10 Dec 2013 ... Lecturer, School of Informatics, University of Edinburgh, 2004-2012 ....
International Conference on Development and Learning (ICDL-08 ....
development of visual maps with intracortical connections, v2.0 (1998) – v5.0 (
2004).
CURRICULUM VITAE James A. Bednar, Ph.D. Continuum Analytics, Inc. 221 W. 6th St. #1550 Austin, TX 78701 USA
[email protected] +1 512 952 8977 homepages.inf.ed.ac.uk/jbednar U.S. and U.K. Citizen
• Degrees Doctor of Philosophy in Computer Science, University of Texas at Austin, 2002. Master of Arts in Computer Science, University of Texas at Austin, 1997. Bachelor of Arts in Philosophy, University of Texas at Austin, 1994. Bachelor of Science in Electrical Engineering, University of Texas at Austin, 1993. • Career since graduation Senior Solutions Architect, Continuum Analytics, Austin, TX, since 1/2017. Solutions Architect, Continuum Analytics, Austin, TX, 6/2015-2016. Honourary Fellow, School of Informatics, University of Edinburgh, since 1/2016. Visiting Scholar, Center for Computational Biology and Bioinformatics, University of Texas at Austin, 10/2014–10/2015. Reader (Associate Professor), School of Informatics, University of Edinburgh, 2014-2015. Senior Lecturer, School of Informatics, University of Edinburgh, 2012-2014. Lecturer (Assistant Professor), School of Informatics, University of Edinburgh, 2004-2012. Postdoctoral researcher, Department of Computer Sciences, University of Texas at Austin, 2002-2004. • Principal research grants Engineering and Physical Sciences Research Council grant EP/F500385/1, LSI Doctoral Training Centres - Neuroinformatics and Computational Neuroscience, October 1, 2008 – March 31, 2018. PI: J.A. Bednar. Co-PI: M. van Rossum. Previous PI: D. Willshaw. £4,782,908 ($7,500,000). Biotechnology and Biological Sciences Research Council grant BB/F529254/1, LSI Doctoral Training Centres - Neuroinformatics and Computational Neuroscience, September 1, 2008 – August 31, 2015. PI: J.A. Bednar. Co-PI: M. van Rossum. Previous PI: D. Willshaw. £458,080 ($715,000). National Institute of Mental Health (Human Brain Project) grant #1R01-MH66991, Computational Modeling of Cortical Maps, April 22, 2002 – May 31, 2006. PI: R. Miikkulainen. Co-investigator: J.A. Bednar. $765,500. • PhD research student supervision: PhD theses completed since 2007 Philipp R¨udiger (2017). Development and Encoding of Visual Statistics in the Primary Visual Cortex. Ph.D. thesis, School of Informatics, The University of Edinburgh, UK. Jean-Luc Stevens (2017). Spatiotemporal Properties of Evoked Neural Response in the Primary Visual Cortex. Ph.D. thesis, School of Informatics, The University of Edinburgh, UK. Christopher E. Ball (2015). Modeling the Emergence of Perceptual Color Space in the Primary Visual Cortex. Ph.D. thesis, School of Informatics, The University of Edinburgh, UK.
Stuart P. Wilson (2011). Figuring Time by Space: Representing Sensory Motion in Cortical Maps. Ph.D. thesis, Department of Psychology, The University of Sheffield, England, UK. Co-supervised with Tony J. Prescott. Now Lecturer at U. Sheffield (UK). Chen Zhao (2011). Neural Mechanisms for Face and Orientation Aftereffects. Ph.D. thesis, School of Informatics, The University of Edinburgh, UK. Next position: Chief Technology Officer, FH Square Co., (California). Jan Antolik (2010). Unified Developmental Model of Maps, Complex Cells and Surround Modulation in the Primary Visual Cortex. Ph.D. thesis, School of Informatics, The University of Edinburgh, UK. Next position: Postdoc at UCL. Now postdoc at CNRS-Gif (France). Judith S. Law (2009). Modeling the Development of Organization for Orientation Preference in Primary Visual Cortex. Ph.D. thesis, School of Informatics, The University of Edinburgh, UK. Next position: Postdoc with Mark van Rossum (U. Edinburgh). Christopher M. Palmer (2009). Topographic and Laminar Models for the Development and Organisation of Spatial Frequency and Orientation in V1. Ph.D. thesis, School of Informatics, The University of Edinburgh, UK. Marina Papoutsi (2008). Phonetic Encoding, Verbal Working Memory, and the Role of Broca’s Area. Ph.D. thesis, School of Informatics, The University of Edinburgh, UK. Next position: Postdoc at Cambridge. Now postdoc at UCL (UK). Judah Ben De Paula (2007). Modeling the Self-Organization of Color Selectivity in the Visual Cortex. Ph.D. thesis, Department of Computer Sciences, The University of Texas at Austin, TX. Co-supervised with R. Miikkulainen (U. Texas). Next position: Software developer, Enthought (Texas). PhD committee member/non-primary supervisor Aleksej Stolicyn, Institute for Adaptive and Neural Computation, University of Edinburgh (2014-2015), Paul Ardin, Institute of Perception, Action, and Behavior, University of Edinburgh (2013-2015), Donal Stewart, Institute for Adaptive and Neural Computation, University of Edinburgh (2013-2015), Alexander Enoch, Institute of Perception, Action, and Behavior, University of Edinburgh (2009-2015), Rui Costa, Institute for Adaptive and Neural Computation, University of Edinburgh (2011-2014), Stuart Yarrow, Institute for Adaptive and Neural Computation, University of Edinburgh (2010-2014), Michael Thomas Smith, Institute for Adaptive and Neural Computation, University of Edinburgh (2010-2013), Ian Saunders, Institute for Adaptive and Neural Computation, University of Edinburgh (2007-2012), David Reichert, Institute for Adaptive and Neural Computation, University of Edinburgh (2009-2010), Xavier Oliver Duocastella, Institute for Adaptive and Neural Computation, University of Edinburgh (2008-2011), Matthew Down, Institute for Adaptive and Neural Computation, University