Ricardo Henao | Scholars@Duke

Ricardo Henao
Assistant Professor in Biostatistics and Bioinformatics

Current Appointments & Affiliations

Assistant Professor in Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2017
Assistant Professor in the Department of Electrical and Computer Engineering, Electrical and Computer Engineering, Pratt School of Engineering 2018
Member of the Duke Clinical Research Institute, Duke Clinical Research Institute, Institutes and Centers 2017

Contact Information

2400 Pratt Street, 8044 North Pavilion, Durham, NC 27705
Duke Box 3850, Durham, NC 27710
ricardo.henao@duke.edu (919) 668-0647

Background
Education, Training, & Certifications
- Ph.D., Technical University of Denmark (Denmark) 2011
Duke Appointment History
- Assistant Research Professor in the Department of Electrical and Computer Engineering, Electrical and Computer Engineering, Pratt School of Engineering 2015 - 2017
Recognition
In the News
- MAR 16, 2016
  
  New Collaborative Seed Grant Program Gives Eight Awards
Research
Selected Grants
- Non-Invasive Diagnosis of Pediatric Pulmonary Invasive Mold Infections awarded by National Institutes of Health 2018 - 2023
- Postdoctoral Training in Genomic Medicine Research awarded by National Institutes of Health 2017 - 2022
- QuBBD: Deep Poisson Methods for Biomedical Time-to-Event and Longitudinal Data awarded by National Institutes of Health 2017 - 2020
- Novel host-based diagnostics of febrile illness in the warfighter awarded by Department of Defense 2016 - 2019
- Host-derived biomarker signatures to differentiate acute viral, bacterial, and fungal infection awarded by National Institutes of Health 2017 - 2019
- PREdicting contagion using Systems And GEnomic analysis (PRESAGE) awarded by Defense Advanced Research Projects Agency 2017 - 2019
- Development and Application of Mathematical Methods for Tracking Biochronicity and Baseline Variation awarded by Defense Advanced Research Projects Agency 2016 - 2018
- Role of the Stroma in Fibrolamellar Hepatocellular Carcinoma awarded by Fibrolamellar Cancer Foundation 2016 - 2018
- Deep learning driven angiographic analysis to enhance evaluation of coronary artery stenosis awarded by Vigilant Medical 2018
- CTOT Ancillary Studies Fund Carry Forward BAL awarded by Mount Sinai School of Medicine 2016 - 2017
- Hyaluronan in Acute Rejection and Chronic Lung Allograft Dysfunction after Human Lung Transplantation awarded by Mount Sinai School of Medicine 2016 - 2017
- HARDAC+:Reproducible HPC for next-generation genomics awarded by North Carolina Biotechnology Center 2016 - 2017
- Feasibility for Predicting Warfighter Health Using Transcriptional Markers on the MAP Platform awarded by Ibis Biosciences, Inc. 2016
Publications & Artistic Works
Selected Publications
- Book Sections
  - Gan, Z, Yuan, X, Henao, R, Tsalik, EL, and Carin, L. "Inference of gene networks associated with the host response to infectious disease." Big Data over Networks. Ed. S Cui, AOH III, Z-Q Luo, and JMF Moura. Cambridge University Press, 2016. 365-390.
- Conference Papers
  - Fan, K, Zhang, Y, Henao, R, and Heller, K. "Triply stochastic variational inference for non-linear beta process factor analysis." January 31, 2017. Full Text
