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计算系统生物学中心

计算系统生物学中心

在数学、物理学、化学、信息科学等学科的交叉与渗透下，生命科学正经历着革命性的蓬勃发展。 计算系统生物学中心基于大数据分析与生命科学实验技术的交叉融合，建设生命科学形态计算仿真与数理技术应用的平台。开展认知、注意、学习与记忆过程的脑科学实验研究，建立大脑学习记忆过程的大尺度计算模型，揭示大脑信息处理机制，启发类脑智能学习新理论、新算法；发展非线性、复杂性与系统科学的新理论与新方法，分析和理解物理、生态、生物、化学、环境、金融、社会等领域中复杂性系统演化的规律，并应用于现实复杂系统的调控；发展统计、动力系统和随机过程新的数值和理论方法，致力于进化生物学和遗传学中的定量化建模与分析，以及数学和理论生物学的交叉研究。

团队PI人员

冯建峰 |

主要研究方向

方向一：神经形态计算与仿真

主要研究神经信息与代码、神经计算模型、神经系统非线性动力学、局部神经回路和大尺度神经网络的计算模拟。光遗传学、多通道电生理、多尺度脑影像等的数据挖掘与建模。

方向二：非线性科学及复杂性系统科学

主要研究非线性动力学建模与分析和数据同化等方法，以及物理、生物、环境与社会领域中复杂性系统演化的个性与共性机制，研究对于现实世界中复杂系统调控的新方法。

方向三：进化和遗传计算模型

主要研究数学和理论生物学等方面的交叉领域，研究各类进化生物学和遗传学中的定量化模型，发展数学、统计、数值的新理论和新方法。

研究进展

揭示具有一般划分结构与拓扑结构分群同步的网络特性

相对于完全协同，分群协同更为广泛出现在生物、物理和工程等自然和人造系统中，也是系统实现其功能的重要特征。以往的研究都局限于仅考虑群内同步、简单的分群划分、简单的拓扑结构。我们首次完整严格的刻画了分群协同的数学定义，将分群协同定义为：群内同步、群间异步和轨道有界三个部分。我们发展了新的代数方法研究群内同步，提出了新的图代数性质与概念—分群生成树，证明了在一定条件下，网络实现分群协同的充要条件是每个划分的节点子集具有分群生成树结构。由此揭示了群内连接与群间连接对于实现分群协同的作用。特别的，如图1所示，相互之间没有任何连接的节点子集仍可能实现群内同步。

这个工作受到国内外同行的广泛关注，荷兰，英国等国外知名学者的研究论文明确指出他们的一些方法来自我们的工作。参考文献3在Chaos(2010-2016) 所有期刊中引用次数排名第3。

References:

  1. Han, Yujuan; Lu, Wenlian; Chen, Tianping, Achieving Cluster Consensus in Continuous-Time Networks of Multi-Agents With Inter-Cluster Non-Identical Inputs [J] IEEE TRANSACTIONS ON AUTOMATIC CONTROL, 2015, 60(3): 793-798.

  2. Han, Yujuan; Lu, Wenlian; Chen, Tianping, Cluster Consensus in Discrete-Time Networks of Multiagents With Inter-Cluster Nonidentical Inputs [J] IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS, 2013, 24(4): 566-578.

  3. Lu, Wenlian; Liu, Bo; Chen, Tianping, Cluster synchronization in networks of coupled nonidentical dynamical systems [J] CHAOS, 2010, 20(1): 013120.

计算机网络病毒传播动力学行为研究

定量化网络安全度量是网络安全科学最核心的问题之一。近年来，我们基于生物病毒传播模型提出了一系列计算机网络病毒传播与防御动力学模型，包括具有主动感染的传播模型、（竞争/合作）的多病毒传播网络模型、主动式防御模型和移动目标防御模型。在此基础上，我们利用控制、优化和博弈的方法建立病毒传播与防御的分析与计算模型，由此定义防御策略的效率，这可为理解和定量网络安全度量提供有效方法。

References:

  1. Xu, Shouhuai; Lu, Wenlian; Xu, Li; Zhan, Zhenxin. Adaptive Epidemic Dynamics in Networks: Thresholds and Control [J] ACM TRANSACTIONS ON AUTONOMOUS AND ADAPTIVE SYSTEMS, 2014, 8(4): 19.

  2. Xu, Shouhuai; Lu, Wenlian; Xu, Li, Push- and Pull-Based Epidemic Spreading in Networks: Thresholds and Deeper Insights [J] ACM TRANSACTIONS ON AUTONOMOUS AND ADAPTIVE SYSTEMS, 2012, 7(3): 32.

  3. Xu, Shouhuai; Lu, Wenlian; Zhan, Zhenxin, A Stochastic Model of Multivirus Dynamics [J] IEEE TRANSACTIONS ON DEPENDABLE AND SECURE COMPUTING, 2012, 9(1): 30-45.

