Journal Publications

  • Clune J, Mouret J-B, Lipson H (2013) The evolutionary origins of modularity. Proceedings of the Royal Society B. 280: 20122863. (pdf) (two-minute video summary)
  • Clune J, Pennock RT, Ofria C, Lenski RE (2012) Ontogeny tends to recapitulate phylogeny in digital organisms. The American Naturalist. 180: E54–E63. (pdf)
  • Clune J, Stanley KO, Pennock RT, Ofria C (2011) On the performance of indirect encoding across the continuum of regularity. IEEE Transactions on Evolutionary Computation. 15(3): 346-367. (pdf)
  • Clune J, Goldsby HJ, Ofria C, and Pennock RT (2011) Selective pressures for accurate altruism targeting: Evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory. Proceedings of the Royal Society. 278: 666-674. (pdf)
  • Clune J, Misevic D, Ofria C, Lenski RE, Elena SF, and Sanjuán R (2008)
    Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. PLoS Computational Biology 4(9): e1000187. (pdf) (cover article)

Peer Refereed Conference Publications


  • Huizinga J, Mouret JB, Clune J (2014) Evolving Neural Networks That Are Both Modular and Regular: HyperNeat Plus the Connection Cost Technique. Proceedings of the Genetic and Evolutionary Computation Conference. (pdf) (video)
  • Velez R, Clune J (2014) Novelty Search Creates Robots with General Skills for Exploration. Proceedings of the Genetic and Evolutionary Computation Conference. (pdf) (video)
  • Coleman O, Blair A, Clune J (2014) Automated Generation of Environments to Test the General Learning Capabilities of AI Agents. Proceedings of the Genetic and Evolutionary Computation Conference. (pdf) (video)
  • Clune J, Chen A, Lipson H (2013) Upload Any Object and Evolve it: Injecting Complex Geometric Patterns into CPPNs for Further Evolution. Proceedings of the IEEE Congress on Evolutionary Computation. 3395-3402 (pdf)
  • Cheney N, MacCurdy R, Clune J, Lipson H (2013) Unshackling evolution: evolving soft robots with multiple materials and a powerful generative encoding. Proceedings of the Genetic and Evolutionary Computation Conference. 167-174 (pdf) (video)
  • Lee S, Yosinski J, Glette K, Lipson H, Clune J (2013) Evolving gaits for physical robots with the HyperNEAT generative encoding: the benefits of simulation. Applications of Evolutionary Computing. 540-549. (pdf) (video)
  • Lohmann S, Yosinski J, Gold E, Clune J, Blum J, Lipson H (2012) Aracna: An Open-Source Quadruped Platform for Evolutionary Robotics. Proceedings of the Artificial Life Conference. 387-392. Winner of best presentation award (presenter: Jason Yosinski). (pdf) (video)
  • Clune J, Lipson H (2011) Evolving three-dimensional objects with a generative encoding inspired by developmental biology. Proceedings of the European Conference on Artificial Life. 144-148. Note: This article is the proper cite for EndlessForms.com and describes its technology. (pdf)
  • Yosinski J, Clune J, Hidalgo D, Nguyen S, Cristobal Zagal J, Lipson H (2011) Evolving robot gaits in hardware: the HyperNEAT generative encoding vs. parameter optimization. Proceedings of the European Conference on Artificial Life. 890-897. (pdf)
  • Suchorzewski M, Clune J (2011) A novel generative encoding for evolving modular, regular and scalable networks. Proceedings of the Genetic and Evolutionary Computation Conference. 1523-1530. (pdf)
  • Clune J, Beckmann BE, McKinley PK, and Ofria C (2010) Investigating whether HyperNEAT produces modular neural networks. Proceedings of the Genetic and Evolutionary Computation Conference. 635-642. (pdf)
  • Clune J, Beckmann BE, Pennock RT, and Ofria C (2009) HybrID: A hybridization of indirect and direct encodings for evolutionary computation. Proceedings of the European Conference on Artificial Life (ECAL). Vol. 2: 134: 141.  (pdf)
  • Goldsby HJ, Knoester DB, Clune J, McKinley PK, Ofria C (2009). The evolution of division of labor. Proceedings of the European Conference on Artificial Life. Vol. 2: 10-18. (pdf)
  • Clune J, Pennock RT, and Ofria C (2009). The sensitivity of HyperNEAT to different geometric representations of a problem. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO). 675-682. (pdf) Winner of best paper award.

