Clare Bates Congdon

Home Brief CV Projects Publications Teaching Contact

Clare Bates Congdon: Publications

* denotes undergraduate, MS, or high-school co-authors

Categories:

Recent papers in Digital Humanities and Social Sciences
Bioinformatics
Intelligent Agents
Evolutionary Design
Computer Science and STEM Pedagogy
Soar

Recent papers in Digital Humanities and Social Sciences

“Measuring the relative importance of different agricultural inputs to global and regional crop yield growth since 1975”. E. Nelson, and C. B. Congdon, F1000Research 2016, 5:2930 (doi: 10.12688/f1000research.10419.1)
"Using Clustering to Explore Teacher Communication on Twitter". S. Houser, C. B. Congdon, D. Santoro, and J. Hochman. International Workshop on Social Media Mining and Analysis, June 2017, Exeter, UK.
"Wandering Words: Tracing Changes in Words Used by Teacher Tweeters Over Time". S. Houser, C. B. Congdon, D. Santoro, and J. Hochman. International Workshop on Social Media World Sensors, held in conjunction with HT2017: 28th ACM Conference on Hypertext and Hypermedia 2017, July 2017, Prague, CZ.

Bioinformatics

Journal Papers

"Effects of Vitamin A Deficiency in the Postnatal Mouse Heart - Role of Hepatic Retinoid Stores", M. A. Asson-Batres, S. V. Ryzhov, O. Tikhomirov, C. W. Duarte, C. B. Congdon, C. R. Lessard*, S. McFarland*, C. Rochette-Egly, T.-L. Tran, C. L. Galindo, A. J. Favreau-Lessard, D. B. Sawyer. American Journal of Physiology - Heart and Circulatory Physiology, April 2016.
“Common features of microRNA target prediction tools”, S. M. Peterson, J. A. Thompson*, M. L. Ufkin, P. Sathyanarayana, L. Liaw, C. B. Congdon. Frontiers in Genetics 5:23, January 2014.
“No-boundary thinking in bioinformatics research”, X. Huang, B. Bruce, A. Buchan, C. B. Congdon, C. L. Cramer, S. F. Jennings, H. Jiang, Z. Li, G. McClure, R. McMullen, J. H. Moore, B. Nanduri, J. Peckham, A. Perkins, S. W. Polson, B. Rekepalli, S. Salem, J. Specker, D. Wunsch, D. Xiong, S. Zhang, Z. Zhao. BioData Mining 6:19, November 2013.
“Bioinformatic prediction of arthropod/nematode-like peptides in non-arthropod, non-nematode members of the Ecdysozoa”, A. E. Christie, D. H. Nolan*, Z. A. Garcia*, M. D. McCoole, S. M. Harmon*, B. Congdon-Jones*, P. Ohno*, N. Hartline*, C. B. Congdon, K. N. Baer, P. H. Lenz. General and Comparative Endocrinology 170 (2011) 480-486, February 2011.
“An Evaluation of Information Content as a Metric of the Inference of Putative Conserved Noncoding Regions in DNA Sequence Using a Genetic Algorithms Approach”, C. B. Congdon, J. Aman, G. M. Nava, H. R. Gaskins, C. Mattingly. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 5(1), 1-14, January 2008.

Invited Papers and Book Chapters

“It’s Not Junk! The Search for Functional Elements in Noncoding DNA”, C. B. Congdon, H. R.Gaskins, G. M. Nava, C. Mattingly. ACM SIGEVOlution, 3(3), 5-16, Fall 2008.
“EpiSwarm, A Swarm-based System for Investigating Genetic Epistasis”, T. Goth*, C-T Tsai, F-T Chiang, and C. B. Congdon. In Y. Chen and M. H. Lim (eds.), Linkage in Evolutionary Computation, pp. 315-334. Springer. October 2008.
“Phylogenetic Inference Using Evolutionary Algorithms”, C. B. Congdon. In DW Corne, GF Fogel, and Y Pan, editors, Computational Intelligence in Bioinformatics, pp. 237-262. Wiley. December 2007.