of Edinburgh (2008-2011), Gaurav Malhotra, School of Psychology, University of Edinburgh (2008-2009), Rowland Sillito, Institute of Perception, Action, and Behavior, University of Edinburgh (2006-2008), Matthew Szenher, Institute of Perception, Action, and Behavior, University of Edinburgh (2004-2008), Yiu Fai Sit, Department of Computer Sciences, University of Texas at Austin (2004-2009). Andrea Greve, Institute for Adaptive and Neural Computation, University of Edinburgh (2004-2007) • Teaching experience at Edinburgh Courses created Computational Neuroscience of Vision (MSc; taught S2006, S2007, S2008, S2009, S2011, S2012, S2013, S2014, S2015) Neuroinformatics Research (MSc; taught S2005) Software Architecture, Process, and Management (MSc,undergraduate; taught S2006, S2007, S2008, S2012; based on SEOC2) Courses taught Neural Computation (MSc; taught A2010) Software Engineering with Objects and Components 2 (MSc,undergraduate; taught S2005) Principles of Neuroscience (MSc; organizer for Neuroinformatics week A2010, A2011, A2012, A2013) 2
Courses tutored/mentored Informatics 1: Cognitive Science (undergraduate) System Design Project (undergraduate) Introduction to Cognitive Science (undergraduate) • Postgraduate MSc student supervision: 19 completed since 2005. Tobias Fischer (2014). Model of All Known Spatial Maps in Primary Visual Cortex. Master’s thesis, The University of Edinburgh, UK. Giacomo Spigler (2014). Neural Modelling of the McCollough Effect in Colour Vision. Master’s thesis, The University of Edinburgh, UK. Annabelle Gee (2014). Neural Modelling of Congenitally Abnormal Visual Pathways. Master’s thesis, The University of Edinburgh, UK. Yvonne Kneisel (2013). Feasibility of Random Wiring in Primate Colour Vision. Master’s thesis, The University of Edinburgh, UK. Bharath Chandra Talluri (2013). Characterising the Properties of Natural and Laboratory Animal-Rearing Environments and Their Impact on Models of Visual Cortex Development. Master’s thesis, The University of Edinburgh, UK. Bilal Khan (2011). Modelling the Pathway to Auditory Cortex. Master’s thesis, The University of Edinburgh, UK. Konstantin Kudryavtsev (2011). High Performance Cortical Simulator. Master’s thesis, The University of Edinburgh, UK. Registered in Physics via the Edinburgh Parallel Computing Centre. Jean-Luc Stevens (2011). A Temporal Model of Neural Activity and VSD Response in the Primary Visual Cortex. Master’s thesis, The University of Edinburgh, UK. Philipp R¨udiger (2011). Estimating Simple and Complex Cell Receptive Fields from Natural Image Stimuli and 2-Photon Imaging Recordings of V1 in Ferrets. Master’s thesis, The University of Edinburgh, UK. Ravikiran Mattaparthi (2011). User Interface with Real-World Units. Master’s thesis, The University of Edinburgh, UK. Gautham Ganapathy (2011). Reconciling Models of Visual Cortex Development with Anatomical Patterns of Lateral Connectivity. Master’s thesis, The University of Edinburgh, UK. John Jacob (2009). Enhancing the Performance of a Cortical Simulator by Running it on a Graphics Processing Unit. Master’s thesis, The University of Edinburgh, UK. Stuart P. Wilson (2007). Self-Organisation Can Explain the Mapping of Angular Whisker Deflections in the Barrel Cortex. Master’s thesis, The University of Edinburgh, UK. Kateryna Gerasymova (2008). Computational Model of All Known Feature Maps in the Primary Visual Cortex. Master’s thesis, Humboldt-Universitaet zu Berlin, Germany. Visiting student. Tikesh Ramtohul (2006). A Self-Organizing Model of Disparity Maps in the Primary Visual Cortex. Master’s thesis, The University of Edinburgh, Scotland, UK. Veldri Kurniawan (2006). Self-Organizing Visual Cortex Model Using a Homeostatic Plasticity Mechanism. Master’s thesis, The University of Edinburgh, Scotland, UK. Chok Ming Ng (2006). Topographica Model of Somatosensory Cortex. Master’s thesis, The University of Edinburgh, Scotland, UK. Julien Ciroux (2005). Simulating the McCollough Effect in a Self-Organizing Model of the Primary Visual Cortex. Master’s thesis, The University of Edinburgh, Scotland, UK. Christopher Ball (2005). Motion Aftereffects in a Self-Organizing Model of Primary Visual Cortex. Master’s thesis, The University of Edinburgh, Scotland, UK. • Administrative experience Director of the Doctoral Training Centre in Neuroinformatics at the University of Edinburgh, 2010-2015. 3
Deputy Director of the Doctoral Training Centre in Neuroinformatics at the University of Edinburgh, 2005-2010. • Committee membership University of Edinburgh Strategy committee for University of Edinburgh School of Informatics, since 2011. University of Edinburgh ECDF Oversight by Researchers Group (joint Informatics representative), since 2011. Computing committee for University of Edinburgh School of Informatics, 2004-2006. Executive committee for University of Edinburgh Doctoral Training Centre in Neuroinformatics, since 2004. University of Edinburgh Institute for Adaptive and Neural Computation, since 2004. UK Panel member for UK EPSRC ICT Responsive Mode grant proposal reviews, April 2012. International Scientific Advisory Panel for the EU-funded COLUMBO project, 2016-. Editorial board for the Taylor & Francis journal Connection Science, since 2013, and the Springer journal Cognitive Computation, since 2014. Editorial board for the Springer book series The Encyclopedia of Computational Neuroscience, responsible for all articles on the Visual System, since 2012. Review editorial board for Frontiers in Computational Neuroscience, since 2012, and Frontiers in Neuroinformatics, since 2009. Programme committee for International Joint Conference on Neural Networks (IJCNN*2008,2010,2012,2015). INCF short course Towards an Integrative Computational Neuroscience, August 2012. 