2(Suppl 2), S17.
-
Dougherty, E. R., Yoon, B., Qian, X., & Pal, R.
(2012).
Special Issue on Genomic Signal Processing FOREWORD. 20(4), VII-VIII.
-
Adl, A. A., Nowzari-Dalini, A., Xue, B., Uversky, V. N., & Qian, X.
(2012).
Accurate prediction of protein structural classes using functional domains and predicted secondary structure sequences. Journal of Biomolecular Structure and Dynamics.
29(6), 1127-1137.
-
Ahmadi Adl, A., Nowzari-Dalini, A., Xue, B., Uversky, V. N., & Qian, X.
(2012).
Accurate prediction of protein structural classes using functional domains and predicted secondary structure sequences. Journal of Biomolecular Structure and Dynamics.
29(6), 623-633.
-
Yoon, B., Qian, X., & Sahraeian, S.
(2012).
Comparative Analysis of Biological Networks: Hidden Markov model and Markov chain-based approach. IEEE Signal Processing Magazine.
29(1), 22-34.
-
Qian, X., & Dougherty, E. R.
(2012).
Intervention in gene regulatory networks via phenotypically constrained control policies based on long-run behavior. 9(1), 123-136.
-
Ghaffari, N., Ivanov, I., Qian, X., & Dougherty, E. R.
(2011).
A CoD-based stationary control policy for intervening in large gene regulatory networks. 12 Suppl 10(Suppl 10), S10.
-
Qian, X., Sahraeian, S., & Yoon, B.
(2011).
Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores. BMC Bioinformatics.
12 Suppl 10(Suppl 10), S6.
-
Qian, X., & Yoon, B.
(2011).
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. BMC Bioinformatics.
12 Suppl 1(Suppl 1), S19.
-
Qian, X., Ghaffari, N., Ivanov, I., & Dougherty, E. R.
(2010).
State reduction for network intervention in probabilistic Boolean networks. Bioinformatics.
26(24), 3098-3104.
-
Ivanov, I., Simeonov, P., Ghaffari, N., Qian, X., & Dougherty, E. R.
(2010).
Selection Policy-Induced Reduction Mappings for Boolean Networks. IEEE Transactions on Signal Processing.
58(9), 4871-4882.
-
Ghaffari, N., Ivanov, I., Qian, X., & Dougherty, E. R.
(2010).
A CoD-based reduction algorithm for designing stationary control policies on Boolean networks. Bioinformatics.
26(12), 1556-1563.
-
Qian, X., Tagare, H. D., Fulbright, R. K., Long, R., & Antani, S.
(2010).
Optimal embedding for shape indexing in medical image databases. Medical Image Analysis.
14(3), 243-254.
-
Qian, X., & Tagare, H. D.
(2010).
Adapting indexing trees to data distribution in feature spaces. CVGIP. Image understanding.
114(1), 111-124.
-
Dougherty, E. R., Pal, R., Qian, X., Bittner, M. L., & Datta, A.
(2010).
Stationary and structural control in gene regulatory networks: basic concepts. International Journal of Systems Science.
41(1), 5-16.
-
Qian, X., & Yoon, B.
(2009).
Effective identification of conserved pathways in biological networks using hidden Markov models. PLoS ONE.
4(12), e8070-e8070.
-
Qian, X., Ivanov, I., Ghaffari, N., & Dougherty, E. R.
(2009).
Intervention in gene regulatory networks via greedy control policies based on long-run behavior. BMC Systems Biology.
3(1), 61.
-
Qian, X., & Dougherty, E. R.
(2009).
On the long-run sensitivity of probabilistic Boolean networks. Journal of Theoretical Biology.
257(4), 560-577.
-
Qian, X., Sze, S., & Yoon, B.
(2009).
Querying pathways in protein interaction networks based on hidden Markov models. Journal of Computational Biology.
16(2), 145-157.
-
Qian, X., Brennan, M. P., Dione, D. P., Dobrucki, W. L., Jackowski, M. P., Breuer, C. K., Sinusas, A. J., & Papademetris, X.
(2009).
