SCHOOL OF ENGINEERING AND APPLIED SCIENCES, HARVARD UNIVERSITY

CS 266: Biologically-inspired Distributed and Multi-agent Systems

Extended Reading List

This page contains an extended list of papers and sources for the different topics that are relevant to this class -- each year we only cover a small fraction of this, and the course syllabus reflects the topics and readings for that year.

Textbooks | Swarm Intelligence | Amorphous Computing | Immune-based Systems | Evolutionary Computing | Synthetic Biology

TextBooks

Textbooks

For some of the subjects, there are textbooks that give a higher-level view of the subject. These are useful if you are presenting or want to read more about the area. We will maintain a "class library" of these books, so talk to radhika to check out the books for short periods of time.

• Books on Self-Organization and Swarms
• Self-organisation in Biological Systems, Camazine, Deneubourg, Franks, Sneyd, Theraulaz, Bonabeau, Princeton University Press, 2002. [This book covers modelling efforts in a wide variety of swarm behaviors (ants, bees, fireflies, fish, slime mold, etc)].
• Swarm Intelligence, E. Bonabeau, M. Dorigo, G. Theraulaz, Oxford University Press, 1999. [This book covers most of the concepts in social insect inspired algorithms, both the biology experiments and the applications in computer science]
• Turtles, Termites, and Traffic Jams, Mitchel Resnick, MIT Press; 1997. [Overview and simulations of many decentralized phenomena, e.g. traffic jams and forrest fires, with an interesting focus on education].
• The Origins of Order: Self-Organization and Selection in Evolution Stuart A. Kauffman, Oxford University Press, 1993. [Evolutionary view on self-organization, in biology and in artificial systems]
  
  
• Books on Development and Morphogenesis
• Algorithmic Beauty of Plants, Przemyslaw Prusinkiewicz, Aristid Lindenmayer, [Covers L-grammars and their application to modelling plants and cells]
• Algorithmic Beauty of Sea Shells, Hans Meinhardt, P. Prusinkiewicz, D.R. Fowler, Springer, 3rd edition, 2003. [Covers turing patterns and reaction-diffusion systems]
• On Growth and Form, by D'Arcy Wentworth Thompson, 1942. [Classic book on how physical forces and other simple rules guide high-level form and function in nature.]
• Principles of Development, by Wolpert (second edition 2002), and Making of the Fly, by Peter Lawrence, 1992. [Two good introductory books on developmental biology]
  
  
• Books on Distributed Systems and Applications
• Distributed Algorithms, Nancy Lynch, Morgan Kaufmann, 1997. [ Common distrubuted system algorithms and their analysis under different assumptions]
• Computer Networking, Andrew Tanenbaum, 4th edition, Prentice Hall, 2002. [excellent book on networking, from bottom up]
• Autonomous Robots: From Biological Inspiration to Implementation and Control, George Bekey, MIT Press, 2005. covers single and multi-robot systems.
• Multiagent Systems: A Modern Approach to Distributed Artificial Intelligence, Gerhard Weiss, MIT Press, 2000.

Swarm Intelligence

Swarm Intelligence: including ant-inspired approaches, flocking, synchronization, and swarm robotics.

• Intro
• Swarm Smarts, Bonabeau, Theraulaz, Scientific American, March 2000
• Self-organisation in Biological Systems (SBS), Chapter 2.
• For most of the topics below, there are chapters in SBS that give details about the biology and chapters in Swarm Intelligence (SI) that give a review of Computer Science applications.
  
  
• Ant Foraging and Path Finding
• SBS, Chapter 13 "Ant Trails".
• Trails and U-turns in the Selection of a Path by the Ant Lasius Niger. Beckers, R., Deneubourg, J.L., & Goss, S. (1992). In Journal of Theor. Biol. 159, 397-415.
• Modulation of trail laying in the ant Lasius Niger and its role in the collective selection of a food source., Beckers, R. Deneubourg, J.L., & Goss, S. (1993). J. Ins. Behav.
• The self-organising exploratory pattern of the argentine ant, J. Deneubourg, S. Aron, S. Goss, and J. Pasteels, J. Insect Behavior 3 (1990):159-168.
• A Pheromone-Based Utility Model for Collaborative Foraging. Liviu Panait and Sean Luke. Proceedings of 2004 Conference on Autonomous Agents and Multiagent Systems. (2D simulation, also see the movies and the simulation framework)
• Terrain Coverage with Ant Robots: A Simulation Study. S. Koenig and Y. Liu. International Conference on Autonomous Agents (AGENTS), 2001.Provides a theoretical link from pheromone-based graph search to LRTA*. Also, attempted implementation with drawing-robots (terrain covering ant robots)
• SI, Chapter 2 (for a review of ant-inspired routing and optimization research)
• Ant-based load balancing in telecommunication networks, R. Schoonderwoerd, O. Holland, J. Bruten and L. Rothkrantz, Journal of Adaptive Behavior, 5(2):169-207, 1997.
• AntNet: Distributed Stigmergetic Control for Communications Networks, (skip sections 8-10) G. Di Caro and M. Dorigo, Journal of Artificial Intelligence Research, 9:317--365, 1998. (a shorter paper (pdf))
• Physical Deployment of Digital Pheromones Through RFID Technology, M. Mamei, F. Zambonelli, IEEE Swarm Intelligence Symposium, Pasadena (CA), USA, 2005. (fun application and implementation of phereomone-ideas to pervasive computing) ((longer journal version))
  
