Structure-based control of complex networks with nonlinear dynamics

Significance Many biological, technological, and social systems can be encoded as networks over which nonlinear dynamical processes such as cell signaling, information transmission, or opinion spreading take place. Despite many advances in network science, we do not know to what extent the network architecture shapes our ability to control these nonlinear systems. Here we extend a recently developed control framework that addresses this question and apply it to real networks of diverse types. Our results highlight the crucial role of a network’s feedback structure in determining robust control strategies, provide a dynamic-detail-independent benchmark for other control methods, and open up a promising research direction in the control of complex networks with nonlinear dynamics. What can we learn about controlling a system solely from its underlying network structure? Here we adapt a recently developed framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This feedback-based framework provides realizable node overrides that steer a system toward any of its natural long-term dynamic behaviors, regardless of the specific functional forms and system parameters. We use this framework on several real networks, identify the topological characteristics that underlie the predicted node overrides, and compare its predictions to those of structural controllability in control theory. Finally, we demonstrate this framework’s applicability in dynamic models of gene regulatory networks and identify nodes whose override is necessary for control in the general case but not in specific model instances.

[1]  R. F. Cancho,et al.  Topology of technology graphs: small world patterns in electronic circuits. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[2]  Colin Campbell,et al.  Stabilization of perturbed Boolean network attractors through compensatory interactions , 2014, BMC Systems Biology.

[3]  Jure Leskovec,et al.  Community Structure in Large Networks: Natural Cluster Sizes and the Absence of Large Well-Defined Clusters , 2008, Internet Math..

[4]  F. Müller,et al.  Few inputs can reprogram biological networks , 2011, Nature.

[5]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[6]  M. Margaliot Controllability and observability of Boolean control networks , 2012 .

[7]  Panos M. Pardalos,et al.  Algorithm 815: FORTRAN subroutines for computing approximate solutions of feedback set problems using GRASP , 2001, TOMS.

[8]  Tamás Vicsek,et al.  Controlling edge dynamics in complex networks , 2011, Nature Physics.

[9]  Samik Ghosh,et al.  Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways , 2016, npj Systems Biology and Applications.

[10]  Christos Faloutsos,et al.  Graphs over time: densification laws, shrinking diameters and possible explanations , 2005, KDD '05.

[11]  Ian T. Foster,et al.  Mapping the Gnutella Network , 2002, IEEE Internet Comput..

[12]  Noah J. Cowan,et al.  Nodal Dynamics, Not Degree Distributions, Determine the Structural Controllability of Complex Networks , 2011, PloS one.

[13]  David Bryan,et al.  Combinational profiles of sequential benchmark circuits , 1989, IEEE International Symposium on Circuits and Systems,.

[14]  R. Shields,et al.  Structural controliability of multi-input linear systems , 1975, 1975 IEEE Conference on Decision and Control including the 14th Symposium on Adaptive Processes.

[15]  Adilson E Motter,et al.  Local structure of directed networks. , 2007, Physical review letters.

[16]  Eduardo D. Sontag,et al.  Mathematical Control Theory: Deterministic Finite Dimensional Systems , 1990 .

[17]  S. Fortunato,et al.  Statistical physics of social dynamics , 2007, 0710.3256.

[18]  M. Ng,et al.  Control of Boolean networks: hardness results and algorithms for tree structured networks. , 2007, Journal of theoretical biology.

[19]  Bradford A. Hawkins,et al.  EFFECTS OF SAMPLING EFFORT ON CHARACTERIZATION OF FOOD-WEB STRUCTURE , 1999 .

[20]  Donald E. Kirk,et al.  Optimal control theory : an introduction , 1970 .

[21]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[22]  M. Huxham,et al.  Do Parasites Reduce the Chances of Triangulation in a Real Food Web , 1996 .

[23]  D. Lauffenburger,et al.  Physicochemical modelling of cell signalling pathways , 2006, Nature Cell Biology.

[24]  G. Odell,et al.  Design and constraints of the Drosophila segment polarity module: robust spatial patterning emerges from intertwined cell state switches. , 2002, The Journal of experimental zoology.

[25]  L. Glass,et al.  The logical analysis of continuous, non-linear biochemical control networks. , 1973, Journal of theoretical biology.

[26]  Lada A. Adamic,et al.  The political blogosphere and the 2004 U.S. election: divided they blog , 2005, LinkKDD '05.

[27]  J. Pearson,et al.  Structural controllability of multiinput linear systems , 1976 .

[28]  Jeffrey T. Hancock,et al.  Experimental evidence of massive-scale emotional contagion through social networks , 2014, Proceedings of the National Academy of Sciences.