Refereed Conference Papers

“GAMI-CRM: Using de novo motif inference to detect cis-regulatory modules”, J. A. Thompson* and C. B. Congdon, IEEE Congress on Evolutionary Computation, July 2014.
“An Exploration Into Improving DNA Motif Inference by Looking for Highly Conserved Core Regions”, J. A. Thompson* and C. B. Congdon, IEEE Computational Intelligence in Bioinformatics and Computational Biology, pp. 60-67, April 2013.
“GAMID Using Genetic Algorithms for the Inference of DNA Motifs That Are Represented in Only a Subset of Sequences of Interest”, J. A. Thompson* and C. B. Congdon, IEEE Congress on Evolutionary Computation, pp. 1-8, July 2012.
“Preliminary results for GAMMI: Genetic algorithms for motif-module inference”, D. J. Gagne* and C. B. Congdon, IEEE Congress on Evolutionary Computation, pp. 1-8, July 2012.
“Towards Interactive Visualization for Exploring Conserved Motifs in Noncoding DNA Sequence”, C. B. Congdon, H. R. Gaskins, G. M. Nava, and C. Mattingly. IEEE Frontiers in the Convergence of Bioscience and Information Technologies (FBIT 2007), pp. 234-240. October, 2007.
“Initial Results with EpiSwarm, A Swarm-based System for Investigating Genetic Epistasis”, T. Goth*, C-T Tsai, F-T Chiang, and C. B. Congdon. IEEE Congress on Evolutionary Computation, Singapore, pp. 3855-3861. September 2007.
“Preliminary Results for GAMI: A Genetic Algorithms Approach to Motif Inference”, C. B. Congdon, C. W. Fizer*, N. W. Smith*, H. R. Gaskins, J. Aman*, G. Nava, and C. Mattingly. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB-2005), pp 97-104. La Jolla, California, November 2005.
“Phylogenetic Trees Using Evolutionary Search: Initial Progress in Extending Gaphyl to Work with Genetic Data”, C. B. Congdon and K. J. Septor*, Congress on Evolutionary Computation (CEC-2003), Canberra, Australia, December 2003.
“Gaphyl: An Evolutionary Algorithms Approach for the Study of Natural Evolution”, C. B. Congdon, Genetic and Evolutionary Computation Conference (GECCO-2002), New York, NY, July 2002. (Best paper award, Real-World Applications track.)
“An Evolutionary Approach to Phylogenetic Tree Construction”, C. B. Congdon, International Work- shop on Frontiers of Evolutionary Algorithms (FEA-2002), Joint Conference on Information Sciences, Research Triangle park, NC, March 2002.
“Gaphyl: A Genetic Algorithms Approach to Cladistics”, C. B. Congdon, Principles and Practice of Knowledge Discovery in Databases (PKDD 2001), Freiburg, Germany, September, 2001. In L. DeRaedt, A. Siebes (eds.), Principles of Data Mining and Knowledge Discovery, Lecture Notes in Computer Science, Vol. 2168, Springer-Verlag, Berlin, pp 67-78.
“Classification of Epidemiological Data: A Comparison of Genetic Algorithm and Decision Tree Approaches”, C. B. Congdon, IEEE Congress on Evolutionary Computation, San Diego, CA, July, 2000.

Workshop Papers

“Issues in Working on Biological Applications of Evolutionary Computation”, C. B. Congdon, Workshop on Biological Applications of Evolutionary Computation, Genetic and Evolutionary Computation Conference (GECCO-2004), Seattle, WA, June 2004.
“Moving from Phenotypes towards Genotoypes: Revising Gaphyl to Work with DNA Data”, C. B. Congdon, Workshop on Biological Applications of Evolutionary Computation, Genetic and Evolutionary Computation Conference (GECCO-2003), Chicago, IL, July 2003.
“An Evolutionary Algorithms Approach to Phylogenetics”, C. B. Congdon, Workshop on Biological Applications of Evolutionary Computation, Genetic and Evolutionary Computation Conference (GECCO-2002), New York, NY, July 2002.
“Gaphyl: A Genetic Algorithm Approach to Cladistics”, C. B. Congdon and E. F. Greenfest*, Workshop on Data Mining with Evolutionary Algorithms, Genetic and Evolutionary Computation Conference (GECCO-2000), Las Vegas, NV, July 2000.
“Genetic Algorithms in Cladistics”, C. B. Congdon and E. F. Greenfest*, Grace Hopper Celebration of Women in Computing, Cape Cod, MA, September 2000.
“Genetic Algorithms for Identifying Combinations of Genes and Other Risk Factors Associated with Coronary Artery Disease”, C. B. Congdon, C. F. Sing, S. L. Reilly, Workshop on Artificial Intelligence and the Genome, International Joint Conference on Artificial Intelligence, August 1993.