  • Goldsby HJ, Goings S, Clune J, and Ofria C (2009) Problem decomposition using indirect reciprocity in evolved populations. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO). 105-112. (pdf)

  • Clune J, Beckmann BE, Ofria C, and Pennock RT (2009) Evolving coordinated quadruped gaits with the HyperNEAT generative encoding. Proceedings of the IEEE Congress on Evolutionary Computation. 2764-2771. (pdf)(video) (supplementary material)

  • Clune J, Ofria C, and Pennock RT (2008) How a generative encoding fares as problem-regularity decreases. Proceedings of the 10th International Conference on Parallel Problem Solving From Nature. 358-367. (pdf)

  • Clune J, Ofria C, and Pennock RT (2007) Investigating the emergence of phenotypic plasticity in digital organisms. Proceedings of the European Conference on Artificial Life. 74-83. (pdf)

  • Clune J, Goings S, Goodman ED, and Punch W (2005) Investigations in meta-GAs: panaceas or pipe dreams? Proceedings of the Genetic and Evolutionary Computation Conference (GECCO). 235-241. Washington, D.C. (pdf)

  • Goings S, Clune J, Ofria C, and Pennock RT (2004) Kin-Selection: The rise and fall of kin cheaters. Proceedings of the Ninth Conference on Artificial Life. 303-308. (pdf)

Edited Publications

  • Krasnogor N, Auger A, Meyer-Nieberg S, Bernadó-Mansilla E, Ochoa G, Browne WN, Ong Y-S, Clune J, Pelta D, Coello Coello CA, Poulding S, Collet P, Preuss M, Eiben AE, Raidl GR, Engelbrecht AP, Ritchie M, Freitas AA, Schoenauer M, Gagné C, Sipper M, Gallagher MR, Smith J, Gershenson C, Spector L, Gustafson S, Squillero G, Hansen N, Watson J-P, Hornby GS, Witt C, Landa-Silva D, Wong ML, Lozano JA and Yu T (2011) editors, Proceedings of the Genetic and Evolutionary Computation Conference. ACM Press, New York, New York.
  • Branke J, Alba E, Arnold D, Bongard J, Brabazon A, Butz MV, Clune J, Cohen M, Deb K, Engelbrecht A, Krasnogor N, Miller JF, O'Neill M, Sastry K, Thierens D, Vanneschi L, van Hemert J and Witt C (2010) editors, Proceedings of the Genetic and Evolutionary Computation Conference. ACM Press, New York, New York, 2010.

Dissertation


  • Clune J (2010) Evolving Artificial Neural Networks with Generative Encodings Inspired by Developmental Biology. (pdf) (video)

Poster Presentations


  • Clune J, Yosinski J, Doan E, Lipson H (2012) EndlessForms.com: Collaboratively evolving 3D-printable objects online. Proceedings of the Thirteenth Conference on Artificial Life. East Lansing, MI. Best Poster Award.
  • Mouret JB, Clune J (2012) An algorithm to create phenotype-fitness maps. Proceedings of the Thirteenth Conference on Artificial Life. East Lansing, MI. (pdf of two-page abstract) (pdf of poster)
  • Strelioff C, Clune J, Ofria C, Lenski R, Epstein C (2009) Evolution of mutation rates. Workshop for Young Researchers in Mathematical Biology. Columbus, OH.
  • Clune J, Ofria C, and Pennock RT (2008) How generative encodings fare on less regular problems. Poster at the Genetic and Evolutionary Computation Conference (GECCO). Atlanta, GA.

  • Smith JJ, Pennock RT, Clune J, Armstrong E, Braverman M, Brady C (2006) Adapting Avida as an evolution education tool: development of model lesson plans. Sigma Xi, The Scientific Research Society Annual Meeting and Student Research Conference. Detroit, MI.

  • Smith JJ, Pennock RT, Clune J, Armstrong E, Braverman M, Brady C (2006) Adapting Avida as an evolution education tool: development of model lesson plans. Society for the Study of Evolution. Stony Brook, NY.
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