  
• Collective Sorting and Clustering
• The Dynamics of Collective Sorting: Robot-Like Ants and Ant-like Robots, J. Deneubourg, S. Goss, N. Franks, A.Sendova-Franks, C. Detrain, L. Chretien, Simulation of Adaptive Behavior: from animals to animats, MIT Press, Cambridge, MA, 1990.
• From Local Actions to Global Tasks: Stigmergy and Collective Robotics, R. Beckers, O. Holland, J. Deneubourg, Artificial Life, MIT Press, Cambridge, MA, volume 4, 1994.
  
  
• Division of Labor (Task Allocation)
• Quantitative study of the fixed threshold model for the regulation of division of labor in insect societies. Bonabeau, Theraulaz, Deneubourg, Proceedings of the Royal Society of London Series B-Biological Sciences, 263: 1565-1569, 1996.
• Fixed response thresholds and the regulation of division of labour in insect societies, Bonabeau, Theraulaz, Deneubourg, Bulletin of Mathematical Biology, 60, p.753-807, 1998;
• Self-Organised Task Allocation in a Group of Robots, Labella T.H., Dorigo M., Deneubourg J.-L. International Symposium on Distributed Autonomous Robotic Systems (DARS04), June 23-25, 2004.
• Dynamic Task Assignment in Robot Swarms, James McLurkin and Daniel Yamins, Robotics: Science and Systems Conference, June 8, 2005.
  
  
• Collective Construction and Stigmergy
• Coordination in Distributed Building,Theraulaz and Bonabeau, Science, 269:686-688, 1995.
• Modeling the collective building of complex architectures in social insects with lattice swarms, Theraulaz and Bonabeau, Journal of Theoretical Biology, 1995.
• Distributed Construction by Mobile Robots with Enhanced Building Blocks, Werfel, Bar-Yam, Rus, Nagpal, IEEE International Conference on Robotics and Automation (ICRA), May 2006.
• Extended Stigmergy in Collective Construction Justin Werfel and Radhika Nagpal IEEE Intelligent Systems 21(2): 20-28 (2006).
  
  
• Towards a Swarm Language for Ant-like Robots
• Designing and Understanding Adaptive Group Behavior, M. Mataric, Adaptive Behavior 4:1, Dec 1995, 51-80. [defines a set of basis behaviors for programming ant-like robots]
• Stupid Robot Tricks: A Behavior-Based Distributed Algorithm Library for Programming Swarms of Robots James McLurkin, Master's Thesis, M.I.T., 2004,
• A Principled Design Methodology for Minimalist Multi-Robot System Controllers, Chris Jones, PhD Thesis (University of Southern California), May 2005.
• Behavior-Based Coordination in Multi-Robot Systems, Chris Jones and Maja Mataric, Autonomous Mobile Robots: Sensing, Control, Decision-Making, and Applications, Sam S. Ge and Frank L. Lewis, eds., Marcel Dekker, Inc., 2005. (survey of behavior-based techniques for programming robot swarms)
• SWARM-BOT: From Concept to Implementation, Mondada, et al, IROS 2003.
  
  
• Flocking
• SBS, Chapter 11, "Fish Schooling".
• Flocks, Herds, and Schools: A Distributed Behavioral Model, C. Reynolds, SIGGRAPH, 1987.
• Stable Flocking of Mobile Agents, Part I and Part II, Tanner, Jadbabaie, Pappas, IEEE Conference on Decision and Control 2003.
• Flocking with Obstacle Avoidance: Cooperation with Limited Communication in Mobile Networks, R. Olfati-Saber, R. Murray, IEEE Conference on Decision and Control 2003. Also see, Distributed geodesic control laws for flocking of nonholonomic agents, N. Moshtagh, A. Jadbabaie, K. Daniilidis. Proceedings of ECC-CDC 2005.
• Robust and Self-repairing Formation Control for Swarms of Mobile Agents, Jimming Cheng, Winston Cheng, Nagpal, National Conference on Artificial Intelligence (AAAI '05), July 2005.
  