  4. Zheng, Ren; Lu, Wenlian; Xu, Shouhuai, Active Cyber Defense Dynamics Exhibiting Rich Phenomena[C]. HotSoS ’15, April 21 – 22, 2015, Urbana, IL, USA

  5. Han, Yujuan Han; Lu, Wenlian Lu; Xu, Shouhuai, Characterizing the Power of Moving Target Defense via Cyber Epidemic Dynamics [C], HotSoS ’14, April 08 – 09 2014, Raleigh, NC, USA

  6. Lu, Wenlian Lu; Xu, Shouhuai; Yi, Xinlei, Optimizing Active Cyber Defense[C], GameSec 2013, LNCS 8252, pp. 206–225, 2013

发表成果（2015-2016）

  1. Pan Li, Wei Lin, and Konstantinos Efstathiou [2017] Isochronous dynamics in pulse coupled oscillator networks with delay, CHAOS, vol. 27 (5), art. no. 053103.

  2. Yao Guo, Wei Lin*, Yuming Chen, and Jianhong Wu [2017], Instability in time-delayed switched systems induced by fast and random switching, Journal of Differential Equations, vol. 263 (2), 880-909.

  3. Kunquan Lan and Wei Lin [2017] Population models with quasi-constant-yield harvest rates, Mathematical Biosciences and Engineering, vol. 14 (2), 467-490.

  4. Yao Guo, Wei Lin*, and Daniel W. C. Ho [2016] Discrete-time systems with random switches: From systems stability to networks synchronization, CHAOS, vol. 26 (3), Article no. 033113.

  5. Wei Cheng, Edmund T. Rolls, Jiang Qiu, Wei Liu, Yanqing Tang, Chu-Chung Huang, XinFa Wang, Jie Zhang, Wei Lin, Lirong Zheng, JunCai Pu, Shih-Jen Tsai, Albert C. Yang, Ching-Po Lin, Fei Wang, Peng Xie, Jianfeng Feng* [2016] Medial reward and lateral non-reward orbitofrontal cortex circuits change in opposite directions in depression, Brain, vol. 139 (12) 3296-3309.

  6. Pei Yu and Wei Lin [2016] Complex dynamics in biological systems arising from multiple limit cycle bifurcation, Journal of Biological Dynamics, vol. 10 (1), pp. 263-285.

  7. Siyang Leng, Wei Lin*, and Jürgen Kurths, [2016] Basin stability for delayed dynamics, Scientific Reports, vol. 6, Article no. 21449.

  8. Kunquan Lan and Wei Lin [2016] Uniqueness of nonzero positive solutions of Laplacian elliptic equations arising in combustion theory, Discrete and Continuous Dynamical System-B, vol. 21, no. 3, pp. 849-861.

  9. Rodrigues, F. A., Peron, T. K. D., Ji, P.  & Kurths, J. (2016).  Kuramoto model in complex networks, \textbf{Physics Reports} 610(26). (IF 16.24)

  10. Han, X.,  Xia, F.,  Ji, P.,  Bi, Q., & Kurths, J.. Hopf -bifurcation-delay-induced bursting patterns in a modified circuit system. Communications in Nonlinear Science and Numerical Simulation, 36, 2016 (IF 2.834)

  11. Huang, L., Qu H., Ji. P, Liu X., and Zhen F. "A novel coordinated path planning method using k-degree smoothing for multi-UAVs." Applied Soft Computing 48 (2016): 182-192.(IF 2.857)

  12. Ji, P., Lu, W, & Kurths, J. (2015).  Onset and suffusing transitions towards synchronization in complex networks.  Europhysics Letters, 109(6), 60005. (IF 2.095)

  13. Peron, T. K. D., Ji, P., Rodrigues, F. A., & Kurths, J. (2015).  Effects ofassortative mixing in the second-order Kuramoto model.  Physical Review E, 91, 052815. (IF 2.228)

  14. Han X., Bi S., Ji P. & Kurths, J., (2015). Fast-slow analysis for parametrically and externally excited systems with two low excitation frequencies. Physical Review E, 92, 012911. (IF 2.228)

  15. Huanfei Ma, Daniel W. C. Ho, Ying-Cheng Lai, and Wei Lin* [2015] Detection meeting control: Unstable steady states in high-dimensional nonlinear dynamical systems, Physical Review E, vol. 92 (4), Article no. 042902.

  16. Yongzheng Sun* and Wei Lin* [2015] A Positive role of multiplicative noise on the emergence of flocking in a stochastic Cucker-Smale system, CHAOS, vol. 25, Article no. 083118.

  17. Bing Xu and Wei Lin* [2015] Parameters identification by a piecewise adaptive rule with a fractional power, International Journal of Bifurcation and Chaos, vol. 25 (12), Article no. 1550166.

  18. Chengwen Chen, Ye Yao, Liang Zhang, Minjie Xu, Jianping Jiang, Tonghai Dou, Wei Lin, Guoping Zhao, Minren Huang, and Yan Zhou* [2015], A comprehensive analysis of the transcriptomes of Marssonina brunnea and infected poplar leaves to capture vital events in host-pathogen interactions, PLoS ONE, vol. 10 (7), Article no. e0134246.

  19. Jun Guo, Wei Wang, Zhi-cheng Sun, Xin-sheng Wu, Mei Hao, Jian-long Ge, Pan-tong Yao, Jian-bing Zhu, Wei Lin, and Lei Xue* [2015] A three-pool model dissecting readily releasable pool replenishment at the calyx of held, Scientific Reports, vol. 5, Article no. 9517.



上海市浦东新区张江高科技园区张衡路825号复旦大学张江校区

  • 复旦大学类脑智能科学与技术研究院,复旦大学类脑研究院