Reviewed/Published Abstracts

“A Preliminary Investigation of Genes Associated with Increased Cancer Survival Time”, J. A. Thompson*, C. Duarte, P. Marks, C. B. Congdon. ACM International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, p. 627-628, September, 2014.
“A Workflow for the Computational Identification of Candidate Regulatory Elements in Noncoding DNA”, J. A. Thompson*, C. R. Lessard*, S. McFarland*, R. L. Morris, C. B. Congdon. ACM International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, p. 643-644, September, 2014.
“Initial Results In Using de Novo Motif Inference to Detect Cis-Regulatory Modules”, J. A. Thompson* and C. B. Congdon, ACM International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, p. 687, September, 2013.
“A Genetic Algorithms Approach to the Inference of Cis-Regulatory Modules”, D. J. Gagne* and C. B. Congdon, IEEE Bioinformatics and Biomedicine, p. 1004, November 2011.
“Using Genetic Algorithms for the Inference of Motifs That Are Represented In Only a Subset of Sequences of Interest”, J. A. Thompson* and C. B. Congdon, IEEE Bioinformatics and Biomedicine, p. 1005, November 2011.

PhD Thesis (and Tech Report)

“A Comparison of Genetic Algorithms and Other Machine Learning Systems on a Complex Classification Task from Common Disease Research”, Ph.D. thesis, University of Michigan, Computer Science and Engineering Division, Dept. of Electrical Engineering and Computer Science, February 1995.

Intelligent Agents

Journal Papers:

“Costly information and the evolution of self-organization in a small, complex economy”, J. Wilson, J. Hill, M. Kersula, C.L. Wilson, L. Whitsel, L. Yan, J. Acheson, Y. Chen, C. Cleaver, C. B. Congdon, A. Hayden, P. Hayes, T. Johnson, G. Morehead, R. Steneck, R. Turner, R. Vadas, C.J. Wilson. Journal of Economic Behavior & Organization, 90(supplement), pp. S76-S93, June 2013.
“Integrated Mobile Robot Design: Winning the AAAI-92 Robot Competition”, D. Kortenkamp, M. Huber, C. Cohen, U. Raschke, C. Bidlack, C. Congdon, F. Koss, and T. Weymouth. IEEE Expert 8(4) (August, 1993), pp. 61-73.

Invited Papers and Book Chapters

“Learning and Game AI”, H. Munoz-Avila, C. Bauckhage, M. Bida, C. B. Congdon, G, Kendall. In Artificial and Computational Intelligence in Games, Ed. S. M. Lucas, M. Mateas, M. Preuss, P. Spronck, J Togelius, Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, Dagstuhl, Germany, 6, pp 33-43, December, 2013.
“General Video Game Playing”, J. Levine, C. B. Congdon, M. Ebner, G. Kendall, S. M. Lucas, R. Miikkulainen, T. Schaul, T. Thompson. In Artificial and Computational Intelligence in Games, Ed. S. M. Lucas, M. Mateas, M. Preuss, P. Spronck, J Togelius, Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, Dagstuhl, Germany, 6, pp 77-83 December, 2013.
“Artificial and Computational Intelligence for Games on Mobile Platforms” C. B. Congdon, P. Hingston, G. Kendall. In Artificial and Computational Intelligence in Games, Ed. S. M. Lucas, M. Mateas, M. Preuss, P. Spronck, J Togelius, Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, Dagstuhl, Germany, 6, pp 101-108 December, 2013.
“Integrating High-Speed Obstacle Avoidance, Global Path Planning, and Vision Sensing on a Mobile Robot”, D. Kortenkamp, M. Huber, C. Cohen, U. Raschke, F. Koss, and C. Congdon. In Artificial Intelligence and Mobile Robots: Case Studies of Successful Robot Systems, Ed. D. Kortenkamp, P. Bonasso, and R. Murphy, MIT Press, Cambridge, MA, 1998.
“Carmel vs. Flakey: A Comparison of Two Winners”, C. B. Congdon, M. Huber, D. Kortenkamp, K. Konolige, K. Meyers, A Saffioti. AI Magazine, v. 14, n. 1, Spring 1993. (A longer version of this paper is also available as AAAI Press Tech Report #RC-92-01.)

