Lingyu Ma 马凌宇 (M.Sc. & PhD candidate)

Affiliation:

Department of Computer Science, University of Freiburg

Address:

Zi.Nr.01-023, Georges-Koehler-Allee, Gebaeude 052, 79110 Freiburg, Germany

Telephone:

+49-(0)761-203-8258

Fax:

+49-(0)761-203-8262

Email:

malingyu@informatik.uni-freiburg.de

Scientific Interests

Protein Secondary Structure Identification
3D Invariance in Pattern Recognition and Machine Learning
Content Based Shape Retrieval

Publications

2011

Lingyu Ma, Marco Reisert, and Hans Burkhardt.
"RENNSH: A Novel Alpha-helix Identification Approach for Intermediate Resolution Electron Density Maps"
IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 2011, in press. bibtex
Abstract: Accurate identification of protein secondary structures is beneficial to understand three-dimensional structures of biological macromolecules. In this paper, a novel refined classification framework is proposed, which treats alpha-helix identification as a machine learning problem by representing each voxel in the density map with its Spherical Harmonic Descriptors (SHD). An energy function is defined to provide statistical analysis of its identification performance, which can be applied to all the alpha-helix identification approaches. Comparing with other existing alpha-helix identification methods for intermediate resolution electron density maps, the experimental results demonstrate that our approach gives the best identification accuracy and is more robust to the noise.
Lingyu Ma, Marco Reisert, Christophe Wirth, Carola Hunte, Olaf Ronneberger, and Hans Burkhardt.
"ALPHA HELIX PREDICTION BASED ON METROPOLIS-HASTINGS SAMPLING"
2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro. 2011, in press. bibtex
Abstract: Accurate identification of protein secondary structures is beneficial to the structural interpretation of low-resolution X-ray and EM electron density maps. Existing alpha helix identification methods mainly focus on locally voxelwise classification and then link the helix-voxels based on post-processing processes. In this paper, a novel alpha helix identification approach, named as SSEPredictor, based on Metropolis-Hastings sampling is proposed, which can provide both locally and globally optimized prediction for alpha helical structures in low-resolution electron density maps. The approach has been tested on X-ray crystallographic electron density maps at 8 angstrom resolution. The experimental results show that the identification accuracy is promising.

2007

Liguo Chen, Lining Sun, Lingyu Ma, and Weibin Rong.
"Automatic Flexible Wire Bonder for MEMS Sensor Packaging Based on Zoom Lens System"
Proc. of MicroNanoChina07. January 2007.

2006

Liguo Chen, Lingyu Ma, Lining Sun, and Weibin Rong.
"Zoom Microscope Based Micropositioning for MEMS Sensor Packaging System"
The 32nd Annual Conference of the IEEE Industrial Electronics Society (IECON06). November 2006.

Thesis

Multipurpose Image Watermarks Algorithm and Applications, Bachelor degree
Research on Micro Vision System for Automatic MEMS Wire Bonding, Master degree

Project

In March 2006, accomplishment of developing "MEMS (micro-electromechanical system) Automatic Wire-bonding System", particularly for MEMS pressure transducers bonding

Teaching

Supervised Diploma thesis: "Alpha-helix Identification Benchmark for Intermediate Resolution Density Maps", Daniel Huhn, winter term 2009/10

CV

2007.09 - present PhD Candidate, Institute for Pattern Recognition and Image Processing, Computer Science Department, University of Freiburg, Germany
2004.09 - 2006.07 Master of Science, Robotics Institute of Harbin Institute of Technology, China
1999.09 - 2003.07 Bachelor of Engineering, Department of Automatic Testing and Control, Harbin Institute of Technology, China

Others

Outstanding Undergraduate Students Fellowship in 2000, 2001, and 2002
Chairman of the student union of Electronic Engineering Department of Harbin Institute of Technology in 2001, 2002
Transfer student in 2002 to Phillips Academy Andover, USA, as one of the top 5 undergraduate students of Harbin Institute of Technology