  - Zhang, Y, Zhao, Y, David, L, Henao, R, and Carin, L. "Dynamic poisson factor analysis." January 31, 2017. Full Text
  - Gan, Z, Pu, Y, Henao, R, Li, C, He, X, and Carin, L. "Learning Generic Sentence Representations Using Convolutional Neural Networks." Association for Computational Linguistics, 2017.
  - Komives, E, Rusincovitch, SA, Paat, J, Carin, L, Costello, D, Gao, M, Hammill, BG, Henao, R, Neely, NB, Rogers, U, Sangvai, D, Schilder, M, and Huang, E. "Guiding Principles for the Duke Connected Care Predictive Modeling Pilot." AMIA, 2017.
  - Li, C, Liu, H, Chen, C, Pu, Y, Chen, L, Henao, R, and Carin, L. "ALICE: Towards Understanding Adversarial Learning for Joint Distribution Matching." 2017.
  - Li, C, Liu, H, Chen, C, Pu, Y, Chen, L, Henao, R, and Carin, L. "ALICE: Towards understanding adversarial learning for joint distribution matching." January 1, 2017.
  - Pu, Y, Gan, Z, Henao, R, Li, C, Han, S, and Carin, L. "VAE Learning via Stein Variational Gradient Descent." 2017.
  - Pu, Y, Gan, Z, Henao, R, Li, C, Han, S, and Carin, L. "VAE learning via Stein variational gradient descent." January 1, 2017.
  - Pu, Y, Wang, W, Henao, R, Chen, L, Gan, Z, Li, C, and Carin, L. "Adversarial Symmetric Variational Autoencoder." 2017.
  - Rusincovitch, SA, Henao, R, Gao, M, Carin, L, Rogers, U, Neely, NB, Schilder, M, Costello, D, Komives, E, and Huang, E. "Rationale and Design for the Duke Connected Care Predictive Modeling Pilot with a Medicare Shared Savings Program Population." AMIA, 2017.
  - Zhang, Y, Chen, C, Gan, Z, Henao, R, and Carin, L. "Stochastic Gradient Monomial Gamma Sampler." PMLR, 2017.
  - Zhang, Y, Gan, Z, Fan, K, Chen, Z, Henao, R, Shen, D, and Carin, L. "Adversarial Feature Matching for Text Generation." PMLR, 2017.
  - Zhang, Y, Shen, D, Wang, G, Gan, Z, Henao, R, and Carin, L. "Deconvolutional Paragraph Representation Learning." 2017.
  - Patel, YA, Henao, R, Moylan, CA, Guy, CD, Piercy, DL, Diehl, AM, and Abdelmalek, MF. "Vitamin D is Not Associated with Histologic Severity in NAFLD: Results of a Paired Clinical and Hepatic Gene Expression Profile Analysis." October 2016. Link to Item
  - Wegermann, K, Henao, R, Pan, Y, Diehl, AM, Abdelmalek, MF, and Moylan, CA. "BCAT1 is Associated with Clinical Decompensation in NAFLD: A Pilot Study." October 2016. Link to Item
  - Pu, Y, Gan, Z, Henao, R, Yuan, X, Li, C, Stevens, A, and Carin, L. "Variational autoencoder for deep learning of images, labels and captions." January 1, 2016.
  - Pu, Y, Gan, Z, Henao, R, Yuan, X, Li, C, Stevens, A, and Carin, L. "Variational Autoencoder for Deep Learning of Images, Labels and Captions." 2016.
  - Song, Z, Henao, R, Carlson, DE, and Carin, L. "Learning Sigmoid Belief Networks via Monte Carlo Expectation Maximization." JMLR.org, 2016.
  - Yizhe, Z, Henao, R, Li, C, and Carin, L. "Bayesian dictionary learning with Gaussian processes and sigmoid belief networks." January 1, 2016.
  - Zhang, Y, Chen, C, Henao, R, and Carin, L. "Laplacian Hamiltonian Monte Carlo." January 1, 2016. Full Text
  - Zhang, Y, Wang, X, Chen, C, Henao, R, Fan, K, and Carin, L. "Towards unifying hamiltonian Monte Carlo and Slice sampling." January 1, 2016.
  - Zhang, Y, Wang, X, Chen, C, Henao, R, Fan, K, and Carin, L. "Towards Unifying Hamiltonian Monte Carlo and Slice Sampling." 2016.