7th International Workshop on Self-Organizing Maps (WSOM 2009). International Conference on Development and Learning (ICDL-08,ICDL-09). International Conference on Machine Learning (ICML-2004). Review committee for the Computational Neuroscience Conference (CNS 2005,2006,2008,2011,2012,2013,2014,2015). Scientific Advisory Panel for the EU-funded BIOTACT project (biotact.org), 2009-2012. Board of Directors for the Organization for Computational Neuroscience, 2005-2008. • Invited international presentations “How Does the Brain Encode the Visual Environment to Guide Future Behavior?”: University of Texas at Austin Center for Perceptual Systems seminar, September 29, 2014. “A Mechanistic Model of the Development and Function of the Primary Visual Cortex”: University of Texas at Austin Forum for Artificial Intelligence, April 10, 2014. How to Read a Map: Understanding Structure-Function Relationships in the Brain workshop at the Janelia Farm Research Campus, Virginia, USA, April 6-9, 2014. Keynote speech at Kongsberg Vision Meeting, Kongsberg, Norway, December 10, 2013. “How Far Can Rate Neurons Go?”: Computational Neuroscience Group, Norwegian University of Life Sciences (UMB), Oslo, December 9, 2013. Brain Corporation, San Diego, July 9, 2012. “Visual Cortex as a General-Purpose Information-Processing Device”: Biological and Computer Vision Interfaces workshop at the 12th European Conference on Computer Vision, Florence, Italy, October 12-13, 2012. 4
“Param: Declarative programming using Parameters”: SciPy 2012: Scientific Computing with Python, Austin, Texas, July 19, 2012. “Building a Comprehensive Model for the Development and Function of the Visual Cortex”: Neuromathematics and Models of Perception lecture series, Institut Henri Poincar´e, Paris, France, December 5, 2011. Ladislav Tauc Conferences & GDR MSPC Neurosciences Joint Meeting, CNRS, Gif-sur-Yvette, France, December 16, 2010. Fitzpatrick Lab, Duke University Medical Center, January 25, 2010. Department of Computer Sciences, University of Texas at Austin, August 4, 2009. Glion2008 Workshop on Learning and Dynamics in Vision, Glion, Switzerland, October 28, 2008. “Computational Maps in the Visual Cortex”: Faculty of Mathematics and Physics, Charles University, Prague, October 19, 2007. Department of Neurobiology and Anatomy, University of Texas Medical School at Houston, Texas, July 6, 2005. Department of Computer Science and Engineering, Oregon Graduate Institute School of Science & Engineering, Oregon Health & Sciences University, April 6, 2004. Department of Electrical Engineering and Computer Science, Tulane University, April 2, 2004. Department of Computer Science, Colorado State University, March 25, 2004. Department of Electrical & Computer Engineering, University of Houston, Texas, March 22, 2004. Department of Computer Science and Engineering, University of South Carolina, March 5, 2004. “Modeling Cortical Function and Development with Topographica”. FACETS CodeJam workshop #1, the University of Heidelberg, April 3, 2007. Center for Perceptual Systems, University of Texas at Austin, November 18, 2002. “Learning to See: Modeling the Development of Visual Function”: Life Sciences Department (INSERM U483), Universit´e Pierre et Marie Curie, Paris, November 26, 2002. Department of Computer Science & Engineering, Michigan State University, May 7, 2002. Department of Computer Science, Georgetown University, March 18, 2002. • Invited UK presentations “Software for Reproducible Science“: Open.ED workshop on Open Knowledge, University of Edinburgh, UK, March 9, 2015. “A Mechanistic Model of the Development and Function of the Primary Visual Cortex”: IDEAS Research Institute, School of Computing Science and Digital Media, Robert Gordon University, Aberdeen, February 7, 2014. Vision Sciences group, School of Health and Life Sciences, Glasgow Caledonian University, November 20, 2013. “What Informatics Can Give to Neuroscience”: Edinburgh Neuroscience Autumn School, October 30, 2013. “Building a Comprehensive Model for the Development and Function of the Visual Cortex”: Bristol Vision Institute, University of Bristol, March 8, 2013. Visual Cognition Lab, University of Edinburgh, December 4, 2009. Department of Psychology, University of Sheffield, November 28, 2008. UK-COLAMN Workshop on Cortical Microcircuitry, University College London, September 4, 2008. 5
“Semi-Declarative Model Specification in Python” BrainScaleS CodeJam Workshop #5, Edinburgh, UK, March 14, 2012. “Computational Maps in the Visual Cortex”: Department of Physiology, University College London, March 28, 2008. School of Biology, University of Newcastle, March 28, 2006. Centre for Theoretical and Computational Neuroscience, University of Plymouth, May 25, 2005. “Learning to See: Modeling the Development of Visual Function”: Centre for Brain & Cognitive Development, School of Psychology, Birkbeck, University of London, September 17, 2002. • Guest lecturing: “Corso Interdisciplinare in Neuroinformatics”: University of Catania, Scuola Superiore, March 29–April 2, 2009. One-week full-time version of my Computational Neuroscience of Vision course. “Modeling Topographic Maps in the Visual System”: INCF short course in neuroinformatics, University of Edinburgh, August 30, 2012. Principles of Neuroscience MSc course, University of Edinburgh, 2005-2011, 2013. Edinburgh Neuroinformatics Summer School, University of Edinburgh, August 26, 2004. Edinburgh Neuroinformatics Summer School, University of Edinburgh, September 13, 2002.
