Journal
- Li, Y., Zarei, Z., Tran, P., Wang, Y., Baskaran, A., Fraden, S., Hagan, M.F., Hong, P. A Machine Learning Approach to Robustly Determine Director Fields and Analyze Defects in Active Nematics. Soft Matter 2024. DOI: 10.1039/D3SM01253K
- Ni, Y., Murray, N.B., Archer-Hartmann, S., Pepi, L.E., Helm, R.F., Azadi, P., Hong, P. Toward Automatic Inference of Glycan Linkages Using MSn and Machine Learning - Proof of Concept Using Sialic Acid Linkages. Journal of the American Society for Mass Spectrometry 2023. DOI: 10.1021/jasms.3c00132s
- Wang, Y.; Chen, S.; Chen, G.; Shurberg, E.; Liu, H.; Hong, P. Motif-Based Graph Representation Learning with Application to Chemical Molecules. Informatics 2023, 10, 8. DOI: 10.3390/informatics10010008
- Yue, H., Hong, P., Liu, H. (2022). Graph-Graph Similarity Network. IEEE Transactions on Neural Networks and Learning Systemss. PMID: 36374897. DOI: 10.1109/TNNLS.2022.3218936
- Yang, T., Wang, Y., Sha, L., Engelbrecht, J., and Hong, P. (2022). Knowledgebra: An Algebraic Learning Framework for Knowledge Graph. Machine Learning and Knowledge Extraction. DOI: 10.3390/make4020019
- Tan, W., Zhang, Q., Quiñones-Frías, M.C., Hsu, A.Y., Zhang, Y., Rodal, A., Hong, P., Luo, H.R., and Xu, B. (2022). Enzyme-Responsive Peptide Thioesters for Targeting Golgi Apparatus. J. Am. Chem. Soc. DOI: 10.1021/jacs.2c02238
- Tan, W., Zhang, Q., Hong, P., and Xu, B. (2022). A Self-Assembling Probe for Imaging the States of Golgi Apparatus in Live Single Cells. Bioconjugate Chemistry. DOI: 10.1021/acs.bioconjchem.2c00084
- Chen, Z., Wei, J., Tang, Y., Lin, C., Costello, C.E., and Hong, P. (2022). GlycoDeNovo2: An Improved MS/MS-Based De Novo Glycan Topology Reconstruction Algorithm. Journal of the American Society for Mass SpectrometryDOI:10.1021/jasms.1c00288
- Wang, Y., Tang, J., Vimal, V.P., Lackner, J., DiZio, P. and Hong, P. (2022). Crash Prediction Using Deep Learning in a Disorienting Spaceflight Analog Balancing Task. Front. Physiol. DOI: 10.3389/fphys.2022.806357
- Du, H.*, Chen, F.*, Liu, H., and Hong, P. (* equal contribution) (2021). Network-based Virus-Host Interaction Prediction with Application to SARS-CoV-2. Cell Patterns. DOI: 10.1016/j.patter.2021.100242
- Zhou, Z., Joshi, C., Liu, R., Norton, M. M., Lemma, L., Dogic, Z., Hagan, M. F., Fraden, S., and Hong, P. (2020). Machine Learning Forecasting of Active Nematics. Soft Matter. DOI: 10.1039/D0SM01316A
- Yang, T., Sha, L., and Hong, P. (2020). NagE: Non-Abelian Group Embedding for Knowledge Graphs. ACM International Conference on Information and Management.
- Yang, T., Sha, L., Li, J. and Hong, P. (2020). A Deep Learning Approach for COVID-19 Trend Prediction. International Workshop on Epidemiology meets Data Mining and Knowledge
Discovery
- Vimal, V. P., Zheng, H., Hong, P., Fakharzadeh, L. N., Lackner, J. R., DiZio, P. (2020). Characterizing Individual Differences in a Dynamic Stabilization Task using Machine Learning. Aerospace Medicine and Human Performance, 91(6):479-488. https://doi.org/10.3357/amhp.5552.2020.