A non-parametric vessel detection method for complex vascular structures. Medical Image Analysis.
13(1), 49-61.
-
Qian, X., & Dougherty, E. R.
(2008).
Effect of function perturbation on the steady-state distribution of genetic regulatory networks: Optimal structural intervention. 56(10), 4966-4976.
-
Qian, X., & Tagare, H. D.
(2005).
Optimal embedding for shape indexing in medical image databases. Lecture Notes in Computer Science.
8(Pt 2), 377-384.
-
Wells, K. M., He, K., Pandey, A., Cabello, A., Zhang, D., Yang, J., ... de Figueiredo, P.
Brucella activates the host RIDD pathway to subvert BLOS1-directed immune defense. eLife.
11, e73625.
-
Qian, X., Yoon, B., Arryave, R., Qian, X., & Dougherty, E. R.
(2023).
Knowledge-driven learning, optimization, and experimental design under uncertainty for materials discovery. 4(11), 100863-100863.
-
chapter
-
Lu, M., He, K., Huang, J. Z., & Qian, X.
(2018).
Principal Component Analysis for Exponential Family Data. Advances in Principal Component Analysis.
(pp. 193-223).
Springer Nature.
-
Lu, M., He, K., Huang, J. Z., & Qian, X.
(2018).
Principal Component Analysis for Exponential Family Data. Advances in Principal Component Analysis.
(pp. 193-223).
Springer Nature.
-
conference paper
-
Bin Abdul Qayyum, A., Qian, X., & Yoon, B.
(2023).
Enhancing Cryo-EM Particle Picking Through Consistency Model-based Latent Space Denoiser. 1-1.
-
Hu, H., Fang, Y., Jin, R., Xiong, W., Qian, X., Dou, D., & Phan, H.
(2018).
Recursive Structure Similarity: A Novel Algorithm for Graph Clustering. Proceedings - International Conference on Tools with Artificial Intelligence, ICTAI.
395-400.
-
Dehghannasiri, R., Qian, X., & Dougherty, E. R.
(2018).
Robust Smoothing for State-Space Models with Unknown Noise Statistics. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
1024-1028.
-
Karbalayghareh, A., Qian, X., & Dougherty, E. R.
(2018).
Optimal Bayesian Transfer Learning for Classifying Multivariate Gaussian Observations. 1-4.
-
Boluki, S., Dadaneh, S. Z., Qian, X., & Dougherty, E. R.
(2018).
Optimal Clustering with Missing Values. 593-594.
-
Zamani Dadaneh, S., Zhou, M., & Qian, X.
(2018).
Covariate-dependent negative binomial factor analysis of RNA sequencing data. Bioinformatics.
i61-i69.
-
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.
-
Hajiramezanali, E., Dadaneh, S. Z., Zhou, M., Karbalayghareh, A., & Qian, X.
(2018).
Bayesian multi-domain learning for cancer subtype discovery from next-generation sequencing count data. Advances in Neural Information Processing Systems.
9115-9124.
-
Hsu, K., Tsai, C., Lin, Y., Qian, X., & Chuang, Y.
(2018).
Unsupervised CNN-Based Co-saliency Detection with Graphical Optimization. Lecture Notes in Computer Science.
502-518.
-
Dehghannasiri, R., Qian, X., & Dougherty, E. R.
(2017).
An Objective-Based Experimental Design Framework for Signal Processing in the Context of Canonical Expansions. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
789-793.
-
Dehghannasiri, R., Esfahani, M. S., Qian, X., & Dougherty, E. R.
(2017).
Bayesian Kalman Filtering in the Presence of Unknown Noise Statistics Using Factor Graphs. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
166-170.
-
Xu, E. L., Qian, X., Yu, Q., Zhang, H., & Cui, S.
(2017).
Feature Selection with Interactions in Logistic Regression Models using Multivariate Synergies for a GWAS Application. 760-761.
-
Tsai, C., Qian, X., & Lin, Y.
(2017).
Segmentation Guided Local Proposal Fusion for Co-Saliency Detection. Proceedings / IEEE International Conference on Multimedia and Expo. IEEE International Conference on Multimedia and Expo.
