Hongyu Su

Ph.D.

Office:

Computer Science Building, Room B333 (3nd floor), Konemiehentie 2, FI-02150 Espoo, Finland

Postal Address:

Department of Computer Science, PO Box 15400, FI-00076 Aalto, Finland

Telephone:

+358 442793169

Work:

+358 504305448

Email:

GitHub:

https://github.com/hongyusu

Permement site:

https://hongyusu.github.io

About Me

I am a Postdoctoral researcher in Department of Computer Science, Aalto University, Finland. My research is along the direction of Machine Learning for Structured Data. Currently I focus on developing accurate learning models for structured output prediction. In general, I am interested in

• Structured Output Prediction / Max-Margin Learning for Multilabel Classification
• Kernel Methods for Complex Data
• Optimization Methods for Large-scale Data
• Social Network / Influence Network Data Analysis
• Bioinformatics, Metagenomics

Education

I did my PhD in the field of Information and Computer Science from Aalto University and Helsinki Institute for Information Technology HIIT during 2012.3 - 2015.4. Before that, I got my Master's degree from University of Helsinki (U.H.) and HIIT in 2010. I got my Bachelor of Engineering from Xidian University, China, in 2007.

Outside Research

I enjoyed aggressive sport like basketball before I broke my knee cruciate ligament. Now I opt to bouldering, scuba diving (holding OWD license), snowboarding (downhill) that explores the unknown part of my life. I also enjoy hiking and traveling a lot for which I share some of the pictures on flickr.

Recent Activity

• We won the Aalto Data Science Hackathon 2015 as the Best Hacks in Fitness (wearables).
• I defended my dissertation on 27th March 2015.
• I will join the evaluation process of the applications for Master programme in Machine Learning and Data Mining 2015 (Macademia).
• With Prof. John Shawe-Taylor, Prof. Mario Marchand, Prof. Juho Rousu, Assi. Prof. Emilie Morvant, we are presenting out paper on NIPS 2014 conference.
• My talk at the International Conference on Machine Learning (ICML2014) is now online at TechTalk.

Refereed Publications

Journal Articles

• Su, Hongyu; Rousu, Juho. Multilabel Classification through Random Graph Ensembles. Machine Learning, Volume 99, Issue 2 (2015), Page 231-256, DOI: 10.1007/s10994-014-5465-9. [online] [preprint]

Conference Articles

• Mario Marchand, Hongyu Su, Emilie Morvant, Juho Rousu, John Shawe-Taylor Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks. In Advances in Neural Information Processing Systems 27(NIPS 2014), 873--881 [preprent] [original] [code] [code with new inference algorithm] [data]
• Su, Hongyu; Gionis, Aristides; Rousu, Juho. Structured Prediction of Network Response. In Proceedings of the 31th International Conference on Machine Learning (ICML 2014), Journal of Machine Learning Research (JMLR) W&CP 32:442--450 [original] [code] [data] [video]
• Su, Hongyu; Rousu, Juho. Multilabel Classification through Random Graph Ensembles. In Proceedings of the 5th Asian Conference on Machine Learning (ACML 2013), Journal of Machine Learning Research (JMLR) W&CP 29:404--418 [original]
• Su, Hongyu; Rousu, Juho. Multi-task Drug Bioactivity Classification with Graph Labeling Ensembles. In Proceedings of the 6th International Conference on Pattern Recognition in Bioinformatics (PRIB 2011), Springer Lecture Note in Computer Science (LNCS) 7035:157--167 [original] [data]
• Su, Hongyu; Heinonen, Markus; Rousu, Juho. Structured Output Prediction of Anti-cancer Drug Activity. In Proceedings of the 5th International Conference on Pattern Recognition in Bioinformatics (PRIB 2010), Springer Lecture Note in Computer Science (LNCS) 6282:265--273 [original] [data]
• Dong, Anguo; Lin, Gao; Zhou, Xiaofeng; Su, Hongyu. An Algebra Approach for Finding Frequent Subgraphs with Hamiltonian Cycle. In Proceedings of the 4th International Conference on Fuzzy Systems and Knowledge Discovery (FSDK 2007), IEEE Computer Society 3:288--292 [original]

Doctoral Dissertation

• Su, Hongyu. Multilabel Classification through Structured Output Learning - Methods and Applications. Doctoral Dissertation, Aalto University School of Science, Feb 2015. [Library] [GitHub] [Draft] [Slides]