• Workshop organisation Co-chair (with Sharon Crook and Hans Ekkehard Plesser), Creating, Documenting, and Sharing Network Models, Edinburgh, UK, September 20-21 2011. Chair, “Modeling Cortical Map Development,” workshop at the Fifteenth Annual Computational Neuroscience Meeting (CNS-2006, Edinburgh, UK), July 2006. Co-chair (with Risto Miikkulainen), “Modeling Cortical Map Development,” workshop at the Tenth Annual Computational Neuroscience Meeting (CNS-2001, San Francisco, CA), July 2001. • Open-source software packages Topographica Python software for flexible simulation of hierarchies of interconnected topographic maps. Eleven releases since 2005 available at http://topographica.org. FeatureMapper Python library for estimating visual or other sensory feature maps. Supports any map that can be calculated from responses to a parameterized set of input patterns, whether from a model or experimental data. Version 0.8 released December 2013 at http://ioam.github.com/featuremapper. HoloViews Python library for flexible visualization of scientific and engineering data. Version 1.0 released February 2015 at http://ioam.github.com/holoviews. Winner of the 2015 UK Open Source Award, in the student-developed category. ImaGen generic Python library for 0D, 1D, and 2D pattern distributions. Version 1.0.1 released November 2014 at http://ioam.github.com/imagen. Param generic Python library for declarative programming using user-definable parameters. Version 1.2.1 released July 2014 at http://ioam.github.com/param and http://ioam.github.com/paramtk. LISSOM (Laterally Interconnected Synergetically Self-Organizing Map) C++ software for simulating the development of visual maps with intracortical connections, v2.0 (1998) – v5.0 (2004).
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• Reviewing Reviewer for the funding agencies National Science Foundation (USA) (2015), European Research Council (2014), Biotechnology and Biological Sciences Research Council (BBSRC) (2014,2009,2006), Engineering and Physical Sciences Research Council (EPSRC) (2012 as panel member, 2006,2005), Medical Research Council (MRC) (2010,2009), Economic and Social Research Council (ESRC) (2006), Neurological Foundation of New Zealand (2006), The Wellcome Trust (2005). Reviewer for the journals Proceedings of the Royal Society of London, Series B (2014), Developmental Neurobiology (2014), Connection Science (2014,2005), PLoS Computational Biology (2013, 2011), Frontiers in Neural Circuits (2013), Journal of the Royal Society Interface (2013), Frontiers in Computational Neuroscience (2013,2012), Vision Research (2012,2010), Network — Computation in Neural Systems (2012,2005,2002,2001,1999), Frontiers in Neuroinformatics (2012,2008), Journal of Computational Neuroscience (2011,2010), Physical Review E (2011,2010). IEEE Transactions on Autonomous Mental Development (2011), Developmental Science (2011,2010,2008), Neuroinformatics (2010), Neural Computation (2009,2008,2007,2006,2005), Proceedings of the Royal Society of London, Series A (2009), Neural Networks (2017,2016,2008,2004), Cerebral Cortex (2005), IEEE Transactions on Evolutionary Computation (2005), Biological Cybernetics (2016,1997).
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LIST OF PUBLICATIONS 2013 ISI/JCR impact factors are shown where available. 1. Books published Risto Miikkulainen, James A. Bednar, Yoonsuck Choe, and Joseph Sirosh (2005). Computational Maps in the Visual Cortex. Springer, Berlin. 2. Books/collections edited Andrew P. Davison, Markus Diesmann, Marc-Oliver Gewaltig, Satrajit S. Ghosh, Fernando Perez, Eilif B. Muller, James A. Bednar, Bertrand Thirion, and Yaroslav Halchenko (eds.) (2015). Python in Neuroscience II. Frontiers Media SA. Research topic in Frontiers in Neuroinformatics. 29 articles. e-Book in press. Eilif Muller, James A. Bednar, Markus Diesmann, Marc-Oliver Gewaltig, Michael Hines, and Andrew P. Davison (eds.) (2015). Python in Neuroscience. Frontiers Media SA. 3. Un-refereed journal articles 4. Refereed journal articles James A. Bednar and Stuart P. Wilson (2015). Cortical maps. The Neuroscientist. In press. Impact factor: 7.618 Stuart P. Wilson and James A. Bednar (2015). What, if anything, are topological maps for?. Developmental Neurobiology, 75:667–681. Impact factor: 4.189 Eilif Muller, James A. Bednar, Markus Diesmann, Marc-Oliver Gewaltig, Michael Hines, and Andrew P. Davison (2015). Python in neuroscience. Frontiers in Neuroinformatics, 9:11. Laurent U. Perrinet and James A. Bednar (2015). Edge co-occurrences can account for rapid categorization of natural versus animal images. Nature Scientific Reports, 5:11400. Impact factor: 5.078 Jean-Luc R. Stevens, Judith S. Law, Jan Antolik, and James A. Bednar (2013). Mechanisms for stable, robust, and adaptive development of orientation maps in the primary visual cortex. Journal of Neuroscience, 33:15747–15766. Impact factor: 6.747 Jean-Luc R. Stevens, Marco Elver, and James A. Bednar (2013). An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook. Frontiers in Neuroinformatics, 7:44. James A. Bednar (2012). Building a mechanistic model of the development and function of the primary visual cortex. Journal of Physiology (Paris), 106:194–211. 