523-528.
-
Tsai, C., Qian, X., & Lin, Y.
(2017).
Image Co-Saliency Detection via Locally Adaptive Saliency Map Fusion. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
1897-1901.
-
Yoon, B., Qian, X., & Kahveci, T.
(2017).
CNB-MAC'17. 750-750.
-
Li, W., Qian, X., & Ji, J.
(2017).
Noise-Tolerant Deep Learning for Histopathological Image Segmentation. Proceedings / ICIP ... International Conference on Image Processing.
3075-3079.
-
Wang, Y., & Qian, X.
(2016).
Stochastic block coordinate Frank-Wolfe algorithm for large-scale biological network alignment. EURASIP Journal on Bioinformatics and Systems Biology.
9-1413.
-
Xue, D., Balachandran, P. V., Yuan, R., Hu, T., Qian, X., Dougherty, E. R., & Lookman, T.
(2016).
Accelerated search for BaTiO3-based piezoelectrics with vertical morphotropic phase boundary using Bayesian learning. Proceedings of the National Academy of Sciences of the United States of America.
13301-13306.
-
Wang, Y., & Qian, X.
(2016).
Finding Low-Conductance sets with Dense interactions (FLCD) for better protein complex prediction. 537-538.
-
Apaydin, M., Zeng, B. o., & Qian, X.
(2016).
A Reliable Alternative of OptKnock for Desirable Mutant Microbial Strains. 573-576.
-
Wang, Y., Yoon, B., & Qian, X.
(2016).
CO-SEGMENTATION OF MULTIPLE IMAGES THROUGH RANDOM WALK ON GRAPHS. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
1811-1815.
-
Dehghannasiri, R., Qian, X., & Dougherty, E. R.
(2016).
OPTIMAL EXPERIMENTAL DESIGN IN CANONICAL EXPANSIONS WITH APPLICATIONS TO SIGNAL COMPRESSION. 2016 IEEE Global Conference on Signal and Information Processing (GlobalSIP).
94-98.
-
Xu, E. L., Qian, X., Liu, T., & Cui, S.
(2016).
PAIRWISE INTERACTION ANALYSIS OF LOGISTIC REGRESSION MODELS. 2016 IEEE Global Conference on Signal and Information Processing (GlobalSIP).
187-191.
-
Wang, Y., & Qian, X.
(2015).
A computational framework for finding functional modules across multiple biological networks. 649-650.
-
Apaydin, M., Zeng, B. o., Ren, S., & Qian, X.
(2015).
A computationally efficient solution strategy for optimal gene knockouts for targeted overproduction. 653-654.
-
Ren, S., Huang, S., Onofrey, J., Papademetris, X., & Qian, X.
(2015).
A Scalable Algorithm for Structured Kernel Feature Selection. JMLR workshop and conference proceedings.
781-789.
-
Lin, Y., Liu, K., Byon, E., Qian, X., & Huang, S.
(2015).
Domain-knowledge driven cognitive degradation modeling for Alzheimer's disease. 721-729.
-
Wang, Y., & Qian, X.
(2014).
Stochastic Coordinate Descent Frank-Wolfe Algorithm for Large-Scale Biological Network Alignment. 1410-1413.
-
Wang, Y., & Qian, X.
(2014).
Biological network clustering by robust NMF. 688-689.
-
Adl, A. A., & Qian, X.
(2014).
Network-regularized bi-clique finding for tumor stratification. 686-687.
-
Wang, Y., & Qian, X.
(2014).
JOINT CLUSTERING OF PROTEIN INTERACTION NETWORKS BY BLOCK MODELING. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
1616-1620.
-
Ren, S., & Qian, X.
(2014).
Structured Sparse PCA to Identify Mirna Co-Regulatory Modules. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
2828-2832.
-
Lin, B., Sun, Y. u., Sanchez, J., & Qian, X.
(2014).
VESSELNESS BASED FEATURE EXTRACTION FOR ENDOSCOPIC IMAGE ANALYSIS. Proceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging.