- Yoong, L. F., Lim, H. K., Tran, H., Lackner, S., Zheng, Z., Hong, P., Moore, A. W. (2020). Atypical Myosin Tunes Dendrite Arbor Subdivision. Neuron, 106:1–16. https://doi.org/10.1016/j.neuron.2020.02.002
- Zhao, R., Hong, P., and Liu, J.S. (2020). IMMIGRATE: A Margin-based Feature Selection Method with Interaction Terms. Entropy, 22(3):291. https://doi.org/10.3390/e22030291
- Xing, X., Sha, L., Hong, P., Shang, Z., Liu, J.S. (2020). Probabilistic Connection Importance Inference and Lossless Compression of Deep Neural Networks. International Conference on Learning Representations 2020.
- Wei, J., Tang, Y., Bai, Y., Zaia, J., Costello, C., Hong, P., Lin, C. (2020). Towards Automatic and Comprehensive Glycan Characterization by On-line PGC-LC-EED MS/MS. American Chemical Society. 92(1):782-791. https://doi.org/10.1021/acs.analchem.9b03183
- Wang, L.*, Sha, L*, Lakin, J. R., Bynum, J., Bates, D. W., Hong, P., Zhou, L. (2019). 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):e196972.
- Tang Y., Pu Y., Gao J., Hong P., Costello C., Lin C.. (2018) De Novo Glycan Sequencing by Electronic Excitation Dissociation and Fixed-Charge Derivatization. Analytical Chemistry
- Hong P., Sun H., Sha L., Pu Y., Khatri K., Yu X., Tang Y., Lin C. (2017) GlycoDeNovo -- an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra. Journal of The American Society for Mass Spectrometry. Note: Machine Learning in Chemistry (Glycomics). Download software
- Bei Y. and Hong P. (2016) Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes. BMC Bioinformatics. Note: Machine Learning in Differential Analysis (False Discovery Rate)
- Vinayagam A., Kulkarni M.M., Sopko R., Sun X., Hu Y., Nand A., Villalta C., Moghimi A., Yang X., Mohr S.E., Hong P., Asara J.M., Perrimon N. (2016). An Integrative Analysis of the InR/PI3K/Akt Network Identifies the Dynamic Response to Insulin Signaling. Cell Reports.
- 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. (2016). A Cross-Species Study of PI3K Protein-Protein Interactions Reveals the Direct Interaction of P85 and SHP2. Scientific Reports.
- Kwon Y., Vinayagam A., Sun X., Dephoure N., Gygi S.P., Hong P., and Perrimon P. (2013). The Hippo Signaling Pathway Interactome. Science.
- Bei Y. and Hong P. (2013) A Novel Approach to Minimize False Discovery Rate in Significance Analysis. BMC Systems Biology
- Sun X. and Hong P. (2013) PPIRank - An Advanced Method for Ranking Protein-Protein Interations in TAP/MS Data. BMC Proteome Science
- Schulte J., Sepp K. J., Wu C., Hong P., Littleton J. T. (2011) High-Content Chemical and RNAi Screens for Suppressors of Neurotoxicity in a Huntington's Disease Model. PLoS One
- 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. (2011) Proteomic and Functional Genomic Landscape of Receptor Tyrosine Kinase and Ras to Extracellular Signal-Regulated Kinase Signaling. Science Signaling 4(196)
- Warner J. L., Anick P., Hong P., and Xue N. (2011) Natural Language Processing and the Oncologic History: Is There a Match? Journal of Oncology Practice 2011 July; e15-e-19.
- Shang Y., Haynes P., Pírez N., Harrington K. I., Guo F., Pollack J., Hong P., Griffith L. C., and Rosbash M. (2011) Imaging analysis of clock neurons reveals light buffers the wake-promoting effect of dopamine. Nature Neuroscience, 14, 889-895.
- Li L., Karabacaka N. M., Cobba J. S., Wang Q., Hong P*, Agara J.N.*. (2010) Memory Efficient Calculation of the Isotopic Mass States of a Molecule. Rapid Communications in Mass Spectrometry, 2010 Sep 30; 24(18):2689-2696.
- Wu C., Schulte J., Sepp K.J., Littleton J.T., and Hong P. (2010) Automatic Robust Neurite Detection and Morphological Analysis of Neuronal Cell Cultures in High-content Screening. Neuroinformatics. 2010 Jun;8(2):83-100.