24 pages. Review. Invited contribution. Impact factor: 2.345 Sharon M. Crook, James A. Bednar, Sandra Berger, Robert Cannon, Andrew P. Davison, Mikael Djurfeldt, Jochen Eppler, Birgit Kriener, Steve Furber, Bruce Graham, Hans E. Plesser, Lars Schwabe, Leslie Smith, Volker Steuber, and Sacha van Albada (2012). Creating, documenting and sharing network models. Network – Computation in Neural Systems, 23(4):131–149. Jan Antolik and James A. Bednar (2011). Development of maps of simple and complex cells in the primary visual cortex. Frontiers in Computational Neuroscience, 5:17. Impact factor: 2.233 Chen Zhao, Peggy Seri`es, Peter J. B. Hancock, and James A. Bednar (2011). Similar neural adaptation mechanisms underlying face gender and tilt aftereffects. Vision Research, 51(18):2021–2030. Impact factor: 2.381 Stuart P. Wilson, James A. Bednar, Tony J. Prescott, and Ben Mitchinson (2011). Neural computation via neural geometry: A place code for inter-whisker timing in the barrel cortex?. PLoS Computational Biology, 7(10):e1002188. Impact factor: 4.829 Stuart P. Wilson, Judith S. Law, Ben Mitchinson, Tony J. Prescott, and James A. Bednar (2010). Modeling the emergence of whisker direction maps in rat barrel cortex. PLoS One, 5(1):e8778. Impact factor: 3.534 8
Marina Papoutsi, Jacco A. De Zwart, J. Martijn Jansma, Martin Pickering, James A. Bednar, and Barry Horwitz (2009). From phonemes to articulatory codes: An fMRI study of the role of Broca’s area in speech production. Cerebral Cortex, 19:2156–2165. Impact factor: 8.305 James A. Bednar (2009). Topographica: Building and analyzing map-level simulations from Python, C/C++, MATLAB, NEST, or NEURON components. Frontiers in Neuroinformatics, 3:8. 9 pages. Invited contribution. James A. Bednar (2008). Understanding neural maps with Topographica. Brains, Minds, and Media, 3:bmm1402. 8 pages. Invited contribution. Vinod Valsalam, James A. Bednar, and Risto Miikkulainen (2007). Developing complex systems using evolved pattern generators. IEEE Transactions on Evolutionary Computation, 11(2):181–198. Impact factor: 5.545 James A. Bednar and Risto Miikkulainen (2006). Joint maps for orientation, eye, and direction preference in a self-organizing model of V1. Neurocomputing, 69(10–12):1272–1276. Stefanie Jegelka, James A. Bednar, and Risto Miikkulainen (2006). Prenatal development of ocular dominance and orientation maps in a self-organizing model of V1. Neurocomputing, 69:1291–1296. James A. Bednar, Judah B. De Paula, and Risto Miikkulainen (2005). Self-organization of color opponent receptive fields and laterally connected orientation maps. Neurocomputing, 65–66:69–76. James A. Bednar and Risto Miikkulainen (2004). Prenatal and postnatal development of laterally connected orientation maps. Neurocomputing, 58-60:985–992. James A. Bednar, Yoonsuck Choe, Judah De Paula, Risto Miikkulainen, Jefferson Provost, and Tal Tversky (2004). Modeling cortical maps with Topographica. Neurocomputing, 1129–1135. James A. Bednar, Amol Kelkar, and Risto Miikkulainen (2004). Scaling self-organizing maps to model large cortical networks. Neuroinformatics, 2:275–302. Impact factor: 3.102 James A. Bednar and Risto Miikkulainen (2003). Self-organization of spatiotemporal receptive fields and laterally connected direction and orientation maps. Neurocomputing, 52–54:473–480. James A. Bednar and Risto Miikkulainen (2003). Learning innate face preferences. Neural Computation, 15(7):1525–1557. Impact factor: 1.694 James A. Bednar, Amol Kelkar, and Risto Miikkulainen (2002). Modeling large cortical networks with growing self-organizing maps. Neurocomputing, 44–46:315–321. James A. Bednar and Risto Miikkulainen (2000). Tilt aftereffects in a self-organizing model of the primary visual cortex. Neural Computation, 12(7):1721–1740. Impact factor: 1.694 5. Refereed book chapters James A. Bednar and Christopher K. I. Williams (2016). Neural maps: Their function and development. In: From Neuron to Cognition via Computational Neuroscience, Michael A. Arbib and James J. Bonaiuto, eds., 409–432. MIT Press, Cambridge, MA. Invited contribution to textbook. James A. Bednar (2014). Hebbian learning of the statistical and geometrical structure of visual input. In: Neuromathematics of Vision, Giovanna Citti and Alessandro Sarti, eds. Springer. Invited contribution. James A. Bednar (2013). Constructing complex systems via activity-driven unsupervised Hebbian self-organization. In: Growing Adaptive Machines: Combining Development and Learning in Artificial Neural Networks, Studies in Computational Intelligence. Springer, Berlin. Invited contribution. James A. Bednar (2014). Visual aftereffects. In: The Encyclopedia of Computational Neuroscience, Dieter Jaeger and Ranu Jung, eds. Springer, Berlin. Invited contribution. James A. Bednar (2014). Topographica. In: The Encyclopedia of Computational Neuroscience, Dieter Jaeger and Ranu Jung, eds. Springer, Berlin. Invited contribution. James A. Bednar and Risto Miikkulainen (2007). Constructing visual function through prenatal and postnatal learning. In: Neuroconstructivism, Vol. 2: Perspectives and Prospects, Denis Mareschal, Mark H. Johnson, Sylvain Sirois, Michael Spratling, Michael S. C. Thomas, and Gert Westermann, eds., 13–37. Oxford University Press, Oxford, UK. Invited contribution. 9
Risto Miikkulainen, James A. Bednar, Yoonsuck Choe, and Joseph Sirosh (1997). Self-organization, plasticity, and low-level visual phenomena in a laterally connected map model of the primary visual cortex. In: Perceptual Learning, R. L. Goldstone, P. G. Schyns, and D. L. Medin, eds., volume 36 of Psychology of Learning and Motivation, 257–308. Academic Press, San Diego, CA. 6. Book chapters James A. Bednar (2003). The role of internally generated neural activity in newborn and infant face preferences. In: Face Perception in Infancy and Early Childhood, Olivier Pascalis and Alan Slater, eds., 133–142. NOVA Science Publishers, New York. Invited contribution. Risto Miikkulainen, James A. Bednar, Yoonsuck Choe, and Joseph Sirosh (1999). Modeling self-organization in the visual cortex. In: Kohonen Maps, Erkki Oja and Samuel Kaski, eds. Elsevier, Amsterdam. Joseph Sirosh, Risto Miikkulainen, and James A. Bednar (1996). Self-organization of orientation maps, lateral connections, and dynamic receptive fields in the primary visual cortex. In: Lateral Interactions in the Cortex: Structure and Function, Joseph Sirosh, Risto Miikkulainen, and Yoonsuck Choe, eds. The UTCS Neural Networks Research Group, Austin, TX. Electronic book, ISBN 0-9647060-0-8, http://nn.cs.utexas.edu/web-pubs/htmlbook96. 7. Refereed conference proceedings papers Jean-Luc R. Stevens, Philipp J. F. Rudiger, and James A. Bednar (2015). Holoviews: Building complex visualizations easily for reproducible science. In: Proceedings of the 14th Python in Science conference, SciPy 2015. Laurent Perrinet and James A. Bednar (2015). Sparse coding of natural images using a prior on edge co-occurrences. In: Proceedings of the 23rd European Signal Processing Conference (EUSIPCO), Marc Antonini, Nicholas Evans, and Cedric Richard, eds. IEEE. In press. James A. Bednar (2012). Visual cortex as a general-purpose information-processing device. In: ECCV 2012 Workshops, A. Fusiello et al., eds., Part I, Lecture Notes in Computer Science 7583, 480–485. Springer, Berlin. Gaurav Malhotra, Martin Pickering, Holly P. Branigan, and James A. Bednar (2008). On the persistence of structural priming: Mechanisms of decay and influence of word-forms. In: Proceedings of the 30th Annual Conference of the Cognitive Science Society, B. C. Love, K. McRae, and V. M. Sloutsky, eds., 657–662. Austin, TX: Cognitive Science Society. Vinod Valsalam, James A. Bednar, and Risto Miikkulainen (2006). Establishing an appropriate learning bias through development. In: Proceedings of the Fifth International Conference on Development and Learning (ICDL-2006). Vinod Valsalam, James A. Bednar, and Risto Miikkulainen (2005). Constructing good learners using evolved pattern generators. In: Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2005, H.-G. Beyer et al., eds., 11–18. New York: ACM. Winner of the Best Paper award for A-Life, Evolutionary Robotics, and Adaptive Behavior. James A. Bednar and Risto Miikkulainen (2002). Neonatal learning of faces: Environmental and genetic influences. In: Proceedings of the 24th Annual Conference of the Cognitive Science Society, Wayne Gray and Christian Schunn, eds., 107–112. Erlbaum, Hillsdale, NJ. James A. Bednar and Risto Miikkulainen (2000). Self-organization of innate face preferences: Could genetics be expressed through learning?. In: Proceedings of the 17th National Conference on Artificial Intelligence and the 12th Annual Conference on Innovative Applications of Artificial Intelligence, 117–122. AAAI Press, Menlo Park, CA. Risto Miikkulainen, James A. Bednar, Yoonsuck Choe, and Joseph Sirosh (1998). A self-organizing neural network model of the primary visual cortex. In: Proceedings of the Fifth International Conference on Neural Information Processing, Shiro Usui and Takashi Omori, eds., volume 2, 815–818. Tokyo: IOS Press.
