Tutorial 13: Biological Signal Processing and Molecular Network Informatics

Presented by

Jian-Qin Liu (National Institute of Information and Communications Technology), Haruhiko Nishimura (University of Hyogo)


Recently years, new challenging issues are continuing to be emerged while the application fields of signal processing have been greatly extended. Bioinformatics is one of the most important application fields of signal processing. This tutorial is designed as the assistance to answering major questions with respect to applying advanced signal processing technology in the bioinformatics of the cell communication. The tutorial is unified by the clue of the kernel theory of signal processing for complex networked information processing in biological systems, especially, the cell.

Towards systematically understanding the cellular functions, the major aspects of the study on the communication mechanism of signaling pathway networks in the cell are presented as follows:

  1. Bioinformatics models for signaling pathway networks:
    Considering the biochemistry features of signaling pathway networks, the computational methods are applied in the simulation of cellular signaling. Here computational complexity is also an important factor for the feasibility of reconstruction of signaling pathway networks.

  2. Robustness analysis of biomolecular networks under discrete state transitions:
    Robustness has been intensively studied in several fields such as control theory, signal processing, and systems biology. Among the major features of cells, specificity is a key to understand the cellular signaling mechanism that sustains the robustness of cells. With the methods of system identification and signal estimation, it is possible to quantitatively analyze the parametric specificity of signaling pathway networks. In contrast to the widely applied analysis methods for the continuous-valued form of signaling pathways, nonsmooth analysis is a promising method to analyze the signaling mechanism of state transitions among different areas of steady states.

  3. Spatial dynamics of cellular signaling pathway networks:
    Besides the codes formulated for signaling pathway networks, the channel unit is introduced into the dynamics model of cellular communication where the joint temporal and spatial dynamics can be investigated. With the supporting technology from communication engineering, it is feasible to study the effect of the channel loss, the delay, and the capacity of cellular signaling processes on the dynamical characteristics such as stability.

  4. NCS-based analysis of cellular communication:
    Based on the knowledge of signaling pathway networks in network dynamics and information theory, NCS (Networked Control Systems) is a powerful tool in theory to help us to understand how the collective behavior of cellular functions are emerged in the cell, which is a complex system where a signaling pathway network within the cell is also a complex network.

  5. Towards systematically understanding cellular communication by communication theory and communication engineering:
    In the eyes of communication theory and communication engineering, a software simulator can be developed as a test-bed in order to carry out the performance analysis of a cellular communication system, by which the network structure of the cellular communication system will be explored for their potential applications in nanobiotechnology such as synthetic biology for biomedical engineering and nano-medicine. It is also noticeable that the pathways of neuro-transmitters in the cellular communication processes are crucial in molecular neuroscience, which covers broad fields including sympathetic/parasympathetic nervous systems and cellular signaling pathways for LTP. With the methodology of complex networks, it is expected to systematically understanding the fine-grained network architecture of cellular communication systems in nature.


  1. Overview of filter theory: successful tools and challenges (Liu)
  2. The dynamics of complex networks (Liu and Nishimura)
  3. Filtering theory for bioinformatics (Liu)
  4. Dynamics of cellular signaling pathway networks (Liu)
  5. Biomedical image processing and neural signal processing for neuroscience (Liu and Nishimura)
  6. The state-of-the-art of biological signal processing (Liu)

Speaker Biography

Jian-Qin Liu received the B.S. degree in computer science and system science from Nankai University, Tianjin, China, in 1986, the M.S. degree in automatic control theory and applications from Xi'an Jiaotong University, Xi'an, China, in 1992, the Ph.D. degree in industrial automation from Central South University, Changsha, China, in 1997 and the Ph.D. degree in informatics from Kyoto University, Kyoto, Japan, in 2006.

He worked as an Assistant Lecturer at Xi'an Jiaotong University from 1986 to 1991 and a Lecturer from 1991 to 1994, a Visiting Researcher at Information and Communication R & D Center, Ricoh Co. Ltd., Yokohama, Japan, from 1994 to 1995, an Associate Professor at Central South University from 1995 to 2000, where he became a Professor in 2000. From 1999 to 2006, he worked as a Researcher at Advanced Telecommunication Research Institute International (ATR), Kyoto, Japan, where he became a Senior Researcher in 2003. Since 2006, he has been an Expert Researcher at Kobe Advanced ICT Research Center, National Institute of Information and Communications Technology, Kobe, Japan.

His current research interests include signal processing, bioinformatics, and communication networks. He had been giving lectures on the courses of signal processing, pattern recognition and neural networks, and control theory in universities in China. He had given tutorials at ECAI'02, ECAL'03, "MEMS,NANO&Smart Systems"2004, IEEE/ASME-AIM'07, SICE'07, IEEE-NANO'09, ICST-Nano-Net'09. He is the first/sole author of three books in which the latest one is "Biomolecular Computation for Bionanotechnology (Boston|London: Artech House, 2007)", more than 40 papers published in academic journals including IEEE Transactions on Nanobioscience and IEEE Transactions on Systems, Man, and Cybernetics (Part C).

Dr. Liu received the Chen Xinmin Award from Central South University in 1998 and the Research Award from Advanced Telecommunication Research Institute International in 2005.

He is a Vice Co-chair of Nano-Scale, Molecular, and Quantum Networking Subcommittee of Emerging Technologies Committee, IEEE Communications Society, a Program Co-chair of the first IEEE MoNaCom Workshop (in conjunction with IEEE INFOCOM 2011), an Area Associate Editor of Special Issues on Emerging Technologies in Communications: Area 8"Nanoscale and Molecular Networking", IEEE Journal on Selected Areas in Communications, and a member of the Editorial Board of Nano Communication Networks Journal (Elsevier), Journal of Frontiers of Computer Science in China (Higher Education Press and Springer), and CAAI (Chinese Association for Artificial Intelligence) Transactions on Intelligent Systems.

He is a member of the IEEE P1906.1 standards working group.


Haruhiko Nishimura graduated from the Department of Physics, Shizuoka University in 1980 and completed the doctoral program at Kobe University, and received the PhD degree in 1985.

After working in the Faculty of Medicine of Hiroshima University, he joined Hyogo University of Education as an associate professor in 1990 and became a professor in 1999. Since 2004, he has been a professor in the Graduate School of Applied Informatics, University of Hyogo. He is currently the director of the information science research center for social applications, University of Hyogo.

His research field is intelligent systems science by several architectures such as neural networks and complex systems. He is also presently engaged in research on biomedical, healthcare, and high confidence sciences. He has published more than 100 papers in international journals and international conferences.

He is currently serving as a Committee Member of the "Task Force on Complex-valued Neural Networks", IEEE Computational Intelligence Society, and as a Member of the editorial board of the Journal of the Society of Kansei Engineering.

He is a member of the IEEE, IEICE, IPSJ, ISCIE, JNSS and others and was awarded ISCIE paper prize in 2001 and JSKE paper prize in 2010.