1295-1298.
-
Lin, B., Johnson, A., Qian, X., Sanchez, J., & Sun, Y. u.
(2013).
Simultaneous Tracking, 3D Reconstruction and Deforming Point Detection for Stereoscope Guided Surgery. Lecture Notes in Computer Science.
35-44.
-
Wang, Y., & Qian, X.
(2013).
Identifying Overlapping Functional Modules in Biological Networks by Markov Random Walk. 2016 IEEE Global Conference on Signal and Information Processing (GlobalSIP).
89-92.
-
Dai, W., Sun, Y. u., & Qian, X.
(2013).
Functional Analysis of Grasping Motion. Proceedings of the ... IEEE/RSJ International Conference on Intelligent Robots and Systems. IEEE/RSJ International Conference on Intelligent Robots and Systems.
3507-3513.
-
Qian, X., & Dougherty, E. R.
(2013).
PHENOTYPICALLY CONSTRAINED BOOLEAN NETWORK INFERENCE WITH PRESCRIBED STEADY STATES. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
82-83.
-
Lin, B., Sun, Y. u., & Qian, X.
(2013).
Thin plate spline feature point matching for organ surfaces in minimally invasive surgery imaging. Proceedings of SPIE.
867112-867112-7.
-
Wang, Y., & Qian, X.
(2013).
Blockmodel module identification in protein interaction networks through Markov random walk. European Signal Processing Conference.
-
Qian, X.
(2012).
A NEW PHENOTYPICALLY CONSTRAINED CONTROL POLICY IN BOOLEAN NETWORKS BASED ON BASINS OF ATTRACTION. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
54-57.
-
Adl, A. A., Qian, X., Xu, P., Vehik, K., & Krischer, J. P.
(2012).
FEATURE RANKING BASED ON SYNERGY NETWORKS TO IDENTIFY PROGNOSTIC MARKERS IN DPT-1. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
66-69.
-
Lu, M., Lee, H., Hadley, D., Huang, J. Z., & Qian, X.
(2012).
Logistic Principal Component Analysis for Rare Variants in Gene-Environment Interaction Analysis. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
122-125.
-
Sajjadi, S. J., Qian, X., & Zeng, B. o.
(2012).
Network-Based Methods to Identify Highly Discriminating Subsets of Biomarkers. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
139-142.
-
Lu, M., Huang, J. Z., & Qian, X.
(2012).
Supervised logistic principal component analysis for pathway based genome-wide association studies. 52-59.
-
Qian, X., Yoon, B., & Dougherty, E. R.
(2012).
STRUCTURAL INTERVENTION OF GENE REGULATORY NETWORKS BY GENERAL RANK-K MATRIX PERTURBATION. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
729-732.
-
Wang, Y., & Qian, X.
(2012).
Functional module identification by block modeling using simulated annealing with path relinking. 123-130.
-
Kayes, I., Qian, X., Skvoretz, J., & Iamnitchi, A.
(2012).
How influential are you: Detecting influential bloggers in a blogging community. Lecture Notes in Computer Science.
29-42.
-
Qian, X., Yoon, B., & Dougherty, E. R.
(2011).
UNCERTAINTY-BASED ESSENTIALITY IN GENE REGULATORY NETWORKS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
17-20.
-
Qian, X., & Yoon, B.
(2011).
CONTOUR-BASED HIDDEN MARKOV MODEL TO SEGMENT 2D ULTRASOUND IMAGES. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
705-708.
-
Qian, X., & Dougherty, E. R.
(2010).
A COMPARATIVE STUDY ON SENSITIVITIES OF BOOLEAN NETWORKS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-4.
-
Suh, J. W., Scheinost, D., Qian, X., Sinusas, A. J., Breuer, C. K., & Papademetris, X.
(2010).
SERIAL NONRIGID VASCULAR REGISTRATION USING WEIGHTED NORMALIZED MUTUAL INFORMATION. Proceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging.
25-28.
-
Qian, X., & Yoon, B.
(2010).
SHAPE MATCHING BASED ON GRAPH ALIGNMENT USING HIDDEN MARKOV MODELS. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
934-937.