Refereed Conference Papers

“Mobile games with intelligence: A killer application?”, P. Hingston, C. B. Congdon, and G. Kendall, IEEE Computational Intelligence in Games, pp. 1-7, August 2013.
“FRIGHT: A flexible rule-based intelligent ghost team for Ms. Pac-Man”, D. J. Gagne* and C. B. Congdon, IEEE Computational Intelligence and Games (CIG 2012), pp. 273-280, September 2012.
“Personality profiles for generating believable bot behaviors”, C. Rosenthal* and C. B. Congdon, IEEE Computational Intelligence and Games (CIG 2012), pp. 124-131, September 2012.
“REALM: A Rule-Based Evolutionary Computation Agent that Learns to Play Mario”, S. Bojarski* and C. B. Congdon, IEEE Computational Intelligence in Games (CIG 2010), pp. 83-90, August 2010.
“RAMP: A Rule-Based Agent for Ms. Pac-Man”, A. Fitzgerald* and C. B. Congdon. IEEE Congress on Evolutionary Computation (CEC-2009), pp. 2646-2653, May 2009.
“Agent Smith: An Evolutionary Agent for Interactive Dynamic Games”, R. Small* and C. B. Cong- don. IEEE Congress on Evolutionary Computation (CEC-2009), pp. 660-666, May 2009.
“GENCEM: A Genetic Algorithms Approach to Coordinated Autonomous Multi-Robot Exploration and Mapping”, C. C. Sotzing*, W. M. Htay*, C. B. Congdon, IEEE Congress on Evolutionary Computation (CEC-2005), pp. 2317-2324, August 2005.
“Integrating Obstacle Avoidance, Global Path Planning, Visual Cue Detection and Landmark Triangulation in a Mobile Robot”, D. Kortenkamp, M. Huber, C. B. Congdon, S. Huffman, C. Bidlack, C. Cohen, F. Koss, U. Raschke, T. Weymouth, SPIE Mobile Robots VII, Boston MA, November 1992.

Reviewed/Published Abstracts

“Winning the AAAI Robot Competition”, D. Kortenkamp, M. Huber, C. Cohen, U. Raschke, C. Bidlack, C. B. Congdon, F. Koss, T. E. Weymouth, American Association for Artificial Intelligence Conference (AAAI-1993), pp 858-859.

Workshop Papers

“A Complex Adaptive Systems Investigation of the Social-Ecological Dynamics of Three Fisheries”, P. S. Hayes, J. Wilson, C. B. Congdon, L. Yah, J. Hill, J. Acheson, Y. Chen, C. Cleaver, A. Hayden, T. Johnson, M. Kersula, G. Morehead, R. Steneck. Association for the Advancement of Artificial Intelligence (AAAI) Fall Symposium on Complex Adaptive Systems: Energy, Information, and Intelligence, November 2011.
“Adaptive Agent-based Modeling of Gulf of Maine Fisheries”, P. Hayes, J. Wilson, C. B. Congdon, Workshop on Agent-Based Computational Economics and Finance, IEEE Congress on Evolutionary Computation (CEC), New Orleans, 2011.
“RAMP: A Rule-Based Agent for Ms. Pac-Man”, A. Fitzgerald, P. Kemeraitis*, and C. B. Congdon, entry for Ms. Pac-Man Competition, World Congress on Computational Intelligence (WCCI), Hong Kong, June 2008.
“RCS: A Learning Classifier System for Evolutionary Robotics”, N. W. Smith*, C. B. Congdon, Eighth International Workshop on Learning Classifier Systems (IWLCS-2005), Genetic and Evolutionary Computation Conference (GECCO-2005), Washington, DC June 2005.