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James A. Bednar and Risto Miikkulainen (1998). Pattern-generator-driven development in self-organizing models. In: Computational Neuroscience: Trends in Research, 1998, J. M. Bower, ed., 317–323. New York: Plenum Press. James A. Bednar and Risto Miikkulainen (1997). A neural network model of visual tilt aftereffects. In: Proceedings of the 19th Annual Conference of the Cognitive Science Society, Michael G. Shafto and Pat Langley, eds., 37–42. Hillsdale, NJ: Erlbaum. 8. Conference poster and talk abstracts Steven M. Silverstein, Docia L. Demmin, and James A. Bednar (2017). Computational modeling of contrast sensitivity and orientation tuning in schizophrenia. In: Proceedings of the 6th Computational and Mathematical Models in Vision Workshop (MODVIS 2017). Steven M. Silverstein, Docia L. Demmin, and James A. Bednar (2017). Computational modeling of low level visual processing impairments in schizophrenia. In: Proceedings of the 16th International Congress on Schizophrenia Research (ICOSR 2017). James A. Bednar, Jim Crist, Joseph Cottam, and Peter Wang (2016). Datashader: Revealing the structure of genuinely big data. In: Proceedings of the 15th Python in Science conference, SciPy 2016. Philipp J. F. Rudiger, Jean-Luc R. Stevens, and James A. Bednar (2016). Holoviews: Let your data reveal itself. In: Proceedings of the 15th Python in Science conference, SciPy 2016. Jean-Luc R. Stevens, Philipp J. F. Rudiger, and James A. Bednar (2015). Holoviews: Building complex visualizations easily for reproducible science. In: Proceedings of the 14th Python in Science conference, SciPy 2015. Laurent U. Perrinet and James A. Bednar (2014). Edge co-occurrences are sufficient to categorize natural versus animal images. Journal of Vision, 14(10):1310. Abstract presented at VSS 2014. Philipp R¨udiger and James A. Bednar (2014). Relating the diversity of interneuronal subtypes to their functional roles in development, homeostasis and sensory processing. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 115.16. Jean-Luc R. Stevens, Sandrine Chemla, Giacomo Benvenuti, Frederic Chavane, and James A. Bednar (2014). A model relating temporal processing across spatial and temporal scales using electrophysiological and optical imaging data in primate V1. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 155.19. Philipp R¨udiger, Jean-Luc R. Stevens, Bharath Chandra Talluri, Laurent Perrinet, and James A. Bednar (2014). Relationship between natural image statistics and lateral connectivity in the primary visual cortex. In: Cosyne Abstracts 2014. Salt Lake City, USA. Philipp R¨udiger and James A. Bednar (2013). Unifying anatomical, psychophysical, and developmental circuit models of primary visual cortex. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 639.11. Philipp R¨udiger, Judith S. Law, Jan Antolik, and James A. Bednar (2013). Developing orientation maps using realistic patterns of lateral connectivity. In: BMC Neuroscience, Gennady S. Cymbalyuk and Astrid A. Prinz, eds., volume 14(Suppl 1), P22. Proceedings of the Twenty-Second Annual Computational Neuroscience Meeting (CNS*2013). Jean-Luc R. Stevens, Marco Elver, and James A. Bednar (2013). An automated simulator-independent workflow for reproducible simulation and analysis using Lancet and IPython Notebook. In: BMC Neuroscience, Gennady S. Cymbalyuk and Astrid A. Prinz, eds., volume 14(Suppl 1). Proceedings of the Twenty-Second Annual Computational Neuroscience Meeting (CNS*2013). Philipp R¨udiger, Jean-Luc Stevens, and James A. Bednar (2012). A spatio-temporally calibrated model of feature map development and neuronal activity in primate V1. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 568.11/AA11. Jean-Luc R. Stevens and James A. Bednar (2012). A temporal model of neural activity and VSD response in V1. In: BMC Neuroscience, volume 13(Suppl 1), 180. Proceedings of the Twenty-First Annual Computational Neuroscience Meeting (CNS*2012). 11
James A. Bednar and Christopher E. Ball (2012). ImaGen: generic library for 0D, 1D and 2D pattern distributions. In: SciPy 2012: Scientific Computing with Python. Stuart P. Wilson, Ben Mitchinson, Tony J. Prescott, and James A. Bednar (2012). Orthogonal coding of tactile stimulus features in a self-organising model of barrel cortex development. In: FENS Abstracts. www.fens.org. Judith S. Law, Jan Antolik, and James A. Bednar (2011). Stable and robust development of orientation maps and receptive fields. In: BMC Neuroscience, volume 12(Suppl 1), S23. Proceedings of the Twentieth Annual Computational Neuroscience Meeting (CNS*2011). Stuart P. Wilson, James A. Bednar, Tony J. Prescott, and Ben Mitchinson (2011). Neural computation via neural geometry: A place code for inter-whisker timing in the barrel cortex? In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 495.22. Laurent Perrinet, David Fitzpatrick, and James A. Bednar (2011). Edge statistics in natural images versus laboratory animal environments: Implications for understanding lateral connectivity in V1. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 530.04. Christopher E. Ball, Julien B. Ciroux, and James A. Bednar (2010). Orientation-contingent color aftereffects (the McCollough effect) can arise through Hebbian synaptic adaptation of horizontal connections. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 892.15. Chen Zhao and James A. Bednar (2010). Curve adaptation effects on high-level facial-expression judgments are predicted to have the same form as low-level aftereffects. Perception, 39 ECVP Abstract Supplement:91. Jan Antolik, Judith S. Law, and James A. Bednar (2009). Reconciling models of V1 development and adult function. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 765.5. Stuart P. Wilson, Ben Mitchinson, Martin Pearson, James A. Bednar, and Tony J. Prescott (2009). Learning multi-whisker spatial-temporal cortical receptive fields from robotic whisker input. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 174.4. Christopher E. Ball and James A. Bednar (2009). A self-organizing model of color, ocular dominance, and orientation selectivity in the primary visual cortex. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 756.9. Stuart P. Wilson, Ben Mitchinson, Martin Pearson, James A. Bednar, and Tony J. Prescott (2009). Learning cortical representations from multiple whisker inputs. In: BMC Neuroscience, volume 10(Suppl 1), P334. Proceedings of the Eighteenth Annual Computational Neuroscience Meeting (CNS*2009). Judith S. Law, Jan Antolik, and James A. Bednar (2009). Homeostatic and gain control mechanisms in a developmental model of orientation map formation in V1. Frontiers in Systems Neuroscience. Poster presented at the 2009 Computational and Systems Neuroscience meeting (COSYNE 09). doi: 10.3389/conf.neuro.06.2009.03.341. Jan Antolik and James A. Bednar (2009). Modeling the development of maps of complex cells. In: BMC Neuroscience, volume 9(Suppl 1), P96. Proceedings of the Seventeenth Annual Computational Neuroscience Meeting (CNS*2009). Jan Antolik and James A. Bednar (2008). Developing maps of complex cells in a computational model of V1. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 811.5. Jan Antolik and James A. Bednar (2008). Developing maps of complex cells in a computational model. In: FENS Abstracts vol 4, A054.1. www.fens.org. Chen Zhao, Peter J. B. Hancock, and James A. Bednar (2008). Modelling face adaptation aftereffects. Perception, 37 ECVP Abstract Supplement:158. Gaurav Malhotra, Martin Pickering, Holly P. Branigan and James Bednar (2008) On the Persistence of Structural Priming: Mechanisms of Decay and Influence of Word Forms. Conference on Human Sentence Processing, CUNY2008.
