刘飞 中国
暂无描述
副教授||博士生导师
目前就职航天学院
所在学科 控制科学与工程
永久地址 http://homepage.hit.edu.cn/liufei

General information

Fei Liu

(Associate Professor)

Control and Simulation Center
Harbin Institute of Technology
Harbin, China


Biological and Medical Simulation Group

Welcome to the biological and medical simulation group. What we are doing involves the following topics:

  • Modeling and simulation techniques
  • Control theory and techniques
  • Biological modeling and simulation
  • Medical Image processing and 3D simulation
  • BioImage processing
  • Machine learning (data mining) and medical data analysis

Upcoming Events

June 22, 2015

BioPPN 2015, Brussels/Belgium, a satellite event of PETRI NETS 2015 and ACSD 2015

August 21-24, 2015

The 9th International Conference on Systems Biology (ISB 2015)  Luoyang, China

News

April 11, 2016

Attended Yamaguchi Lunch Seminar and gave a talk on "A Colored Hybrid Petri Net Model for the Delta-Notch Dependent Boundary Formation in the Drosophila Large Intestine"

March 21, 2016

Attended Yamaguchi Workshop on Computational Network Biology and gave a talk on "A Colored Hybrid Petri Net Model for the Delta-Notch Dependent Boundary Formation in the Drosophila Large Intestine"

March 14-16, 2016

Attended Awaji Yumebutai workshop and gave a talk on "colored Petri nets for multiscale systems biology"

March 3-4, 2016

Attended the IEICE Workshop of Technical Committee on Mathematical Systems Science and its applications (IEICE-MSS) and gave a talk on "A Colored Hybrid Petri Net Model for the Delta-Notch Dependent Boundary Formation in the Drosophila Large Intestine"

February 12, 2016

Visisted Lab of systems microbiology, Nara Institute of Scinece and Technology and gave a talk on "colored Petri nets for multiscale systems biology"

 

October 14- November 20, 2015

Visit Network Science Lab led by Professor Matsuno, Yamaguchi University, Japan,

as a JSPS invitation fellow funded by JSPS

October 12, 2015

The Sino-German Workshop on Multiscale spatial computational systems biology has been successfully finished.

August 18, 2015

We received the funding confirmation for our Sino-German Workshop on Multiscale spatial computational systems biology which will be held in Beijing, October 08 – 12, 2015

July 08- September 15, 2015

Visit Network Science Lab led by Professor Matsuno, Yamaguchi University, Japan,

as a JSPS invitation fellow funded by JSPS

March 16-23, 2015

Visited Network Science Lab led by Professor Matsuno, Yamaguchi University, Japan

and give a talk "Modelling and simulating reaction-diffusion systems using coloured Petri net".

November 18-28, 2014

Attended Dagstuhl Seminar, Germany &

Visited BTU Cottbus, Germany

August 17-23, 2014

Presented in 2014 International Workshop and Summer School on "Biological Big Bytes" a satellite meeting of the international workshop/summer school on Crops, Chips & Comp, Harbin, China

March 22-23, 2014

Prof. Hiroshi Matsuno and Dr. Zhongyuan Tian visited HIT and presented their work.

September 12-15, 2013

Presented in 2013 International Workshop and Summber School on Crops, Chips, and Computers (C3 2013), Tongliao, China

July 7 - August 6, 2013

Visited Network Science Lab led by Professor Matsuno, Yamaguchi University, Japan

and give a talk "Colored Petri nets for multiscale systems biology".

December 8-16, 2012

Presented in 2012 Winter Simulation Conference, Berlin, Germany &

Visited BTU Cottbus, Germany

Short Biography

April 2013 - Present, PhD advisor

Dec. 2009 – Present, Associate Professor at Control and Simulation Center, Harbin Institute of Technology.

Feb. 2009 – Feb. 2012, Scientific Staff Member at Department of Computer Science, Brandenburg University of Technology Cottbus.

Sept. 2007 – Jan. 2009, Postdoc at school of Astronautics, Harbin Institute of Technology.

Dec. 2006 – Dec. 2009, Lecturer at the Control and Simulation Center, Harbin Institute of Technology.

Education

  • Dr. rer. nat., Computer Science, Brandenburg University of Technology Cottbus, Germany, January 2012
  • PhD, Control Science and Engineering, Harbin Institute of Technology, China, November 2006
  • M.E., Control Science and Engineering, Harbin Institute of Technology, China, May 2004
  • B.E., Automatic testing and control, Harbin Institute of Technology, China, July 2001

Research Interests

  • Modeling and Simulation
    • Stochastic/continuous/hybrid simulation algorithms
    • Qualitative/stochastic/continuous/hybrid Petri nets
    • Colored qualitative/stochastic/continuous/hybrid Petri nets
    • Multiscale modeling and simulation in systems biology
  • Modeling and Control
    • Modeling and control for complex systems
    • Intelligent data analysis (data mining)
    • Design of control systems
  • Medical image processing
    • Image segmentation
    • 3D image reconstruction

Publications

 

2016

  • Fei Liu, Deshun Sun and Hiroshi Matsuno. Modeling and Analysis of the Delta-Notch Dependent Boundary Formation in the Drosophila Large Intestine. International Conference on Systems biology, Weihai,  Shandong, 19-22, August, 2016.