  
• Collective Synchronization
• Coupled oscillators and biological synchronization Strogatz, S. and Stewart, I., Scientific American 269 (6):102-09, 1993. Synchronization of pulse-coupled biological oscillators (skip section 3) (Famous paper on firefly synchronization), Mirollo, R.and Strogatz, S., SIAM J. Appl. Math. 50: 1645-1662, 1990;
• Bard Ermentrout. An adaptive model for synchrony in the firefly pteroptyx malaccae. Journal of Mathematical Biology, 29(6):571-585, June 1991. (unlike the MS model, this adapts both phase and frequency)
• Two original historical papers on firefly synchronization:
  A Historical Note on the Synchronous Flashing of Fireflies, E. W. Gudger, Science, 1919;
  The Supposed Synchronal Flashing Of Fireflies P. Laurent, Science, 1917.
  SBS, chapter 10 "Synchronized Flashing amongst Fireflies" (gives very nice historical survey)
• Decentralized Synchronization Protocols with Nearest Neighbor Communication, Lucarelli, Wang, ACM Conference on Embedded Networked Sensor Systems (Sensys), 2004. (Mathematical Analysis of Multi-hop Sync)
• Firefly-Inspired Sensor Network Synchronicity with Realistic Radio Effects, Werner-Allen, Tewari, Patel, Welsh, Nagpal, ACM Conference on Embedded Networked Sensor Systems (SenSys), Nov 2005 (Implementation on real (MoteLab) networks)
• Firefly-inspired Heartbeat Synchronization in Overlay Networks, Ozalp Babaoglu, Toni Binci, Mark Jelasity, IEEE Conference on Self-Adaptive and Self-Organizing Systems (SASO), July 2007. (uses the Ermentrout model of synchronization with frequency adaptation for p2p networks)
• DESYNC: Self-Organizing Desynchronization and TDMA on Wireless Sensor Networks. Julius Degesys, Ian Rose, Ankit Patel, Radhika Nagpal. International Conference on Information Processing in Sensor Networks (IPSN), April 2007.
  
  
• Analysis of Distributed Concensus
• Consensus and Cooperation in Networked Multi-Agent Systems, R. Olfati-Saber, J. A. Fax, and R. M. Murray., Proceedings of the IEEE, vol. 95, no. 1, pp. 215-233, Jan. 2007.
• Flocking for Multi-Agent Dynamic Systems: Algorithms and Theory. R. Olfati-Saber, IEEE Trans. on Automatic Control, vol. 51(3), pp. 401-420, Mar. 2006.

Amorphous Computing

Amorphous Computing: including patterning and morphogenesis models, algorithmic and programmable self-assembly, gradient-based approaches, self-reconfigurable robotics and global-to-local languages and theory

• Morphogenesis and development
• Visual Models of Morphogenesis, Przemyslaw Prusinkiewicz, Mark Hammel, and Radomir Mech, 1997. [Focus on Reaction-Diffusion and L-systems]
• Principles of Development, Chapter 1, Lewis Wolpert.
• Principles of Development, Chapter 13 on Regeneration.
• The Chemical Basis of Morphogenesis, A. M. Turing, Phil. Trans. of the Royal Society of London, 1952 [classic paper].
• Morphogens: Measuring dimensions - the regulation of size and shape, Day and Lawrence, Review Article, Development 127, 2977-2987, 2000.[describes several very interesting examples of decentralized regulation of development]
• Biological Pattern Formation, Hans Meinhardt.
  
  
• Amorphous Computing: Global-to-local programming of pattern
• Amorphous Computing, Abelson, Allen, Coore, Hanson, Homsy, Knight, Nagpal, Rauch, Sussman, Weiss, Communications of the ACM, Volume 43, Number 5, May 2000.
• Programmable Self-Assembly Using Biologically-Inspired Multiagent Control, R. Nagpal, ACM Joint Conference on Autonomous Agents and Multi-Agent Systems (AAMAS), Bologna, Italy, July 2002.
• Part of chapter 5, and chapter 7, PhD Thesis, Radhika Nagpal (section on repeated structures and scale-independence).
• Biologically-inspired Self-Assembly of 2D Shapes, Using Global-to-local Compilation, A. Kondacs, International Joint Conference on Artificial Intelligence (IJCAI), 2003.
• Programming Methodology for Biologically-Inspired Self-Assembling Systems, R. Nagpal, A. Kondacs, C. Chang, AAAI Spring Symposium, March 2003.
• Towards a Catalog of Biologically-inspired Primitives, Nagpal, Workshop on Engineering Self-organising Applications (ESOA), Autonomous Agents and Multiagents Systems Conference (AAMAS), 2003.
  
