Huibin Shen

Postal Address:

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

Email:

firstname.lastname@aalto.fi

About

I am a PhD student at KEPACO group, led by Professor Juho Rousu. My research focuses on kernel based machine learning and its application to system biology. I had my master in the Department of Computer Science, University of Helsinki. I did my bachelor in East China Normal University under the supervision of Prof. Weining Qian. Projects ara mostly on Github.

News

• Finished the internship at Amazon Berlin in the summer of 2016.
• Attended the Dagstuhl Seminar on Computational Metabolomics 2015.
• Accepted to the Machine Learning Summer School (MLSS) 2014 in Reykjavik, Iceland.
• Accepted to the NIPS workshop MLCB 2013.

Papers

Journal Articles

• Kai Dährkop, Huibin Shen, Marvin Meusel, Juho Rousu and Sebastian Böcker: Searching molecular structure databases with tandem mass spectra using CSI:FingerID. PNAS 112, 12580-12585 (2015). CSI:FingerID
• Huibin Shen, Niocola Zamboni, Markus Heinonen, Juho Rousu: Metabolite identification through machine learning -- tackling casmi challenge using fingerid. Metabolites 3(2), 484--505 (2013).

Conference and Workshop

• Huibin Shen, Sandor Szedmak, Céline Brouard and Juho Rousu: Soft Kernel Target Alignment for Two-stage Multiple Kernel Learning. In proceedings of Discovery Science 2016.
• Céline Brouard, Huibin Shen, Kai Dährkop, Florence d'Alché-Buc, Sebastian Böcker, Juho Rousu: Fast metabolite identification with Input Output Kernel Regression. In proceedings of ISMB 2016, Bioinformatics, 32(12) i28-i36, 2016.
• Huibin Shen, Kai Dährkop, Sebastian Böcker and Juho Rousu: Metabolite Identification through Multiple Kernel Learning on Fragmentation Trees. In proceedings of ISMB 2014, Bioinformatics 30(12), i157-i164 (2014). [code] [pdf]
• Markus Heinonen, Huibin Shen, Niocola Zamboni, Juho Rousu: Metabolite identification and molecular fingerprint prediction through machine learning. In proceedings of MLSB 2012, Bioinformatics 28(18), 2333--2341 (2012).[code] [pdf]

Projects

• FingerID. A web server and a package for metabolite identification through machine learning.
• Distributed suffix sorting algorithm. In this project, we designed and implemented the first distributed suffix sorting algorithm with Professor Veli Mäkinen. A presentation can be found here.

Teaching

• Assistant to ICS-E4030 Kernel Methods in Machine Learning, given by Associate Professor Juho Rousu, Aalto University, 2016.
• Assistant to ICS-E4030 Kernel Methods in Machine Learning, given by Associate Professor Juho Rousu, Aalto University, 2015.
• Assistant to ICS-E4030 Kernel Methods in Machine Learning, given by Associate Professor Juho Rousu, Aalto University, 2014.
• Assistant to T-61.5060 Algorithmic Methods of Data Mining, given by Associate Professor Aristides Gionis, Aalto University, 2013.