  • Fei Liu, Hiroshi Matsuno, Ryutaro Murakami. A Colored Hybrid Petri Net Model for the Delta-Notch Dependent Boundary Formation in the Drosophila Large Intestine. IEICE, 2016, 115(480): 47-52.  http://www.ieice.org/ken/paper/20160303CbhY/

  • Liu F, Heiner M, Yang M (2016) Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters. PLoS ONE 11(2): e0149674. doi:10.1371/journal.pone.0149674
  • F Liu, M Heiner and M Yang: Representing Network Reconstruction Solutions with Colored Petri Nets; Neurocomputing, 2016, 174(A): 483-493, doi:10.1016/j.neucom.2015.04.112

2015

  • Fei Liu: Colored Petri nets for multiscale systems biology; Talk, Sino-German Workshop, Beijing, Sino-German Center for Research Promotion, October 2015.
  • Fei Liu. Colored Petri Nets for Multiscale Systems Biology. Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481). Dagstuhl Reports, Dagstuhl, Germany, 2015, 4(11):160-161.
  • Steven S. Andrews, Satya N. V. Arjunan, Gianfranco Balbo, Arne T. Bittig, Jerome Feret, Kazunari Kaizu, and Fei Liu. Simulating macromolecular crowding with particle and lattice-based methods. Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481). Dagstuhl Reports, Dagstuhl, Germany, 2015, 4(11):170-187.
  • O Pârvu, D Gilbert, M Heiner, F Liu, N Saunders and S Shaw: Spatial-temporal modelling and analysis of bacterial colonies with phase variable genes; ACM Transactions on Modeling and Computer Simulation (TOMACS), 25(2):25p., May 2015.

2014

  • F Liu, MA Blätke, M Heiner and M Yang: Modelling and simulating reaction–diffusion systems using coloured Petri nets;Computers in Biology and Medicine, October 2014, 53:297–308.
  • F Liu, M Heiner and M Yang: Modeling and analyzing biological systems using colored hierarchical Petri nets, illustrated by C. elegans vulval development. Journal of Biological Systems, 2014.9, 22(3): 1-31.
  • Fei Liu, Ming Yang. Compositional colored Petri net approach to multiscale modeling for systems biology. International Journal of Modeling, Simulation, and Scientific Computing. 2014.12, 5(4): 1450017.
  • M Herajy, F Liu and C Rohr: Coloured hybrid Petri nets for systems biology; In Proc. of the 5rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2014, CEUR-WS.org, CEUR Workshop Proceedings, volume 1159, pages 60-76, June 2014.
  • Fei Liu, Zhifa Hu, Ming Yang. Colored Petri Nets-Based Biological Network Reconstruction for Systems Biology. The 2014 International Conference on Life System Modeling and Simulation (LSMS2014) and 2014 International Conference on Intelligent Computing for Sustainable Energy and Environment (ICSEE2014).  Communications in Computer and Information Science, Springer, Volume 461, 2014, pp 150-159.
  •  

2013

  • F Liu and M Heiner: Petri Nets for Modeling and Analyzing Biochemical Reaction Networks. In "Approaches in Integrative Bioinformatics", (M Chen and R Hofestädt, Eds.), Springer, 23 Oct 2013: 245–272.
  • F. Liu and M. Heiner: Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets; IET Systems Biology, 7(4):106-113, 2013.
  • F. Liu and M. Heiner: Modeling membrane systems using colored stochastic Petri nets; Nat. Computing, 12(4):617-629, 2013.
  • F Liu, M Heiner and M. Yang. Colored Petri Nets for Multiscale Systems Biology – Current Modeling and Analysis Capabilities in Snoopy. International Conference on Systems biology, Huangshan, Anhui, 23-25 August, 2013. pp. 24-30.
  • H. Zhang, F. Liu, M. Yang, Simulation of time Petri nets. 4th International Conference on System Science, Engineering Design and Manufacturing Informatization. Guiyang, Guizhou, October, 26-27, 2013.
  • H. Zhang, F. Liu. Simulation of Colored Time Petri Nets. 2013 IEEE International Conference on Information and Automation. Yinchuan, Ningxia. August 26-28, 2013.
  • D. Gilbert, M. Heiner, F. Liu and N. Saunders: Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology; In Proc. PETRI NETS 2013, Milano, Springer, LNCS, volume 7927, pages 230–249, June 2013.
  • O. Parvu, D. Gilbert, M. Heiner, F. Liu, and N. Saunders (2013): Modelling and Analysis of Phase Variation in Bacterial Colony Growth. In Proceedings Computational Methods in Systems Biology; 11th International Conference CMSB 2013, Springer LNCS, volume 8130, pages 78-91, 2013.
  • Liu, F., Yang, M. (2013): Colored Stochastic Petri Nets for Modeling Complex Biological Systems. International Journal of  Hybrid Information Technology. 6(5):11-24, 2013.