  - Henao, R, Hasanaliyeva, N, Bell, LN, Wulff, J, Perichon, R, Moylan, CA, Lu, JT, Guy, CD, Diehl, AM, and Abdelmalek, MF. "Plasma Metabolomic Profiles Predict Advanced Hepatic Fibrosis in Patients with Nonalcoholic Fatty Liver Disease." October 2015. Link to Item
  - Gan, Z, Chen, C, Henao, R, Carlson, D, and Carin, L. "Scalable deep Poisson factor analysis for topic modeling." January 1, 2015.
  - Gan, Z, Henao, R, Carlson, D, and Carin, L. "Learning deep sigmoid belief networks with data augmentation." January 1, 2015.
  - Gan, Z, Li, C, Henao, R, Carlson, DE, and Carin, L. "Deep Temporal Sigmoid Belief Networks for Sequence Modeling." 2015.
  - Henao, R, Gan, Z, Lu, J, and Carin, L. "Deep poisson factor modeling." January 1, 2015.
  - Lian, W, Henao, R, Rao, V, Lucas, J, and Carin, L. "A multitask point process predictive model." January 1, 2015.
  - Raiy, P, Hu, C, Henao, R, and Carin, L. "Large-scale Bayesian multi-label learning via topic-based label embeddings." January 1, 2015.
  - Henao, R, Yuan, X, and Carin, L. "Bayesian nonlinear support vector machines and discriminative factor modeling." January 1, 2014.
  - Ouinones, QJ, Ma, Q, Henao, R, Lucas, J, Riess, ML, Bain, J, Newgard, CB, Barnes, BM, and Podgoreanu, MV. "Proteomnic and Metabolomic Profiling After Isehemia-Reperfusion Injury Reveals Bottlenecks That Underlie Cardioprotection in Hibernating Mammals." November 26, 2013. Link to Item
  - Henao, R, and Winther, O. "Bayesian sparse factor models and DAGs inference and comparison." December 1, 2009.
  - Alvarez, M, Henao, R, Castellanos, G, Godino, JI, Orozco, A, and IEEE, . "Kernel principal component analysis through time for voice disorder classification." 2006. Link to Item
  - Alvarez, M, and Henao, R. "Probabilistic kernel principal component analysis through time." January 1, 2006.
  - Rengifo, CL, Alvarez, DA, Henao, R, Castellanos, G, and Hurtado, JE. "Active learning on the classification of voice pathologies." ISCA, 2004.
- Journal Articles
  - Bradley, T, Peppa, D, Pedroza-Pacheco, I, Li, D, Cain, DW, Henao, R, Venkat, V, Hora, B, Chen, Y, Vandergrift, NA, Overman, RG, Edwards, RW, Woods, CW, Tomaras, GD, Ferrari, G, Ginsburg, GS, Connors, M, Cohen, MS, Moody, MA, Borrow, P, and Haynes, BF. "RAB11FIP5 Expression and Altered Natural Killer Cell Function Are Associated with Induction of HIV Broadly Neutralizing Antibody Responses." Cell 175.2 (October 2018): 387-399.e17. Full Text
  - Sweeney, TE, Azad, TD, Donato, M, Haynes, WA, Perumal, TM, Henao, R, Bermejo-Martin, JF, Almansa, R, Tamayo, E, Howrylak, JA, Choi, A, Parnell, GP, Tang, B, Nichols, M, Woods, CW, Ginsburg, GS, Kingsmore, SF, Omberg, L, Mangravite, LM, Wong, HR, Tsalik, EL, Langley, RJ, and Khatri, P. "Unsupervised Analysis of Transcriptomics in Bacterial Sepsis Across Multiple Datasets Reveals Three Robust Clusters." Critical Care Medicine 46.6 (June 2018): 915-925. Full Text
  - Sweeney, TE, Perumal, TM, Henao, R, Nichols, M, Howrylak, JA, Choi, AM, Bermejo-Martin, JF, Almansa, R, Tamayo, E, Davenport, EE, Burnham, KL, Hinds, CJ, Knight, JC, Woods, CW, Kingsmore, SF, Ginsburg, GS, Wong, HR, Parnell, GP, Tang, B, Moldawer, LL, Moore, FE, Omberg, L, Khatri, P, Tsalik, EL, Mangravite, LM, and Langley, RJ. "A community approach to mortality prediction in sepsis via gene expression analysis." Nature Communications 9.1 (February 15, 2018): 694-null. Full Text