- Schulte J., Sepp K., Jorquera R., Wu C,. Song Y., Hong P., and Littleton J.T. (2010) DMob4/Phocein regulates synapse formation, axonal transport, and microtubule organization. Journal of Neuroscience. 2010, 30(15):5189-5203.
- Schoemans, R., Aigrot M.S., Wu C., Maree R., Hong P., Belachew S., Josse C., Lubetzki C., and Bours V. (2010). Oligodendrocyte development and myelinogenesis are not impaired by high concentrations of phenylalanine or its metabolites. Journal of Inherited Metabolic Disease, 2010 Apr;33(2):113-20.
- Sun X. and Hong P. (2009). Automatic inference of multicellular regulatory networks using informative priors. International Journal of Computational Biology and Drug Design 2009, 2(2):115-133.
- Karabacak N.M., Li L., Tiwari A., Hayward L.J., Hong P., Easterling M.L., and Agar A.N. (2009). Sensitive and specific identification of wild-type and variant proteins from 8 to 669 kDa using top-down mass spectrometry. Molecular & Cellular Proteomics. 2009 Apr;8(4):846-56.
- Zhou R., Hotta I., Denli A.M., Hong P., Perrimon N., and Hannon G.J. (2008). Comparative Analysis of Argonaute-Dependent Small RNA Pathways in Drosophila. Molecular Cell. 2008 Nov 21;32(4):592-9
- Li L., Kresh J.A., Karabacak N.M., Cobb J.S., Agar J.N., and Hong P. (2008). A Hierarchical Algorithm for Calculating the Isotopic Fine Structures of Molecules. Journal of the American Society for Mass Spectrometry, 19(12), pp 1867-1874.
- Sepp K.J., Hong P., Lizarraga S.B., Liu J.S., Mejia L.A., Walsh C.A., Perrimon N. (2008). Identification of neural outgrowth genes using genome-wide RNAi. PLoS Genet. 2008 Jul 4;4(7):e1000111.
- Sun X. and Hong P. Computational Modeling of Caenorhabditis elegans Vulval Induction. Bioinformatics. 2007;23(13):i499-i507.
- Kulkarni M.M., Booker M., Silver S.J., Friedman A., Hong P., Perrimon N., Mathey-Prevots B. (2006) Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays. Nature Methods. 3(10):833-838
- Hong P., Liu X.S., Zhou Q., Lu X., Liu J.S., and Wong W.H. A boosting approach for motif modeling using ChIP-chip Data, Bioinformatics, 21, pp. 2636-2643.
- Hong P. and Wong W.H. GeneNotes: A novel information management software for biologists, BMC Bioinformatics 2005, 6:20.
- Hong P., Zhong S., Wong W.H. (2005) Towards Ubiquitous Bio-information Computing: Data Protocols, Middleware, and Web service for Heterogeneous Bio-information Integration and Retrieval. International Journal Software Engineering and Knowledge Engineering, special issue on Software and Knowledge Engineering Support in Bioinformatics. 15(3), 475-485.
- Hong P. and Huang T.S. (2004) Spatial pattern discovery by learning a probabilistic parametric model from multiple attributed relational graphs. Journal of Discrete Applied Mathematics, vol. 130, pp. 113-135.
- Hong P., Wen Z., and Huang T.S. (2002) Real-time speech-driven expressive synthetic talking faces using neural networks. IEEE Transaction on Neural Networks, 13(4), pp. 916-927.
- Hong P., Wen Z., and Huang T.S. (2001) IFACE: A 3D synthetic talking face. International Journal of Image and Graphics, 1(1), pp. 19-26.
Conference
- Chen, Z.; Li, P.; Liu, H.; Hong, P. Characterizing the Influence of Graph Elements. International Conference on Learning Representations 2023
- Li, P., Wang, Y., Zhao, H., Hong, P., and Liu, H. (2021). On Dyadic Fairness: Exploring and Mitigating Bias in Graph Connections. International Conference on Learning Representations 2021.