  
• Amorphous Computing: More general programming languages
• Programming a Paintable Computer W. Butera, PhD Thesis, MIT Media Lab, 2002 [Browse chapters 1, 3 (esp programming model), and 5 (applications 1 and 2)].
• Infrastructure for Engineered Emergence on Sensor/Actuator Networks, Jacob Beal and Jonathan Bachrach, IEEE Intelligent Systems, (Vol. 21, No. 2) pp. 10-19, March/April 2006.
  
  
• Shape and Self-Assembly in Modular Robotics
• Self-reconfiguring robots Daniela Rus, Zack Butler, Keith Kotay, Marsette Vona, Communications of the ACM, Volume 45, Issue 3, March 2002.
• Self-reconfiguration using Directed Growth, Stoy, Nagpal, Intl Symposium on Distributed Autonomous Robotic Systems (DARs), June 2004
• Self-repair and Scale-independent Self-reconfiguration, Stoy, Nagpal, IROS Sept 2004.
• Generic Decentralized Control for a Class of Self-Reconfigurable Robots, Butler, Kotay, Rus, Tomita, IEEE Conf on Robotics and Automation (ICRA), 2002.
• Self-organizing programmable parts, Bishop et al (Erik Klavin's group) Intl Conf. on Intelligent Robots and Systems (IROS), 2005. (also see Graph grammars for self-assembling robotic systems, ICRA, 2004 for the grammer generating algorithm)
• How to Make a Self-Reconfigurable Robot Run, K. Stoy, Shen, P. Will, Intl. Conf. on Autonomous Agents and Multiagent Systems (AAMAS'02), 2002. (self-repairing locomotion)
• Multiagent Control of Self-Reconfigurable Robots, Bojinov, Casal, Hogg, Intl Conf. on Multiagent Systems (ICMAS), 2000.
  
  
• Hardware Environments
• Pushpin Computing System Overview: A Platform for Distributed, Embedded, Ubiquitous Sensor Networks, Lifton et al, Pervasive Computing 2002. (Also see Pushpin computing website) Pushpin's are the physical incarnation of butera's paintable amorphous computer.
• Self-Organising Impact Sensing Networks in Robust Aerospace Vehicles, Prokopenko et al, In John Fulcher (ed.) Advances in Applied Artificial Intelligence, 186-233, Idea Group, 2006. (Website with simulation movies)
  
  
• Applications of Gradients
• Pheromone Robots, David Payton and Mike Daily and Regina Estkowski and Mike Howard and Craig Lee, Autonomous Robots, 11, 3, 319-324, 2001.
• Motion Coordination for Ubiquitous Agents , Mamei, Mahan, Leonardi, Zambonelli, Workshop on Ubiquitous Agents on embedded, wearable, and mobile devices, AAMAS 2002.
• Co-Fields: A Physically Inspired Approach to Motion Coordination , Mamei, Zambonelli, Leonardi, IEEE Pervasive Computing, 3(2):52-61, 2004.
• Spreading Pheromones in Everyday Environments via RFID Technologies, M. Mamei, F. Zambonelli, 2nd IEEE Symposium on Swarm Intelligence, June 2005.
• Stupid Robot Tricks: A Behavior-Based Distributed Algorithm Library for Programming Swarms of Robots James McLurkin, Master's Thesis, M.I.T., 2004.
• Hormone-inspired self-organization and distributed control of robotic swarms, Shen, W.-M, P. Will, A. Galstyan, C.-M. Chuong, Autonomous Robots, 17:93-105, 2004.