  - Shen, D, Su, Q, Chapfuwa, P, Wang, W, Wang, G, Carin, L, and Henao, R. "NASH: Toward End-to-End Neural Architecture for Generative Semantic Hashing." Corr abs/1805.05361 (2018). Open Access Copy
  - Wegermann, K, Henao, R, Diehl, AM, Murphy, SK, Abdelmalek, MF, and Moylan, CA. "Branched chain amino acid transaminase 1 (BCAT1) is overexpressed and hypomethylated in patients with non-alcoholic fatty liver disease who experience adverse clinical events: A pilot study." Plos One 13.9 (January 2018): e0204308-null. Full Text
  - Zhang, X, Henao, R, Gan, Z, Li, Y, and Carin, L. "Multi-Label Learning from Medical Plain Text with Convolutional Residual Models." CoRR abs/1801.05062 (2018).
  - Hald, DH, Henao, R, and Winther, O. "Gaussian process based independent analysis for temporal source separation in fMRI." NeuroImage 152 (May 2017): 563-574. Full Text
  - Patel, YA, Henao, R, Moylan, CA, Guy, CD, Piercy, DL, Diehl, AM, and Abdelmalek, MF. "Reply to Kim et al." The American journal of gastroenterology 112.5 (May 2017): 807-808. Full Text
  - Burke, TW, Henao, R, Soderblom, E, Tsalik, EL, Thompson, JW, McClain, MT, Nichols, M, Nicholson, BP, Veldman, T, Lucas, JE, Moseley, MA, Turner, RB, Lambkin-Williams, R, Hero, AO, Woods, CW, and Ginsburg, GS. "Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection." Ebiomedicine 17 (March 2017): 172-181. Full Text
  - Li, C, Liu, H, Chen, C, Pu, Y, Chen, L, Henao, R, and Carin, L. "Towards Understanding Adversarial Learning for Joint Distribution Matching." CoRR abs/1709.01215 (2017).
  - Pu, Y, Gan, Z, Henao, R, Li, C, Han, S, and Carin, L. "Stein Variational Autoencoder." CoRR abs/1704.05155 (2017).
  - Pu, Y, Wang, W, Henao, R, Chen, L, Gan, Z, Li, C, and Carin, L. "Adversarial symmetric variational autoencoder." Advances in Neural Information Processing Systems 2017-December (January 1, 2017): 4331-4340.
  - Shen, D, Zhang, Y, Henao, R, Su, Q, and Carin, L. "Deconvolutional Latent-Variable Model for Text Sequence Matching." CoRR abs/1709.07109 (2017).
  - Zhang, Y, Chen, C, Gan, Z, Henao, R, and Carin, L. "Stochastic gradient monomial gamma sampler." 34th International Conference on Machine Learning, Icml 2017 8 (January 1, 2017): 6083-6092.
  - Zhang, Y, Gan, Z, Fan, K, Chen, Z, Henao, R, Shen, D, and Carin, L. "Adversarial Feature Matching for Text Generation." CoRR abs/1706.03850 (2017).
  - Zhang, Y, Shen, D, Wang, G, Gan, Z, Henao, R, and Carin, L. "Deconvolutional Paragraph Representation Learning." CoRR abs/1708.04729 (2017).
  - Patel, YA, Henao, R, Moylan, CA, Guy, CD, Piercy, DL, Diehl, AM, and Abdelmalek, MF. "Vitamin D is Not Associated With Severity in NAFLD: Results of a Paired Clinical and Gene Expression Profile Analysis." The American Journal of Gastroenterology 111.11 (November 2016): 1591-1598. Full Text
  - Henao, R, Lu, JT, Lucas, JE, Ferranti, J, and Carin, L. "Electronic health record analysis via deep poisson factor models." Journal of Machine Learning Research 17 (April 1, 2016).
  - McClain, MT, Henao, R, Williams, J, Nicholson, B, Veldman, T, Hudson, L, Tsalik, EL, Lambkin-Williams, R, Gilbert, A, Mann, A, Ginsburg, GS, and Woods, CW. "Differential evolution of peripheral cytokine levels in symptomatic and asymptomatic responses to experimental influenza virus challenge." Clinical and Experimental Immunology 183.3 (March 2016): 441-451. Full Text
  - Gan, Z, Pu, Y, Henao, R, Li, C, He, X, and Carin, L. "Unsupervised Learning of Sentence Representations using Convolutional Neural Networks." CoRR abs/1611.07897 (2016).
  - Tsalik, EL, Henao, R, Nichols, M, Burke, T, Ko, ER, McClain, MT, Hudson, LL, Mazur, A, Freeman, DH, Veldman, T, Langley, RJ, Quackenbush, EB, Glickman, SW, Cairns, CB, Jaehne, AK, Rivers, EP, Otero, RM, Zaas, AK, Kingsmore, SF, Lucas, J, Fowler, VG, Carin, L, Ginsburg, GS, and Woods, CW. "Host gene expression classifiers diagnose acute respiratory illness etiology." Science Translational Medicine 8.322 (January 2016): 322ra11-null. Full Text Open Access Copy
  - Zhang, Y, Henao, R, Carin, L, Zhong, J, and Hartemink, AJ. "Learning a hybrid architecture for sequence regression and annotation." 30th AAAI Conference on Artificial Intelligence, AAAI 2016 (January 1, 2016): 1415-1421. Open Access Copy
  - Gan, Z, Li, C, Henao, R, Carlson, D, and Carin, L. "Deep temporal sigmoid belief networks for sequence modeling." Advances in Neural Information Processing Systems 2015-January (January 1, 2015): 2467-2475.
  - Vikeså, J, Møller, AKH, Kaczkowski, B, Borup, R, Winther, O, Henao, R, Krogh, A, Perell, K, Jensen, F, Daugaard, G, and Nielsen, FC. "Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin." Bmc Cancer 15 (January 2015): 151-null. Full Text
  - Yuan, X, Henao, R, Tsalik, EL, Langley, RJ, and Carin, L. "Non-Gaussian discriminative factor models via the max-margin rank-likelihood." 32nd International Conference on Machine Learning, ICML 2015 2 (January 1, 2015): 1254-1263. Open Access Copy
  - Tsalik, EL, Langley, RJ, Dinwiddie, DL, Miller, NA, Yoo, B, van Velkinburgh, JC, Smith, LD, Thiffault, I, Jaehne, AK, Valente, AM, Henao, R, Yuan, X, Glickman, SW, Rice, BJ, McClain, MT, Carin, L, Corey, GR, Ginsburg, GS, Cairns, CB, Otero, RM, Fowler, VG, Rivers, EP, Woods, CW, and Kingsmore, SF. "An integrated transcriptome and expressed variant analysis of sepsis survival and death." Genome Medicine 6.11 (January 2014): 111-null. Full Text Open Access Copy
  - Benjamin, AM, Thompson, JW, Soderblom, EJ, Geromanos, SJ, Henao, R, Kraus, VB, Moseley, MA, and Lucas, JE. "A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information." BMC bioinformatics 14 (December 16, 2013): 364-. Full Text Open Access Copy
  - Kurokawa, M, Kim, J, Geradts, J, Matsuura, K, Liu, L, Ran, X, Xia, W, Ribar, TJ, Henao, R, Dewhirst, MW, Kim, W-J, Lucas, JE, Wang, S, Spector, NL, and Kornbluth, S. "A network of substrates of the E3 ubiquitin ligases MDM2 and HUWE1 control apoptosis independently of p53." Science Signaling 6.274 (May 7, 2013): ra32-null. Full Text Open Access Copy
  - Henao, R, Murray, J, Ginsburg, G, Carin, L, and Lucas, JE. "Patient clustering with uncoded text in electronic medical records." AMIA Annual Symposium Proceedings 2013 (January 2013): 592-599.
  - Henao, R, and Winther, O. "Predictive active set selection methods for Gaussian processes." Neurocomputing 80 (March 2012): 10-18. Full Text