[29]  David Murrugarra,et al.  Molecular network control through boolean canalization , 2015, EURASIP J. Bioinform. Syst. Biol..

[30]  Tore Opsahl,et al.  Clustering in weighted networks , 2009, Soc. Networks.

[31]  Duncan Macrae Direct Factor Analysis of Sociometric Data , 2016 .

[32]  Jean M. Vettel,et al.  Controllability of structural brain networks , 2014, Nature Communications.

[33]  Panos M. Pardalos,et al.  Feedback Set Problems , 2009, Encyclopedia of Optimization.

[34]  R. Tsien,et al.  Specificity and Stability in Topology of Protein Networks , 2022 .

[35]  K. Sneppen,et al.  Specificity and Stability in Topology of Protein Networks , 2002, Science.

[36]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[37]  H. Schättler,et al.  Geometric Optimal Control , 2012 .

[38]  F. Fairman Introduction to dynamic systems: Theory, models and applications , 1979, Proceedings of the IEEE.

[39]  Peter Donnelly,et al.  Superfamilies of Evolved and Designed Networks , 2004 .

[40]  Jie Sun,et al.  Controllability transition and nonlocality in network control. , 2013, Physical review letters.

[41]  Alessandro Vespignani,et al.  Epidemic spreading in scale-free networks. , 2000, Physical review letters.

[42]  L. Zeleny,et al.  Adaptation of Research Findings in Social Leadership to College Classroom Procedures , 1950 .

[43]  B. Fiedler,et al.  Dynamics and control at feedback vertex sets. II: a faithful monitor to determine the diversity of molecular activities in regulatory networks. , 2013, Journal of theoretical biology.

[44]  Panos M. Pardalos,et al.  Feedback Set Problems , 1999, Handbook of Combinatorial Optimization.

[45]  M Chaves,et al.  Methods of robustness analysis for Boolean models of gene control networks. , 2006, Systems biology.

[46]  Luis Mateus Rocha,et al.  Control of complex networks requires both structure and dynamics , 2015, Scientific Reports.

[47]  Katherine C. Chen,et al.  Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. , 2003, Current opinion in cell biology.

[48]  Julio Collado-Vides,et al.  RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation , 2007, Nucleic Acids Res..

[49]  M. Resende,et al.  GREEDY RANDOMIZED ADAPTIVE SEARCH PROCEDURES (GRASP) , 1999 .

[50]  N. Gray,et al.  Targeting cancer with small molecule kinase inhibitors , 2009, Nature Reviews Cancer.

[51]  L. Aravind,et al.  Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. , 2006, Journal of molecular biology.

[52]  Robert R. Christian,et al.  Organizing and understanding a winter's seagrass foodweb network through effective trophic levels , 1999 .

[53]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[54]  A. Isidori Nonlinear Control Systems , 1985 .

[55]  S. Shen-Orr,et al.  Networks Network Motifs : Simple Building Blocks of Complex , 2002 .

[56]  Daizhan Cheng,et al.  Controllability and observability of Boolean control networks , 2009, Autom..

[57]  R. Thomas,et al.  Logical analysis of systems comprising feedback loops. , 1978, Journal of theoretical biology.

[58]  Sean N. Brennan,et al.  Observability and Controllability of Nonlinear Networks: The Role of Symmetry , 2013, Physical review. X.

[59]  Jure Leskovec,et al.  Predicting positive and negative links in online social networks , 2010, WWW '10.

[60]  H. Schättler,et al.  Geometric Optimal Control: Theory, Methods and Examples , 2012 .

[61]  Danielle S. Bassett,et al.  Collective Decision Dynamics in the Presence of External Drivers , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[62]  Eugene V. Koonin,et al.  Biological applications of the theory of birth-and-death processes , 2005, Briefings Bioinform..

[63]  R. Kálmán Mathematical description of linear dynamical systems , 1963 .

[64]  Denis Thieffry,et al.  Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework , 2008, Adv. Appl. Math..

[65]  Philippe Galinier,et al.  Applying local search to the feedback vertex set problem , 2013, Journal of Heuristics.

[66]  Panos M. Pardalos,et al.  A Greedy Randomized Adaptive Search Procedure for the Feedback Vertex Set Problem , 1998, J. Comb. Optim..

[67]  Mark Newman,et al.  Networks: An Introduction , 2010 .

[68]  W. Austin Elam,et al.  Physical Biology of the Cell , 2014, The Yale Journal of Biology and Medicine.

[69]  Tatsuya Akutsu,et al.  Structural controllability of unidirectional bipartite networks , 2013, Scientific Reports.

[70]  H. Othmer,et al.  The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. , 2003, Journal of theoretical biology.