- Zheng Z. and Hong P. (2018) Robust Detection of Adversarial Attacks by Modeling the Intrinsic Properties of Deep Neural Networks. Neural Information Processing Systems.
- Sha L. and Hong P. (2017) Neural Knowledge Tracing. In: Frasson C., Kostopoulos G. (eds) Brain Function Assessment in Learning. BFAL 2017. Lecture Notes in Computer Science, vol 10512. Springer, Cham.
- Zheng Z. and Hong P. Incorporate Deep-Transfer-Learning into Automatic 3D Neuron Tracing. International Conference on Neuroscience and Cognitive Brain Information. 2016.
- Bei Y. and Hong P. Maximizing Margin Quality and Quantity. IEEE International Workshop on Machine Learning for Signal Processing. 2015.
- Bei Y., Hong P., Ke F., Zhou Y., Xu L., and Zhu M. Psychiatric Insights into Liver Cirrhosis and Their Correlations with Traditional Chinese Medicine Diagnostics. The IEEE International Conference on Bioinformatics and Biomedicine, 2013. (regular paper)
- Bei Y. and Hong P. Significance Analysis by Minimizing False Discovery Rate. The IEEE International Conference on Bioinformatics and Biomedicine, Philadelphila, USA. October 2012. (regular paper)
- 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, USA. October 2012. (regular paper)
- Anick P., Hong P., Xue N., and Anick D. 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.
- Lin, C. and Hong P. Novel Morphological Phenotypes Discovery in High-Content Screens Using Underused Features. in International Conference on Bioinformatics and Computational Biology. 2010. Honolulu, Hawaii, USA.
- Sun X. and Hong P. Improving Automatic Inference of the Biological Network Governing C. elegans Vulval Induction by Incorporating Interaction Data. Biocomp 2008.
- 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. 2007.
- Hong P. (2006). Interactive Analysis of High-Content Cellular Images via Relevant Feedback. 2006 Workshop on Multiscale Biological Imaging, Data Mining and Informatics, Santa Barbara, CA, USA.
- Hong P., K. J. Sepp, et al. (2006). Intelligent Interfaces for Interactive Analysis of High-Content Cellular Images. Frontiers in Live Cell Imaging, NIH, Bethesda, MD.
- Hong P., Zhong, S., Wong, W. H. (2004) Towards Ubiquitous Bio-information Computing: Data Protocols, Middleware, and Web service for Heterogeneous Bio-information Integration and Retrieval. Proc. IEEE 4th Sym. on Bioinformatics and Bioengineering. 2004:57-64.
- Chai J., Hong P., and Zhou M. X. (2004) A Probabilistic Approach to Reference Resolution in Multimodal User Interface. International Conference on Intelligent User Interfaces, Madeira, Portugal, Jan. 2004.
- Chai J., Hong P., Zhou M., and Prasov Z. (2004) Optimization in Multimodal Interpretation. The 42nd Annual Conference of Association of Computational Linguistics, Barcelona, Spain. July 22-24, 2004.
- Chai J., Prasov Z., and Hong P. (2004) Performance Evaluation and Error Analysis for Multimodal Interpretation in Conversational Systems. In Proceedings of HLT-NAACL, Boston, MA, May 3-7, 2004.
- Hong P. and Huang T.S. (2002) Inexact spatial pattern mining. Workshop on Discrete Mathematics and Data Mining. 2002.
- Hong P., Wen Z., Huang T.S., and Shum H. Y. (2002) Real-time speech-driven 3D face animation. International Symposium on 3D Data Processing Visualization Transmission, Padova, Italy, June 2002.
- Hong P. and Huang T.S. (2002) Multimodal temporal pattern mining. International Conference on Pattern Recognition. 2002.
- Huang T.S. and Hong P. (2002) Exemplar-based face and facial motion tracking. International Conference on Acoustics, Speech, and Signal Processing, 2002.
- Hong P. and Huang T.S. (2002) Unsupervised temporal pattern extraction and association. International Conference on Acoustics, Speech, and Signal Processing, 2002.
- Hong P. and Huang T.S. (2001) Learning the isomorphic sub-graph from multiple attributed relation graphs. IWCIA and ENTCS 2001.
