Hongyu Su

Academic

Machine Learning
Optimization
Structured Prediction

Education

Research Interests

  • Optimization Research and Machine Learning
  • Structured Output Prediction / Kernel Methods
  • Social Network Analysis / Bioinformatics / Metagenomics
  • Deep Learning / Large Scale Learning / Distributed Optimization

Publications

Industry Publications

Cambri. AI Whitepaper. Cambri, 2024. [read]

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]

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]

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. [preprint] [original] [code] [code (new inference)]
  • Su, Hongyu; Gionis, Aristides; Rousu, Juho. Structured Prediction of Network Response. In Proceedings of the 31st International Conference on Machine Learning (ICML 2014), JMLR W&CP 32:442–450. [original] [code] [video]
  • Su, Hongyu; Rousu, Juho. Multilabel Classification through Random Graph Ensembles. In Proceedings of the 5th Asian Conference on Machine Learning (ACML 2013), 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 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 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]

Workshop Articles

  • Simon Cousins, John Shawe-Taylor, Mario Marchand, Juho Rousu, Hongyu Su. Multiple Kernel Learning for Prediction on Unknown Graph Structures. In the 8th NIPS Workshop on Optimization for Machine Learning (OPT 2015) — NIPS 2015.
  • Hongyu Su, Giorgio Valentini, Sandor Szedmak, Juho Rousu. Transporter Protein Classification through Structured Prediction and Multiple Kernel Learning. In Workshops on MLCB & MLSB 2015 — NIPS 2015.
  • Su, Hongyu; Gionis, Aristides; Rousu, Juho. Structured Prediction of Network Response. In International Workshop on Multi-Target Prediction — ECML 2014.
  • Su, Hongyu; Rousu, Juho. Random Graph Ensembles in Multilabel Classification. In Object, Function and Structured Data: towards next Generation Kernel-Based Methods — ICML 2012. [original]
  • Su, Hongyu; Rousu, Juho. Multilabel Classification via Random Graph Labeling. In AISTATS 2012. [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), 67–70. [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. [original]

Funding & Awards

  • 2014 — Chinese Government Award for Outstanding Doctoral Students (top 500 worldwide)
  • 2011 — Fully funded position from Helsinki Doctoral Programme in Computer Science (HeCSE)
  • 2010 — Master thesis grant from Center of Excellence Grant 118653 ALGODAN
  • 2008 — International Master's Degree Student Award, University of Helsinki

Academic Review

  • NIPS 2012, 2015, 2016
  • IEEE Transactions on Knowledge and Data Engineering (TKDE)
  • IEEE Transactions on Neural Networks and Learning Systems (TNNLS)
  • International Conference on Web Search and Data Mining (WDSN 2013)

Thesis Supervision

  • 2015 — Community detection for large-scale metagenomics data, Aalto
  • 2014 — Graph kernels and multiple kernel learning for PPI prediction, Aalto
  • 2012 — Large-scale metagenomics data analysis, Aalto

Teaching

  • Spring 2015 — Lecture in Special Course in Bioinformatics II, Aalto
  • Autumn 2014 — Assistant in Research Project in Computer and Information Science, Aalto
  • Spring 2013 — Lecture in Special Course in Computer and Information Science II, Aalto
  • Autumn 2013 — Assistant in Research Project in Computer and Information Science, Aalto
  • Spring 2012 — Assistant in Computational Methods of System Biology, University of Helsinki