Skip to main content

Mining Structure-Activity Relations in Biological Neural Networks using NeuronRank

  • Chapter
  • 1026 Accesses

Part of the book series: Studies in Computational Intelligence ((SCI,volume 77))

Because it is too difficult to relate the structure of a cortical neural network to its dynamic activity analytically, we employ machine learning and data mining to learn structure-activity relations from sample random recurrent cortical networks and corresponding simulations. Inspired by the PageRank and the Hubs&Authorities algorithms for networked data, we introduce the NeuronRank algorithm, which assigns a source value and a sink value to each neuron in the network. Source and sink values are used as structural features for predicting the activity dynamics of biological neural networks. Our results show that NeuronRank based structural features can successfully predict average firing rates in the network, as well as the firing rate of output neurons reflecting the network population activity. They also indicate that link mining is a promising technique for discovering structure-activity relations in neural information processing.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Mauricio Barahona and Louis M. Pecora. Synchronization in small-world sys-tems. Physical Review Letters, 89 : 054101, 2002.

    Article  Google Scholar 

  2. Valentino Braitenberg and Almut Schüz. Cortex: Statistics and Geometry of Neuronal Connectivity. Springer-Verlag, Berlin,  2nd edition, 1998.

    Google Scholar 

  3. Nicolas Brunel. Dynamics of sparsely connected networks of excitatory and in-hibitory spiking neurons. Journal of Computational Neuroscience, 8(3): 183-208, 2000.

    Article  MATH  Google Scholar 

  4. Soumen Chakrabarti, Byron E. Dom, and Piotr Indyk. Enhanced hypertext categorization using hyperlinks. InLaura M. Haas and Ashutosh Tiwary, editors, Proceedings of SIGMOD-98, ACM International Conference on Management of Data, pages 307-318, Seattle, US, 1998. ACM Press, New York, US.

    Chapter  Google Scholar 

  5. Gregory F. Cooper and Edward Herskovits. A bayesian method for the induction of probabilistic networks from data. Machine Learning, 9(4):309-347, 1992.

    MATH  Google Scholar 

  6. Nello Cristianini and John Shawe-Taylor. An Introduction to Support Vector Machines and Other Kernel-based Learning Methods. Cambridge University Press, March 2000.

    Google Scholar 

  7. Markus Diesmann and Marc-Oliver Gewaltig. NEST: An environment for neural systems simulations. In Theo Plesser and Volker Macho, editors, Forschung und wisschenschaftliches Rechnen, Beiträge zum Heinz-Billing-Preis 2001, volume 58 of GWDG-Bericht, pages 43-70. Ges. für Wiss. Datenverar-beitung, Göttingen, 2002.

    Google Scholar 

  8. Markus Diesmann, Marc-Oliver Gewaltig, and Ad Aertsen. Stable propagation of synchronous spiking in cortical neural networks. Nature, 402(6761):529-533, 1999.

    Article  Google Scholar 

  9. Pedro Domingos. Mining social networks for viral marketing. IEEE Intelligent Systems, 20(1):80-82, 2005.

    Article  MathSciNet  Google Scholar 

  10. Lise Getoor. Link mining: a new data mining challenge. SIGKDD Explorations, 5(1):84-89, 2003.

    Article  MathSciNet  Google Scholar 

  11. Lise Getoor and Christopher P. Diehl. Link mining: a survey. SIGKDD Explo- rations, 7(2):3-12, 2005.

    Article  Google Scholar 

  12. Tayfun Gürel, Luc De Raedt, and Stefan Rotter. Ranking neurons for mining structure-activity relations in biological neural networks: Neuronrank. Neuro-computing, doi:10.1016/j.neucom.2006.10.1064, 2006.

    Google Scholar 

  13. Eugene M. Izhikevich. Polychronization: Computation with spikes. Neural Computation, 18(2):245-282, February 2006.

    Article  MATH  MathSciNet  Google Scholar 

  14. Jon M. Kleinberg. Authoritative sources in a hyperlinked environment. Journal of the ACM, 46(5):604-632, 1999.

    Article  MATH  MathSciNet  Google Scholar 

  15. Shimon Marom and Goded Shahaf. Development, learning and memory in large random networks of cortical neurons: lessons beyond anatomy. Quarterly Reviews of Biophysics, 35(1):63-87, February 2002.

    Article  Google Scholar 

  16. R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon. Network motifs: simple building blocks of complex networks. Science,  298(5594):824-827, October 2002.

    Article  Google Scholar 

  17. Abigail Morrison, Carsten Mehring, Theo Geisel, Ad Aertsen, and Markus Dies-mann. Advancing the boundaries of high connectivity network simulation with distributed computing. Neural Computation, 17(8):1776-1801, 2005.

    Article  MATH  Google Scholar 

  18. Lawrence Page, Sergey Brin, Rajeev Motwani, and Terry Winograd. The pager-ank citation ranking: Bringing order to the web. Technical report, Stanford Digital Library Technologies Project, 1998.

    Google Scholar 

  19. Robert J J. Prill, Pablo A  A. Iglesias, and Andre Levchenko. Dynamic properties of network motifs contribute to biological network organization. Public Library of Science, Biology, 3(11), October 2005.

    Google Scholar 

  20. Ross J. Quinlan. C4.5: Programs for Machine Learning (Morgan Kaufmann Series in Machine Learning). Morgan Kaufmann, January 1993.

    Google Scholar 

  21. Sen Song, Sjöström Per, Markus Reigl, Sacha Nelson, and Dmitri Chklovskii. Highly nonrandom features of synaptic connectivity in local cortical circuits. Public Library of Science, Biology, 3(3):0507-05019, 2005.

    Google Scholar 

  22. Benjamin Taskar, Pieter Abbeel, and Daphne Koller. Discriminative probabilis-tic models for relational data. In Adnan Darwiche and Nir Friedman, editors, Uncertainty in AI, pages 485-492. Morgan Kaufmann, 2002.

    Google Scholar 

  23. D. J. Watts and S. H. Strogatz. Collective dynamics of ‘small-world’ networks. Nature, 393(6684):440-442, June 1998.

    Article  Google Scholar 

  24. Ian H. Witten and Eibe Frank. Data Mining: Practical Machine Learning Tools and Techniques, Second Edition (Morgan Kaufmann Series in Data Manage- ment Systems). Morgan Kaufmann, June 2005.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Gürel, T., Raedt, L.D., Rotter, S. (2007). Mining Structure-Activity Relations in Biological Neural Networks using NeuronRank. In: Hammer, B., Hitzler, P. (eds) Perspectives of Neural-Symbolic Integration. Studies in Computational Intelligence, vol 77. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73954-8_3

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-73954-8_3

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-73953-1

  • Online ISBN: 978-3-540-73954-8

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics