Pengyu Hong

Professor of Computer Science

Departments/Programs

Computer Science
Volen National Center for Complex Systems

Degrees

University of Illinois, Urbana-Champaign, Ph.D.
Tsinghua University, M.S.
Tsinghua University, B.S.

Expertise

Machine Learning, Image Processing, Glycomaterials, Materials Research, Bioinformatics and Biomedical Informatics, FinTech, Intelligent Education

Profile

Dr. Hong’s main research focus on Machine Learning and its applications in Bioinformatics, Biomedical Informatics, Materials Research, FinTech, and Intelligent Education. His lab has developed novel advanced techniques to analyze heterogeneous data, such as, image, video, text, audio, financial data, and so on. He participated into organizing several international conferences. His main contributions include pioneering in developing high-content neuronal screening techniques, pioneering in develop Machine Learning techniques for de novo glycan sequencing using mass spectrometry technology, integrating heterogeneous biological data to automatically infer multi-cellular regulatory networks, detect protein-protein interactions by analyzing Mass Spectrometry data, electronic healthcare record analysis, machine-learning driven image retrieval, audio-driven face animation, probabilistic reasoning in multi-modal human-computer interfaces. He has published ~30 papers in prestigious journals. Webpage

Courses Taught

COSI	101a	Fundamentals of Artificial Intelligence
COSI	123a	Statistical Machine Learning
COSI	149b	Practical Machine Learning with Big Data
COSI	178a	Computational Molecular Biology

Scholarship

Du, H., Chen, F., Liu, H., Hong, P.. "Network-based Virus-Host Interaction Prediction with Application to SARS-CoV-2." Cell Patterns (2021). (forthcoming)

Li, P., Wang, Y., Zhao, H., Hong, P., and Liu, H.. "On Dyadic Fairness: Exploring and Mitigating Bias in Graph Connections." International Conference on Learning Representations, Vienna, Austria. May 4, 2021 – May 8, 2021. (forthcoming)

Yang, T., Sha, L., Li, J. and Hong, P.. "A Deep Learning Approach for COVID-19 Trend Prediction." International Workshop on Epidemiology Meets Data Mining and Knowledge Discovery, San Diego, CA, USA. August 24, 2020.

Vimal, V. P., Zheng, H., Hong, P., Fakharzadeh, L. N., Lackner, J. R., DiZio, P.. "Characterizing Individual Differences in a Dynamic Stabilization Task using Machine Learning." Aerospace Medicine and Human Performance (2020).

Xing, X., Sha, L., Hong, P., Shang, Z., Liu, J.S.. "Probabilistic Connection Importance Inference and Lossless Compression of Deep Neural Networks." International Conference on Learning Representations, Addis Ababa, ETHIOPIA. 04/26/2020 - 04/30/2020.

Yang, T., Sha, L., and Hong, P.. "NagE: Non-Abelian Group Embedding for Knowledge Graphs." ACM International Conference on Information and Management, 2020.

Yoong, L. F., Lim, H. K., Tran, H., Lackner, S., Zheng, Z., Hong, P., Moore, A. W.. "Atypical Myosin Tunes Dendrite Arbor Subdivision." Neuron 106. (2020): 1–16.

Zhao, R., Hong, P., and Liu, J.S.. "IMMIGRATE: A Margin-based Feature Selection Method with Interaction Terms." Entropy 22. 3 (2020): 291.

Zhou, Z., Joshi, C., Liu, R., Norton, M. M., Lemma, L., Dogic, Z., Hagan, M. F., Fraden, S., and Hong, P.. "Machine Learning Forecasting of Active Nematics." Soft Matter (2020).

Wang, L., Sha, L, Lakin, J. R., Bynum, J., Bates, D. W., Hong, P., Zhou, L.. "Development and Validation of a Deep Learning Algorithm for Mortality Prediction in Selecting Patients with Dementia for Earlier Palliative Care Interventions." JAMA Network Open 2. 7 (2019): e196972.

Wei, J., Tang, Y., Bai, Y., Zaia, J., Costello, C., Hong, P., Lin, C.. "Towards Automatic and Comprehensive Glycan Characterization by On-line PGC-LC-EED MS/MS." American Chemical Society. 92. 1 (2019): 782-791.

Tang Y., Pu Y., Gao J., Hong P., Costello C.E., and Lin C.. "De Novo Glycan Sequencing by Electronic Excitation Dissociation and Fixed-Charge Derivatization." Analytical Chemistry 10.1021/acs.analchem.7b04077. (2018).

Zheng, Zhihao; Hong, Pengyu. "Robust Detection of Adversarial Attacks by Modeling the Intrinsic Properties of Deep Neural Networks." Neural Information Processing Systems, Montreal, Canada. 12/3/2018 - 12/8/2018.