[71]  Derek Ruths,et al.  Control Profiles of Complex Networks , 2014, Science.

[72]  Daryl J. Daley,et al.  Epidemic Modelling: An Introduction , 1999 .

[73]  Bryan C. Daniels,et al.  Sloppiness, robustness, and evolvability in systems biology. , 2008, Current opinion in biotechnology.

[74]  Ching-tai Lin Structural controllability , 1974 .

[75]  Ann Lieberman The Hidden Power of Social Networks: Understanding How Work Really Gets Done in Organizations , 2005 .

[76]  Christos Faloutsos,et al.  Graph evolution: Densification and shrinking diameters , 2006, TKDD.

[77]  Jean-Pierre Eckmann,et al.  Entropy of dialogues creates coherent structures in e-mail traffic. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[78]  G. Odell,et al.  The segment polarity network is a robust developmental module , 2000, Nature.

[79]  Wen-Xu Wang,et al.  Intrinsic dynamics induce global symmetry in network controllability , 2015, Scientific Reports.

[80]  U. Alon Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.

[81]  U. Alon An introduction to systems biology : design principles of biological circuits , 2019 .

[82]  Ginestra Bianconi,et al.  Network controllability is determined by the density of low in-degree and out-degree nodes. , 2014, Physical review letters.

[83]  A. Barabasi,et al.  Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets , 2015, Proceedings of the National Academy of Sciences.

[84]  Wen-Xu Wang,et al.  Energy scaling and reduction in controlling complex networks , 2016, Royal Society Open Science.

[85]  Weiping Li,et al.  Applied Nonlinear Control , 1991 .

[86]  Jure Leskovec,et al.  Signed networks in social media , 2010, CHI.

[87]  Neo D. Martinez,et al.  Food-web structure and network theory: The role of connectance and size , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[88]  L. Allen An introduction to stochastic processes with applications to biology , 2003 .

[89]  Uri Alon,et al.  An Introduction to Systems Biology , 2006 .

[90]  Albert-László Barabási,et al.  Limits of Predictability in Human Mobility , 2010, Science.

[91]  Albert-László Barabási,et al.  Control Principles of Complex Networks , 2015, ArXiv.

[92]  Albert-László Barabási,et al.  Controllability of complex networks , 2011, Nature.

[93]  Neo D. Martinez Artifacts or Attributes? Effects of Resolution on the Little Rock Lake Food Web , 1991 .

[94]  Wen-Xu Wang,et al.  A geometrical approach to control and controllability of nonlinear dynamical networks , 2016, Nature Communications.

[95]  B. Fiedler,et al.  Dynamics and Control at Feedback Vertex Sets. I: Informative and Determining Nodes in Regulatory Networks , 2013, Journal of Dynamics and Differential Equations.

[96]  D. Ruths,et al.  Response to Comment on “Control profiles of complex networks” , 2014, Science.

[97]  G. Odell,et al.  Ingeneue: a versatile tool for reconstituting genetic networks, with examples from the segment polarity network. , 2002, The Journal of experimental zoology.

[98]  Jon M. Kleinberg,et al.  Overview of the 2003 KDD Cup , 2003, SKDD.

[99]  Joseph Naor,et al.  Approximating Minimum Feedback Sets and Multicuts in Directed Graphs , 1998, Algorithmica.

[100]  M E J Newman,et al.  Random acyclic networks. , 2009, Physical review letters.

[101]  L. Movileanu,et al.  Physical Models of Living Systems , 2016 .

[102]  S. P. Cornelius,et al.  Realistic control of network dynamics , 2013, Nature Communications.

[103]  Albert-László Barabási,et al.  Observability of complex systems , 2013, Proceedings of the National Academy of Sciences.

[104]  L. Glass Classification of biological networks by their qualitative dynamics. , 1975, Journal of theoretical biology.

[105]  S. Brenner,et al.  The structure of the nervous system of the nematode Caenorhabditis elegans. , 1986, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[106]  Adilson E Motter,et al.  Control of Stochastic and Induced Switching in Biophysical Networks. , 2015, Physical review. X.

[107]  Andrei Z. Broder,et al.  Graph structure in the Web , 2000, Comput. Networks.

[108]  Albert-László Barabási,et al.  Internet: Diameter of the World-Wide Web , 1999, Nature.

[109]  K. Norlen 1 EVA : Extraction , Visualization and Analysis of the Telecommunications and Media Ownership Network , 2002 .

[110]  Réka Albert,et al.  Cell Fate Reprogramming by Control of Intracellular Network Dynamics , 2014, PLoS Comput. Biol..

[111]  Matthew Richardson,et al.  Trust Management for the Semantic Web , 2003, SEMWEB.