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Stuart P. Wilson, Charles W. Fox, Tony J. Prescott, and James A. Bednar (2007). A self-organizing model of whisker deflection maps in the barrel cortex. In: Barrels XX (SfN Satellite Meeting). Stuart P. Wilson, Tony J. Prescott, and James A. Bednar (2007). Self-organization in the barrel cortex. In: Functional Organization of Barrel Cortex Networks. ENI-Net Mini-Symposia in Neurosciences. Jan Antolik and James A. Bednar (2007). Modeling the development of maps of complex cells in V1. Neurons on the Map: The 5th Neuron Satellite Meeting. Jan Antolik and James A. Bednar (2007). Modelling surround modulation in the LGN. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 395.10. Christopher M. Palmer and James A. Bednar (2007). Topographic and laminar organization of spatial frequency and orientation in a developmental model of V1 using natural images. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 395.13. Judith S. Law, Veldri Kurniawan, and James A. Bednar (2007). Homeostatic plasticity in a model of V1 orientation map development. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 395.6. Judith S. Law and James A. Bednar (2007). Reconciling models of surround modulation and V1 feature map development. In: BMC Neuroscience, volume 8(Suppl 2), S23. Proceedings of the Sixteenth Annual Computational Neuroscience Meeting (CNS*2007). Judah De Paula, James A. Bednar, and Risto Miikkulainen (2007). Modeling self-organizing tri-chromatic color selective regions in primary visual cortex. In: BMC Neuroscience, volume 8(Suppl 2), S24. Proceedings of the Sixteenth Annual Computational Neuroscience Meeting (CNS*2007). Marina Papoutsi, Jacco De Zwart, Martijn Jansma, Martin Pickering, James A. Bednar, and Barry Horwitz (2007). The processing of low frequency pseudowords by Broca’s area. In: Abstracts of the 13th Annual Meeting of the Organization for Human Brain Mapping (Chicago, IL). Organization for Human Brain Mapping, www.humanbrainmapping.org. James A. Bednar and Judith Law (2007) Reconciling models of surround modulation and V1 orientation map development. Talk given April 27, 2007 at the workshop “Information Processing in the Visual System” at the Mathematical Biosciences Institute (MBI) of the Ohio State University. Christopher Ball and James A. Bednar (2006). Motion aftereffects in a self-organizing model of the primary visual cortex. In: Fifteenth Annual Computational Neuroscience Meeting (CNS*2006). Judith S. Law and James A. Bednar (2006). Surround modulation by long-range lateral connections in an orientation map model of primary visual cortex development and function. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 546.4. Christopher M. Palmer and James A. Bednar (2006). Modeling the development of topographic and laminar organization for orientation and spatial frequency in the primary visual cortex. In: Society for Neuroscience Abstracts. Society for Neuroscience, www.sfn.org. Program No. 546.3. James A. Bednar, Yoonsuck Choe, Judah De Paula, Risto Miikkulainen, and Jefferson Provost (2005). Modeling the visual cortex using the Topographica cortical map simulator. In: Society for Neuroscience Abstracts. Society for Neuroscience. James A. Bednar, Yoonsuck Choe, Judah De Paula, Risto Miikkulainen, and Jefferson Provost (2005). The Topographica cortical map simulator. Perception. Poster and abstract presented at the European Conference on Visual Perception (A Coru˜na, Spain). Judah Ben De Paula, James A. Bednar, and Risto Miikkulainen (2004). Modeling self-organization of color-opponent receptive fields and laterally connected orientation maps and color blobs in V1. In: Society for Neuroscience Abstracts. Society for Neuroscience. Program No. 174.11. Risto Miikkulainen, James A. Bednar, and Yoonsuck Choe (2004). Sparse, redundancy-reduced visual coding through self-organized lateral connections. In: Society for Neuroscience Abstracts. Society for Neuroscience. Program No. 490.3. James A. Bednar and Risto Miikkulainen (2003). Joint maps for orientation, ocular dominance, and direction preference in a self-organizing laterally connected model of primary visual cortex. In: Society for Neuroscience Abstracts. Society for Neuroscience. Program No. 701.2. 13
James A. Bednar, Yoonsuck Choe, Judah De Paula, Risto Miikkulainen, Jefferson Provost, and Yiu Fai Sit (2005). Topographica: Computational Modeling of Cortical Maps. Poster and demonstration at the 2005 Society for Neuroscience Meeting (Washington, DC), as part of the Human Brain Project of the National Institute of Mental Health. James A. Bednar and Risto Miikkulainen (2002). Self-organization of spatiotemporal receptive fields and laterally connected direction and orientation maps. Poster and abstract presented at the 2002 Society for Neuroscience Meeting Satellite Symposium, Dynamical Neuroscience X: From Experiments and Models to Brain Theory (Orlando, Florida). James A. Bednar and Risto Miikkulainen (1997). A neural network model of visual tilt aftereffects. Perception, 26 Supplement:20. Poster and abstract presented at the European Conference on Visual Perception (Helsinki, Finland). 9. Patents Tim Hayles and James A. Bednar (2000). Attribute-based system and method for configuring and controlling a data acquisition task. U.S. patent 6067584, National Instruments Corporation.
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