Bei, Yuanzhe and Hong, Pengyu. "Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes." BMC Bioinformatics 17. 541 (2017): DOI: 10.1186/s12859-016-1386-x.

Hong P., Sun H., Sha L., Pu Y., Khatri K., Yu X., Tang Y., Lin C.. "GlycoDeNovo -- an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra." Journal of The American Society for Mass Spectrometry 28. 11 (2017): 2288-2301.

Sha L. and Hong P.. "Neural Knowledge Tracing." International Conference on Brain Function Assessment in Learning, Patras, Greece. Sep. 07, 2017.

Vinayagam A., Kulkarni M.K., Sopko R., Sun X., Hu Y., Nand A., Villalta C., Moghimi A., Yang X., Mohr S.E., Hong P., Asara J.M., Perrimon N.. "An Integrative Analysis of the InR/PI3K/Akt Network Identifies the Dynamic Response to Insulin Signaling." Cell Reports 16. 11 (2017): 3062–3074.

Zheng, Zhihao and Hong, Pengyu. "Incorporate Deep-Transfer-Learning into Automatic 3D Neuron Tracing." International Conference on Neuroscience and Cognitive Brain Information, Barcelona, Spain. November 13 - 17, 2016.

Bei, Yuanzhe and Hong, Pengyu. "Maximizing Margin Quality and Quantity." IEEE International Workshop on Machine Learning for Signal Processing, Boston. September 17-20, 2015.

Breitkopf S.B., Yang X., Begley M., Kulkarni M., Chiu Y., Turke A., Lauriol J., Yuan M., Qi J., Engelman J.A., Hong P., Kontaridis M.I., Cantley L.c., Perrimon N. Asara J.M.. "A Cross-Species Study of PI3K Protein-Protein Interactions Reveals the Direct Interaction of P85 and SHP2." Scientific Reports 6. 20471 (2016): DOI: 10.1038.

Bei Y. and Hong P.. "Psychiatric Insights into Liver Cirrhosis and Their Correlations with Traditional Chinese Medicine Diagnostics." IEEE International Conference on Bioinformatics and Biomedicine 2013, Shanghai, China. 12/18/2013 - 12/21/2013.

Bei Y. and Hong P.. "Significance Analysis by Minimizing False Discovery Rate." The IEEE International Conference on Bioinformatics and Biomedicine., Philadelphila, PA, USA. October 2012.

Bei, Yuanzhe and Hong, Pengyu. "A Novel Approach to Minimize False Discovery Rate in Significance Analysis." BMC Systems Biology 7. Suppl 4 (2013): S1.

Kwon Y., Vinayagam A., Sun X., Dephoure N., Gygi S.P., Hong P., and Perrimon P.. "The Hippo Signaling Pathway Interactome." Science 342. 6159 (2013): 737-740.

Sun X., Hong P., Kulkarni M., Kwon Y. and Perrimon N.. "PPIRank - an advanced method for ranking protein-protein interations in TAP/MS data." Proteome Science 11. Suppl 1 (2013): S16.

Sun X., Hong P., Kulkarni M., Kwon Y., and Perrimon N.. "An Advanced Method for Identifying Protein-Protein Interaction by Analyzing TAP/MS Data." The IEEE International Conference on Bioinformatics and Biomedicine, Philadelphila, PA USA. October 2012.

Anick, P., Hong, P., Xue, N. & Yang, Y.. "Coreference resolution for electronic medical records." the 2011 i2b2/VA/Cincinnati Workshop on Challenges in Natural Language Processing for Clinical Data, Washington, DC.. Oct 22, 2011.

Friedman AA., Tucker G., Singh R., Yan D., Vinayagam A., Hu Y., Binari R., Hong P., Sun X., Porto M., Pacifico S., Murali T., Finley Jr. R. L., Asara J. M., Berger B., Perrimon N.. "Proteomic and Functional Genomic Landscape of Receptor Tyrosine Kinase and Ras to Extracellular Signal–Regulated Kinase Signaling." Science Signaling 4. 196 (2011): p. rs10.

Schulte J., Sepp K. J., Wu C., Hong P., Littleton J. T.. "High-Content Chemical and RNAi Screens for Suppressors of Neurotoxicity in a Huntington's Disease Model." PLoS One 6. 8 (2011): e23841..

Shang Y., Haynes P., Pírez N., Harrington K. I., Guo F., Pollack J., Hong P., Griffith L. C., and Rosbash M.. "Imaging analysis of clock neurons: light buffers the wake-promoting effect of dopamine." Nature Neuroscience 14. (2011): 889–895.

Warner J. L., Anick P., Hong P., and Xue N.. "Natural Language Processing and the Oncologic History: Is There a Match?." Journal of Oncology Practice 7. 4 (2011): e15-e19.