  - Rossing, M, Borup, R, Henao, R, Winther, O, Vikesaa, J, Niazi, O, Godballe, C, Krogdahl, A, Glud, M, Hjort-Sørensen, C, Kiss, K, Bennedbæk, FN, and Nielsen, FC. "Down-regulation of microRNAs controlling tumourigenic factors in follicular thyroid carcinoma." Journal of molecular endocrinology 48.1 (February 2012): 11-23. Full Text
  - Carin, L, Hero, A, Lucas, J, Dunson, D, Chen, M, Heñao, R, Tibau-Puig, A, Zaas, A, Woods, CW, and Ginsburg, GS. "High-Dimensional Longitudinal Genomic Data: An analysis used for monitoring viral infections." Ieee Signal Processing Magazine 29.1 (January 2012): 108-123. Full Text
  - Henao, R, Thompson, JW, Moseley, MA, Ginsburg, GS, Carin, L, and Lucas, JE. "Hierarchical factor modeling of proteomics data." 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012 (2012). Full Text
  - Friis, M, Martin-Bertelsen, T, Friis-Hansen, L, Winther, O, Henao, R, Sørensen, MS, and Qvortrup, K. "Gene expression of the endolymphatic sac." Acta Oto Laryngologica 131.12 (December 2011): 1257-1263. Full Text
  - Henao, R, and Winther, O. "Sparse linear identifiable multivariate modeling." Journal of Machine Learning Research 12 (March 1, 2011): 863-905.
  - Henao, R, and Winther, O. "PASS-GP: Predictive active set selection for Gaussian processes." Proceedings of the 2010 IEEE International Workshop on Machine Learning for Signal Processing, MLSP 2010 (November 24, 2010): 148-153. Full Text
  - Borup, R, Rossing, M, Henao, R, Yamamoto, Y, Krogdahl, A, Godballe, C, Winther, O, Kiss, K, Christensen, L, Høgdall, E, Bennedbaek, F, and Nielsen, FC. "Molecular signatures of thyroid follicular neoplasia." Endocrine-related cancer 17.3 (September 2010): 691-708. Full Text
  - Walder, C, Henao, R, Mørup, M, and Hansen, LK. "Semi-Supervised Kernel PCA." CoRR abs/1008.1398 (2010).
  - Alvarez López, MA, Henao, R, and Orozco, A. "Myocardial ischemia detection using Hidden Markov principal component analysis." IFMBE Proceedings 18 (January 1, 2008): 99-103. Full Text
  - Alvarez, M, Henao, R, Castellanos, G, Godino, JI, and Orozco, A. "Kernel Principal Component analysis through time for voice disorder classification." Conference proceedings : .. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference 1 (January 2006): 5511-5514. Full Text
  - Alvarez, M, Henao, R, Castellanos, G, Godino, JI, and Orozco, A. "Kernel Principal Component analysis through time for voice disorder classification." Conference proceedings : .. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference (2006): 5511-5514.
  - Henao, R, Thompson, JW, Moseley, MA, Ginsburg, GS, Carin, L, and Lucas, JE. "Latent protein trees." Annals of Applied Statistics 7.2: 691-713. Full Text Open Access Copy Link to Item
  - Henao, R, and Lucas, JE. "Efficient hierarchical clustering for continuous data." Link to Item
Teaching & Mentoring
Recent Courses
- ECE 899: Special Readings in Electrical Engineering 2017
Scholarly, Clinical, & Service Activities
Outreach & Engaged Scholarship
- Bass Connections Faculty Team Member. Data+. June 2016 - July 2016 2016

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Education, Training, & Certifications

Duke Appointment History

In the News

Selected Grants

Selected Publications

Book Sections

Conference Papers

Journal Articles

Recent Courses

Outreach & Engaged Scholarship