2012

  • Fei Liu. Colored Petri Nets for Systems Biology. PhD thesis. Brandenburg University of Technology Cottbus. January 2012.
  • F Liu, M Heiner and M Yang: An efficient method for unfolding colored Petri nets; In Proceedings of the 2012 Winter Simulation Conference (WSC 2012), Berlin, IEEE, 978-1-4673-4781-5/12, 2012, 1-12.
  • Q Gao, D Gilbert, M Heiner, F Liu, D Maccagnola and D Tree: Multiscale Modelling and Analysis of Planar Cell Polarity in the Drosophila Wing; IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(2):337-351, 2013.
  • Monika Heiner, Mostafa Herajy, Fei Liu, Christian Rohr, Martin Schwarick. Snoopy – a unifying Petri net tool. International Conference on Application and Theory of Petri Nets and Concurrency. LNCS, volume 7347, 398–407, June 2012.

2011

  • Q Gao, F Liu, D Gilbert, M Heiner and D Tree: A Multiscale Approach to Modelling Planar Cell Polarity in Drosophila Wing using Hierarchically Coloured Petri Nets; In Proc. 9th International Conference on Computational Methods in Systems Biology (CMSB 2011), Paris, ACM digital library, pages 209–218, September 2011.
  • Q Gao, F Liu, D Tree and D Gilbert: Multi-cell Modelling Using Coloured Petri Nets Applied to Planar Cell Polarity; In Proc. of the International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2011, CEUR-WS.org, CEUR Workshop Proceedings, volume 724, pages 135–150, June 2011.

2010

  • F Liu and M Heiner: Computation of Enabled Transition Instances for Colored Petri Nets; In Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), CEUR-WS.org, CEUR Workshop Proceedings, volume 643, pages 51–65, October 2010.
  • F Liu and M Heiner: Colored Petri nets to model and simulate biological systems; In Int. Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010, Braga, Portugal, pages 70-84, June 2010.
  • Shi, P., Liu, F. Yang, M. A modified ANP and its application in simulation credibility evaluation. In: International Journal of Simulation Modelling. 2010, 9(4), 195-207.

2009

  • Liu, F., Yang, M. (2009): An optimal design method for simulation verification, validation and accreditation schemes. In: Simulation. 85(6), 375-386.
  • Liu, F., Ma, P., Yang, M., Wang, Z. (2009) Validation of intelligent models: key problems. In: Journal of Harbin Institute of Technology (New Series). 12(3), 371-375
  • Shi, P., Liu, F., Yang, M. (2009): Quantify simulation verification and validation. Proceedings of the 11th International Conference on Computer Modelling and Simulation at Cambridge, UK, March 2009, 123-128.  
  • Shi, P., Liu, F., Yang, M., Wang, Z. (2009): A fuzzy rules-based approach to analyzing human behavior models. Proceedings of the 11th International Conference on Computer Modelling and Simulation at Cambridge, UK, March 2009, 346-351.  
  • Liu, F., Yang, M., Wang, Z. (2008): VV&A solution for complex simulation systems. In: International Journal of simulation: Systems, Science and Technology. 9(1), 10-18.

Talks

More publications:

 

Scientific service

  • Reviewer of National Natural Science Foundation of China, since 2013.
  • Program Committee member of International Workshop on Biological Processes & Petri Nets (since 2013).
  • Session chair of International Conference on System Simulation and Scientific Computing, 2008.
  • Member of Chinese Association of System Simulation since 2001.
  • Reviewer of some journals and conferences.

Funding

  • National Natural Science Foundation of China, Colored Petri nets-based multi-scale modeling and simulation theory, method and implementation in systems biology (61273226), 2013-2016. (Principle Investigator)
  • Natural Scientific Research Innovation Foundation in Harbin Institute of Technology, High-fidelity human behavior modeling theory and method (HIT.NSRIF.2009005), 2010-2012. (Principle Investigator)
  • China Postdoctoral Science Foundation, Intelligent analysis methods for complex simulation systems (20080430911), 2008-2009. (Principle Investigator)
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