Asara, J., Kulkarni, M., Friedman, A., Yang, X., Hong, P., Engelman, J., and Perrimon, N.. ""Interact-ome" of Components in the Insulin Signaling Pathway in Drosophila and Compared to Human Cancer Cells." US HUPO Proteomics -- from Bench to Clinic, Denver, Colorado, USA. March 7 - 10, 2010.

Li L., Karabacak1 N.M., Cobb J.S., Wang Q., Hong P., Agar1 J.N.. "Memory-efficient calculation of the isotopic mass states of a molecule." Rapid Communications in Mass Spectrometry 24. 18 (2010): 2689-2696.

Lin C., Hong P., Bakal C., and Perrimon N.. "Novel Morphological Phenotypes Discovery in High-Content Screens Using Underused Features.." International Conference on Bioinformatics and Computational Biology, Honolulu, Hawaii, USA. March 24-26, 2010.

Peter Anick, Pengyu Hong, Nianwen Xue, David Anick. "I2B2 2010 Challenge: Machine Learning for Information Extraction from Patient Records." Fourth i2b2/VA Shared-Task and Workshop Challenges in Natural Language Processing for Clinical Data, Washington, DC. November 2010.

Schoemans R., Aigrot M.S., Wu C., Marée R., Hong P., Belachew S., Josse C., Lubetzki C. and Bours V.. "Oligodendrocyte development and myelinogenesis are not impaired by high concentrations of phenylalanine or its metabolites." Journal of Inherited Metabolism Disease (2010).

Schulte J., Sepp K., Jorquera R., Wu C., Song Y., Hong P., and Littleton J.T.. "DMob4/Phocein regulates synapse formation, axonal transport, and microtubule organization." Journal of Neuroscience (2010).

Wu C., Schulte J., Sepp K.J., Littleton J.T., and Hong P.. "Automatic Robust Neurite Detection and Morphological Analysis of Optical Microscopy Neuron Cell Culture Images in High-Content Screening." Neuroinformatics (2010).

Karabacak N.M., Li L., Tiwari A., Hayward L.J., Hong P., Easterling M.L., and Agar A.N.. "Sensitive and specific identification of wild-type and variant proteins from 8 to 669 kDa using top-down mass spectrometry." Molecular & Cellular Proteomics 8. 4 (2009): 846-856.

Sun X. and Hong P.. "Automatic Inference of Multicellular Regulatory Networks Using Informative Priors." International Journal of Computational Biology and Drug Design 2. 2 (2009): 115-133.

Karabacak NM, Li L, Tiwari A, Hayward LJ, Hong P, Easterling ML, and Agar AN. "Sensitive and specific identification of wild-type and variant proteins from 8 to 669 kDa using top-down mass spectrometry." Molecular & Cellular Proteomics (2008).

Li L, Kresh JA, Karabacak NM, Cobb JS, Agar JN, and Hong P. "A Hierarchical Algorithm for Calculating the Isotopic Fine Structures of Molecules." Journal of the American Society for Mass Spectrometry 19. 12 (2008): 1867-1874.

Li L., Kresh J.A., Karabacak N.M., Cobb J.S., Agar J.N., and Hong P.. "A Hierarchical Algorithm for Calculating the Isotopic Fine Structures of Molecules." Journal of the American Society for Mass Spectrometry 19. 12 (2008): 1867-1874.

Lin C, Mak W, Hong P, Sepp K, Perrimon N.. "Intelligent Interfaces for Mining Large-Scale RNAi-HCS Image Databases." IEEE International Symposium on Bioinformatics and Bioengineering, Boston, MA, USA. October 14-17, 2007.

Sepp K.J., Hong P., Lizarraga S.B., Liu J.S., Mejia L.A., Walsh C.A., and Perrimon N.. "Identification of neural outgrowth genes using genome-wide RNAi.." PLoS Genet. 4. 7 (2008).

Zhou R., Hotta I., Denli A.M., Hong P., Perrimon N., and Hannon G.J.. "Comparative Analysis of Argonaute-Dependent Small RNA Pathways in Drosophila." Molecular Cell 32. 4 (2008): 592-599.

Hong, Pengyu. "Interactive Analysis of High-Content Cellular Images via Relevant Feedback.." Workshop on Multiscale Biological Imaging, Data Mining and Informatics, Santa Barbara, CA, USA.. Sep 7-8.

Sun, Xiaoyun and Hong, Pengyu. "Computational modeling of Caenorhabditis elegans vulval induction.." Bioinformatics 12. 23 (2007): i499-507.

Kulkarni, M. M., Booker, M., Silver, S. J., Friedman, A., Hong, P., Perrimon, N., Mathey-Prevot, B.. "Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays." Nature Methods 3. 10 (2006): 833-838.