- Hong P., Wen Z., and Huang T.S. (2001) An integrated framework for face modeling, facial motion analysis and synthesis. ACM Multimedia 2001.
- Hong P., Wen Z., and Huang T.S. (2001) Real-time speech-driven avatar with constant short time delay. EUROIMAGE ICAV3D 2001.
- Hong P., Wen Z., Huang T.S., and Chan, M. T. (2001) Speech-driven avatars. Army Research Lab Symposium 2001.
- Hong P., Tian, Q., and Huang T.S. (2000) Incorporate support vector machines to content-based image retrieval with relevant feedback. IEEE International Conference on Image Processing, Vancouver, Canada, Sep. 10-13, 2000.
- Hong P. and Huang T.S. (2000) Learning to extract multi-temporal signal patterns from a temporal signal sequence. International Conference on Pattern Recognition, Barcelona, Spain, Sep 3-7, 2000.
- Hong P., Turk M., and Huang T.S., Constructing finite state machines for fast gesture recognition. International Conference on Pattern Recognition, Barcelona, Spain, Sep 3-7, 2000.
- Wang R., Hong P., and Huang T.S. (2000) An automatic moving object extraction system for video indexing. International Conference on Pattern Recognition, Barcelona, Spain, Sep 3-7, 2000.
- Huang T.S., Cohen I., Hong P., and Li, Y. (2000) IA3: intelligent affective animated agents. International Conference on Image and Graphic Technology toward 21 Century and Beyond, Tianjin, China, August 16-18, 2000.
- Tian, Q., Hong P., and Huang T.S. (2000) Update relevant image weights for content-based image retrieval using support vector machines. IEEE International Conference on Multimedia and Expo, Hilton New York & Towers, New York, NY, July 30 - Aug. 2, 2000.
- Hong P., Wang R., Huang T.S. (2000) Learning patterns from images by combining soft decisions and hard decisions. IEEE Conference on Computer Vision and Pattern Recognition, Hilton Head Island, South Carolina, June 13-15, 2000.
- Hong P., Turk M., and Huang T.S. (2000) Gesture modeling and recognition using finite state machines. IEEE International Conference on Automatic Face and Gesture Recognition, March 28-30, 2000, Grenoble, France.
- Hong P. and Huang T.S. (2000) Extracting the recurring patterns from image. Asian Conference on Computer Vision, Jan. 5-8, 2000, Taipei, Taiwan.
- Hong P. and Huang T.S. (1999) Natural mouse - a novel human-computer interface. International Conference on Image Processing, Oct 24-28, 1999, Kobe, Japan.
- Hong P., Ray S.R., and Huang T.S. (1999) A new scheme for extracting multi temporal sequence patterns. International Joint Conference on Neural Networks, July 10-16, 1999, Washington DC. USA.
- Hong P., Huang T.S., and Lin X. (1998) Mouth motion learning and generating from observations. IEEE Workshop on Multimedia Signal Processing, Dec. 7-9, 1998, Los Angeles, California, USA.
- Si Y., Hong P., et al. (1995) A synchronization model for multimedia presentation with user interaction. National Conference on Multimedia Technology, Nov. 1995, Guangzhou, P. R. China.
Book chapter contributions
- Sun X., Mohr S., Vinayagam A., Hong P., Perrimon N. (2015) Inferring genetic architecture from systems genetics studies. in Linking Phenotypes with Genotypes. editor Markowetz and Boutros, Cambridge University Press. pp. 139-160.
- Wen Z., Hong P., Tu, J., and Huang T.S. (2003) Learning 3D Face Deformation Models: Methods and Applications. in 3D Modeling and Animation: Synthesis and Analysis Techniques for the Human Body, Idea Group Inc., Hershey, PA 17033, USA.
- Hong P., Wen Z., Huang T.S. (2002) Speech-driven face animation. in MPEG-4 Facial Animation - The Standard, implementations and applications, John Wiley & Sons, ISBN 0-470-84465-5.
- Hong P., Wen Z., Li Y., and Huang T.S. (2000) Avatars. in Computer Science Handbook of the Army Research Lab, ADID FedLab.
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