-
Qian, X., & Dougherty, E. R.
(2009).
CONTROL-COMPATIBLE STATE REDUCTION FOR BOOLEAN NETWORKS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
41-42.
-
Qian, X., & Dougherty, E. R.
(2008).
A New Sensitivity Measure for Probabilistic Boolean Networks based on Steady-State Distributions. 136-139.
-
Joshi, A., Qian, X., Dione, D. P., Bulsara, K. R., Breuer, C. K., Sinusas, A. J., & Papademetris, X.
(2008).
Effective visualization of complex vascular structures using a non-parametric vessel detection method. IEEE Transactions on Visualization and Computer Graphics.
1603-1610.
-
Qian, X., & Dougherty, E. R.
(2008).
Analytic formulation of optimal structural intervention strategies in Boolean Networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-2.
-
Qian, X., Brennan, M. P., Dione, D. P., Dobrucki, W. L., Jackowski, M. P., Breuer, C. K., Sinusas, A. J., & Papademetris, X.
(2007).
Detection of Complex Vascular Structures using Polar Neighborhood Intensity Profile. Proceedings / IEEE International Conference on Computer Vision. IEEE International Conference on Computer Vision.
1-8.
-
Qian, X., & Tagare, H. D.
(2006).
Overcoming dropout while segmenting cardiac ultrasound images. 105-108.
-
Qian, X., Tagare, H. D., & Tao, Z.
(2006).
Segmentation of Rat Cardiac Ultrasound Images with Large Dropout Regions. Proceedings / CVPR, IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE Computer Society Conference on Computer Vision and Pattern Recognition.
1-8.
-
Qian, X., & Tagare, H. D.
(2005).
Optimal Embedding for Shape Indexing in Medical Image Databases. Lecture Notes in Computer Science.
377-384.
-
Qian, X., Tagare, H. D., & Fulbright, R. K.
(2005).
Re-embedding vs. clustering as shape indexing strategies for medical image databases. Proceedings of SPIE.
144-151.
-
Tagare, H. D., Qian, X., Fulbright, R. K., Long, R., & Antani, S.
(2004).
Shape based retrieval in NHANES II. 776-779.
-
Qian, X., & Tagare, H. D.
(2002).
Optimally Adapted Indexing Trees for Medical Image Databases. Proceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging.
321-324.
-
Zhang, Z., Ren, S., Qian, X., & Duffield, N.
Learning Flexible Time-windowed Granger Causality Integrating Heterogeneous Interventional Time Series Data. 4408-4418.
-
Zhang, Z., Ren, S., Qian, X., & Duffield, N.
Towards Invariant Time Series Forecasting in Smart Cities. 1344-1350.
-
Bin Abdul Qayyum, A., Qian, X., & Yoon, B.
(2023).
Enhancing Cryo-EM Particle Picking Through Consistency Model-based Latent Space Denoiser. 1-1.
-
institutional repository document
-
Niyakan, S., Yoon, B., Qian, X., & Luo, X.
(2024).
Biologically Interpretable VAE with Supervision for Transcriptomics Data Under Ordinal Perturbations
-
Niyakan, S., Sheng, J., Cao, Y., Zhang, X., Xu, Z., Wu, L., Wong, S., & Qian, X.
(2023).
MUSTANG: MUlti-sample Spatial Transcriptomics data ANalysis with cross-sample transcriptional similarity Guidance
-
Niu, P., Soto, M. J., Huang, S., Yoon, B., Dougherty, E. R., Alexander, F. J., Blaby, I., & Qian, X.
(2022).
Sensitivity analysis of genome-scale metabolic flux prediction
-
Wells, K., He, K., Pandey, A., Cabello, A., Zhang, D., Yang, J., ... de Figueiredo, P.
(2021).
Diverse pathogens activate the host RIDD pathway to subvert BLOS1-directed immune defense
-
Niu, P., Soto, M. J., Yoon, B., Dougherty, E. R., Alexander, F. J., Blaby, I., & Qian, X.
(2021).