Workshop and Other Articles

• Su, Hongyu; Gionis, Aristides; Rousu, Juho. Structured Prediction of Network Response. In International Workshop on Multi-Target Prediction - ECML 2014 workshop, long abstract and oral presentation
• Su, Hongyu; Rousu, Juho. Random Graph Ensembles in Multilabel Classification. In Object, Function and Structured Data: towards next Generation Kernel-Based Methods - ICML 2012 workshop, paper and oral presentation [original]
• Su, Hongyu; Rousu, Juho. Multilabel Classification via Random Graph Labeling. In the 5th International Conference on Artificial Intelligence and Statistics (AISTATS 2012), long abstract and poster presentation [original]
• Su, Hongyu; Heinonen, Markus; Rousu, Juho. Multilabel Prediction of Drug Activity. In Proceedings of the 4th International Workshop on Machine Learning in Systems Biology (MLSB 2010), MLSB 2010 publication 67-70, long abstract and oral presentation [original]
• Su, Hongyu; Heinonen, Markus; Rousu, Juho. Multilabel Classification of Drug-like Molecules via Max-margin Conditional Random Fields. In Proceedings of the 5th European Workshop on Probabilistic Graphical Models (PGM 2010), HIIT 2010 publication 2:67-70, paper and oral presentation [original]

Academic Activities

Presentations and Posters

• Mario Marchand, Hongyu Su, Emilie Morvant, Juho Rousu, John Shawe-Taylor Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks. In Annual Conference on Advances in Neural Information Processing Systems (NIPS 2014), Montreal, Canada, December 8 - December 13, 2014 [poster]
• Su, Hongyu; Gionis, Aristides; Rousu, Juho. Structured Prediction of Network Response. In the 31th International Conference on Machine Learning (ICML 2014), Beijing, China, June 21- June 26, 2014 [poster, slides, video]
• Su, Hongyu; Rousu, Juho. Multilabel Classification through Random Graph Ensembles. In the 5th Asian Conference on Machine Learning (ACML 2013), Canberra, Australia, November 11 - November 15, 2013 [poster, slides]
• Su, Hongyu; Rousu, Juho. Multilabel Classification via Random Graph Labeling. In the 5th International Conference on Artificial Intelligence and Statistics (AISTATS 2012), La Palma, Canary Islands, April 21-23, 2012 [poster]
• Su, Hongyu; Rousu, Juho. Multi-task Drug Bioactivity Classification with Graph Labeling Ensembles. In the 6th International Conference on Pattern Recognition in Bioinformatics (PRIB 2011), Delft, The Netherlands, November 2 - November 4, 2011 [poster, slides]
• Su, Hongyu; Heinonen, Markus; Rousu, Juho. Multilabel Classification of Drug-like Molecules via Max-margin Conditional Random Fields. In the 5th European Workshop on Probabilistic Graphical Models (PGM 2010), Helsinki, Finland, September 13 - September 15, 2010 [poster, slides]

Reviewer

• IEEE Transactions on Knowledge and Data Engineering (TKDE).
• IEEE Transactions on Neural Networks and learning Systems (TNNLS).
• The 6th ACM International Conference on Web Search and Data Mining (WDSM2013).
• The 26th Annual Conference on Neural Information Processing Systems (NIPS2012).

Research Visit

• Prof. Mario Marchand, Prof. Francois Laviolett, Laval University, Quebec city, Canada, December 11 - December 19, 2014
• Prof. Jinzhi Lei, Tsinghua University, Beijing, China, June, 2014
• Prof. John Shawe-Taylor, University College London, March 20 - April 1, 2014
• Dr. Wei Bian, University of Technology, Sydney, November 15 - November 18, 2013

Teaching

• Lecture in T-61.6080 Special Course in Bioinformatics II, Aalto University, Spring 2015.
• Assistant in T-61.5910 Research Project in Computer and Information Science, Aalto University, Autumn 2014.
• Lecture and assistant in T-61.6020 Special Course in Computer and Information Science II, Aalto University, Spring 2013.
• Assistant in T-61.5910 Research Project in Computer and Information Science, Aalto University, Autumn 2013.
• Assistant in 582653 Computational Methods of System Biology, University of Helsinki, Spring 2012.