Evolutionary Design

Refereed Conference Papers

“Preliminary Results with GAUGUIN, an Evolutionary Computation Approach to Creating Art in the Suprematist Style”, T. Cook*, C. B. Congdon. IEEE Congress on Evolutionary Computation, Singapore, pp. 4252-4257. September 2007.
“GenTree: An Interactive Genetic Algorithms System for Designing 3D Polygonal Tree Models”, C.B. Congdon and R. H. Mazza III*, Genetic and Evolutionary Computation Conference (GECCO-2003), Chicago, IL, July 2003. (Nominated for best-paper award, Real-World Applications track.)
“Towards a Genetic Algorithms Approach to Designing 3D Polygonal Tree Models”, R. H. Mazza III* and C. B. Congdon, Congress on Evolutionary Computation (CEC-2002), Honolulu, HI, May 2002.

Computer Science and STEM Pedagogy

Invited Papers and Book Chapters

“Computer Science and Bioinformatics”, P. Tymann, C. B. Congdon, J. Dougherty, D. Evans, M. LeBlanc, J. C. Little, J. Prey, V. Stojkovic, in Math & Bio 2010: Linking Undergraduate Disciplines, L.A. Steen, Editor. The Mathematical Association of America, pp. 75-82, 2005.
“Machine Learning for the Masses”, C. B. Congdon, Curriculum Descant column for Intelligence magazine, Association for Computing Machinery Special Interest Group in Artificial Intelligence, v12, n2, Summer 2001.

Refereed Conference Papers

“Infusing the Creative-Thinking Process Into Undergraduate STEM Education: An Overview”, R. Diluzio and C. B. Congdon, IEEE Integrated STEM Education Conference (ISEC), Princeton, NJ, 2015, pp 52-56.
“Machine Learning in the Liberal Arts Curriculum”, C. B. Congdon, SIGCSE Technical Symposium in Computer Science Education, Austin, TX, March, 2000, pp 100-104.

Conference Abstracts

“Considerations on Undergraduate CS Research”, S. A. Robila, D. Baldwin, C. Congdon, A. Kumar, Consortium for Computing Sciences in Colleges, NorthEastern region (CCSCNE), April 2005 , also Journal of Computing Sciences in Colleges v20(5), May 2005.
“The Use of Robots in the Undergraduate Curriculum: Experience Reports”, M. G. Goldweber, C. Congdon, B. Fagin, D. Hwang, F. Klassner, SIGCSE Technical Symposium in Computer Science Education, Charlotte, NC, February 2001, pp 404-405.
“Teaching advice and support for new and adjunct faculty (panel session): experiences, policies, and strategies”, D. G. Kay, C. B. Congdon, S. Fitzgerald, M. S. King, P. Semmes, SIGCSE Technical Symposium in Computer Science Education, Austin, TX, March, 2000, pp 414-415.

Workshop Papers

“Robots Don’t Rule: Some Thoughts on Using Robots for Introductory CS”, C. B. Congdon, American Association for Artificial Intelligence (AAAI) Robotics and Education Symposium, Spring Symposium Series, Stanford University, March 26-28, 2001.

Soar

Book Chapter

“Learning Control Knowledge in an Unsupervised Planning Domain”, C. B. Congdon, in The Soar Papers: Research on Integrated Intelligence, volume 2, Ed. P. S. Rosenbloom, J. E. Laird, A. Newell, MIT Press, Cambridge, MA, 1993.

Tech Reports

“The Soar User’s Manual: Version 9.6.0”, J. E. Laird, C. B. Congdon, M. Assanie, N. Derbinsky, and J. Xu. July, 2017. (Tech report, University of Michigan EECS Department; online at https://soar.eecs.umich.edu/downloads/SoarManual.pdf)
“The Soar User’s Manual: Version 9.1”, J. E. Laird and C. B. Congdon. June, 2009. (Tech report, University of Michigan EECS Department)
“The Soar User’s Manual: Version 8.0”, J. E. Laird, C. B. Congdon, and K. J. Coulter. May, 1999. (Tech report, University of Michigan EECS Department)
“The Soar User’s Manual: Version 7.0.4”, C. B. Congdon and J. E. Laird, January, 1997.
“The Soar Advanced Applications Manual: Version 7.0”, C. B. Congdon and K. B. Schwamb, 1997.