Immune-inspired Systems

Immune-inspired Systems

• Computer Immunology, S. Forrest, S. Hofmeyr, and A. Somayaji. Communications of the ACM Vol. 40, No. 10, pp. 88-96 (1997).
• An Overview of the Immune System (Web Essay), Steven A Hofmeyr, 1997.
• Simulated evolution of antibody gene libraries under pathogen selection, M. Oprea and S. Forrest. 1998 IEEE International Conference on Systems, Man and Cybernetics
• Immunology as information processing.[read sections 1-3] S. Forrest, S.Hofmeyr. In Design Principles for the Immune System and Other Distributed Autonomous Systems, edited by L.A. Segel and I. Cohen. Santa Fe Institute Studies in the Sciences of Complexity. New York: Oxford University Press (2001).
• A Sense of Self for Unix Processes S. Forrest, S. A. Hofmeyr, A. Somayaji, and T. A. Longstaff. IEEE Symposium on Computer Security and Privacy (1996).
• Randomized Instruction Set Emulation to Disrupt Binary Code Injection Attacks. E.G. Barrantes, D.H. Ackley, S. Forrest, T.S. Palmer, D. Stefanovic, D.D. Zovi. In Proceedings of the 10th ACM Conference on Computer and Communications Security (CCS 2003), pp.281-289 (2003).
• Architecture for an Artificial Immune System, S. Hofmeyr, S. Forrest. Evolutionary Computation 7(1), Morgan-Kaufmann, San Francisco, CA, pp. 1289-1296 (2000).
• More papers on this topic

Evolution-inspired Systems

Evolution-inspired Systems

• Fundamentals of Natural Computing, Chapter 3, de Castro, CRC 2007 (will be handed out in class or scanned in soon).
• Evolving inventions, Koza, Keane, Streeter, Scientific American, Feb 2003.
• What's AI done for me lately? Genetic programming's human-competitive results, Koza et al, IEEE Intelligent Systems, May 2003.
• Evolving cellular automata to perform computations: A review of recent work Mitchell, Crutchfield, and Das.
• Automatic Design and Manufacture of Artificial Lifeforms, Lipson, H., Pollack J. B., (2000), Nature 406, pp. 974-978.
• Automated Damage Diagnosis and Recovery for Remote Robotics, Bongard J., Lipson H. (2004), IEEE International Conference on Robotics and Automation (ICRA04). (optional, also see the hardware demonstration in Resilient machines through continuous self-modeling, same authors, Science, 2007 314: 1118-1121.)
• Evolving an Integrated Phototaxis and Hole-avoidance Behavior for a Swarm-bot, Christensen A.L.., Dorigo M. International Conference on the Simulation and Synthesis of Living Systems (Alife X), 2006. (for more on the hardware system, see
• Cooperative Hole Avoidance in a Swarm-bot Trianni V., Nolfi S., Dorigo M. Robotics and Autonomous Systems, Volume 54, number 2, pp. 97-103
• Evolving Aggregation Behaviors for Swarm Robotic Systems: A Systematic Case Study, Bahceci E., Sahin E., IEEE Swarm Intelligence Symposium, 2005.
• Evolution of cooperation without reciprocity Riolo, Cohen, and Axelrod, Nature 414:441-443, 2001; Tides of Tolerance, Sigmund and Nowak, Nature 414:403-405.
• From Selfish Nodes to Cooperative Networks - Emergent Link-based Incentives in Peer-to-Peer Networks, David Hales, IEEE International Conference on Peer-to-Peer Computing, Aug 2004;

Synthetic Biology

Synthetic Biology, and DNA self-assembly

• Synthetic Biology, Scientific American, May 2004
• Cellular Gate Technology, Knight and Sussman, First International Conference on Unconventional Models of Computation (UMC98), 1998; [optional] for more background see Toward in vivo Digital Circuits, Weiss, Homsy, Knight, DIMACS Workshop on Evolution as Computation, 1999;
• Toggles and oscillators: new genetic circuit designs, Judd EM, Laub MT, McAdams HH, Bioessays. 2000 Jun;22(6):507-9. A synthetic oscillatory network of transcriptional regulators, M. Elowitz and S. Leibler, Nature. 2000 Jan 20;403(6767):335-8;
• Programmed population control by cell-cell communication and regulated killing.You, Cox, Weiss, Arnold, Nature. 2004 Apr 22;428(6985):868-71.[cells coordinate to control population density via quorum-sensing; a population level thermostat]
• DNA Computing by Self-Assembly, Erik Winfree, in the National Academy of Engineering, The Bridge, 33(4):31-38, 2003;
• Design and self-assembly of two-dimensional DNA crystals, Winfree, Liu, Wenzler, Seeman, in Nature 394, 539-544, Aug. 6, 1998. For more info see Winfree's page at Caltech.
• "Molecular Computation of Solutions To Combinatorial Problem," Leonard Adelman, Science, 266: 1021-1024, (Nov. 11) 1994. [Using DNA in a test tube to solve an instance of the travelling salesman problem]