TRIMER: Transcription Regulation Integrated with MEtabolic Regulation
-
Niyakan, S., Yoon, B., Qian, X., & Luo, X.
(2024).
Biologically Interpretable VAE with Supervision for Transcriptomics Data Under Ordinal Perturbations
Research
principal investigator on
- III: Small: Collaborative Research: Combinatorial Collaborative Clustering for Simultaneous Patient Stratification and Biomarker Identification awarded by National Science Foundation - (Arlington, Virginia, United States) 2018 - 2021
- CAREER: Knowledge-driven Analytics, Model Uncertainty, and Experiment Design awarded by National Science Foundation - (Arlington, Virginia, United States) 2016 - 2021
- AF:Small: Collaborative Research: Personalized Environmental Monitoring of Type 1 Diabetes (T1D): A Dynamic System Perspective awarded by National Science Foundation - (Arlington, Virginia, United States) 2017 - 2020
- EAGER: Collaborative Research: Tracking of KOR1 Protein Transport in Arabidopsis using Fluorescent-Timer Imaging System awarded by National Science Foundation - (Arlington, Virginia, United States) 2015 - 2017
- EAGER: Identifying Blockmodel Functional Modules across Multiple Networks awarded by National Science Foundation - (Arlington, Virginia, United States) 2014 - 2017
- Identifying Risk Factors and Interactions for Type 1 Diabetes in Large Studies awarded by National Institutes of Health - (Bethesda, Maryland, United States) 2013 - 2016
- International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2015) awarded by National Science Foundation - (Arlington, Virginia, United States) 2015
co-principal investigator on
- Context-Aware Biomarker Discovery and Health Monitoring by Adaptive Integration of Heterogeneous Smartphone Signals awarded by United States Air Force - (Arlington, Virginia, United States) 2018 - 2022
- Elements: Software: Autonomous, Robust, and Optimal In-Silico Experimental Design Platform for Accelerating Innovations in Materials Discovery awarded by National Science Foundation - (Arlington, Virginia, United States) 2018 - 2021
- DMREF: Accelerating the Development of High Temperature Shape Memory Alloys awarded by National Science Foundation - (Arlington, Virginia, United States) 2015 - 2019
- Quantifying Performance for Classification based on Multi-Gene Dynamics Relative to the Number of Simultaneously Measured Live-Cell Expression Levels awarded by Brookhaven National Laboratory - (Upton, New York, United States) 2018
- International Workshop on Computational Network Biology: Modeling,-Analysis, and Control (CNB-MAC 2016) awarded by National Science Foundation - (Arlington, Virginia, United States) 2016 - 2017
Teaching
teaching activities
- CSCE491 Hnr-research Instructor
- ECEN303 Random Signals & Systems Instructor
- ECEN333 Interface Eng & Life Science Instructor
- ECEN491 Research Instructor
- ECEN684 Professional Internship Instructor
- ECEN684 Professional Internshp-in Ab Instructor
- ECEN685 Directed Studies Instructor
- ECEN689 Sptp: Bayesian Deep Learning Instructor
- ECEN689 Sptp: Bdl Discovery Instructor
- ECEN691 Research Instructor
- ECEN765 Mach Learn With Networks Instructor
- ENGR485 Directed Studies Instructor
- ENGR491 Hnr-research Instructor
- ICPE639 Intro Machine Learning Engy Instructor
Works By Students
chaired theses and dissertations
-
Lu, Meng (2015-11). Probabilistic Models for Aggregate Analysis of Non-Gaussian Data in Biomedicine.
-
Wan, Qing (2016-04). Directed Information and Its Biomedical Applications.
-
Wang, Yijie (2015-08). Module Identification for Biological Networks.
-
Wang, Zhou (2016-12). Structured Rule Discovery from Heterogeneous Longitudinal Data for Complex Disease.
Background
education and training
awards and honors
Contact
first name
- Xiaoning
has last name
- Qian
mailing address
-
Texas A&M University
Electrical Engineering
3128 TAMU
College Station, TX 77843-3128
USA
Other
- xqian@tamu.edu