Publications

The list is mainly the result of internet searches we sometimes perform. Please let us know of items that should be added to this list via the contact form.

A.  Peer reviewed journal publications

11) Kalman filter mixture model for spike sorting of non-stationary data
Journal of Neuroscience Methods (2011) 196:159-169
A. Calabrese and L. Paninski
http://www.sciencedirect.com

10) 1/f Neural Noise Reduction and Spike Feature Extraction using a Subset of Informative Samples
Annals of Biomedical Engineering 39 (2011): 1264-1277
Z. Yang, L. Hoang, Q. Zhao, E. Keefer, and W. Liu
http://www.ece.nus.edu.sg/stfpage/eleyangz/ABME_11.pdf

9) Spike-Train Communities: Finding Groups of Similar Spike Trains
Journal of Neuroscience 9 February 2011, 31 (6):2321-2336
Mark D. Humphries
DOI:10.1523/​JNEUROSCI.2853-10.201
http://www.jneurosci.org/content/31/6/2321.short

8) Eye Movements Show Optimal Average Anticipation with Natural Dynamic Scenes
Cognitive Computation, 2010
Eleonora Vig, Michael Dorr, Thomas Martinetz and Erhardt Barth
DOI: 10.1007/s12559-010-9061-4
http://www.springerlink.com/content/73l4j324g63150n1/

7) A stochastic model of human visual attention with a dynamic Bayesian network
IEEE Transactions on pattern analysis and machine intelligence, Submitted 2010.
Akisato Kimura, Derek Pang, Tatsuto Takeuchi, Kouji Miyazato, Kunio Kashino and Junji Yamato.
NTT Communication Science Laboratories, Kanagawa, Japan.
D. Pang - Department of Electrical Engineering, Stanford University
http://arxiv.org/pdf/1004.0085 [PDF]

6) Generation of Spatiotemporally Correlated Spike Trains and Local Field Potentials Using a Multivariate Autoregressive Process
J Neurophysiol 103: 2912-2930, 2009. 2010. doi:10.1152/jn.00518.2009
Diego A. Gutnisky and Kreimir Josi
Department of Neurobiology and Anatomy, University of Texas–Houston Medical
School; and Department of Mathematics, University of Houston, Houston, Texas.
http://jn.physiology.org/cgi/content/full/103/5/2912

5) A Continuous Entropy Rate Estimator for Spike Trains Using a K-Means-Based Context Tree
Neural Computation
April 2010, Vol. 22, No. 4, Pages 998-1024 (doi:10.1162/neco.2009.11-08-912)
Tiger W. Lin
Revelle College, University of California, San Diego, La Jolla, CA 92092,
U.S.A. and Summer Undergraduate Research Fellow, Rockefeller University, New York, NY 10065
George N. Reeke
Laboratory of Biological Modeling, Rockefeller University, New York, NY 10065
http://www.ncbi.nlm.nih.gov/pubmed/19922298

4) Accurate spike sorting for multi-unit recordings
European Journal of Neuroscience
Volume 31 Issue 2 (January 2010), pages 263 - 272
Takashi Takekawa , Yoshikazu Isomura and Tomoki Fukai
Laboratory for Neural Circuit Theory, RIKEN Brain Science Institute, Hirosawa
2-1, Wako, Saitama 351-0198, Japan.
Department of Complexity Science and Engineering, University of Tokyo,
Kashiwa, Chiba, Japan.
http://www3.interscience.wiley.com/journal/123239648/abstract

3) Of bits and wows: A Bayesian theory of surprise with applications to attention
Neural Networks
Volume 23, Issue 5, June 2010, Pages 649-666
Pierre Baldi, Department of Computer Science, UCI, Irvine
Laurent Itti, Department of Computer Science, USC, Los Angeles
http://linkinghub.elsevier.com/retrieve/pii/S0893608009003256

2) ePPR: a new strategy for the characterization of sensory cells from input/output data
Joaquin Rapela, Gidon Felsen, Jon Touryan, Jerry M. Mendel, Norberto M. Grzywacz
Network: Computation in Neural Systems.
Vol. 21, No. 1-2 , Pages 35-90
http://www.ncbi.nlm.nih.gov/pubmed/20735338

1) A new spike detection algorithm for extracellular neural recordings
Journal of IEEE Transactions on Biomedical Engineering; June 2009
Shahjahan Shahid, Jacqueline Walker, and Leslie S Smith
Department Computing and Mathematics, University of Stirling, Stirling, UK.
Department of Electronic and Computer Engineering, University of Limerick, Limerick, Ireland.
http://www.ncbi.nlm.nih.gov/pubmed/19622433


B.  Conference presentations or abstracts

14) Human-motion saliency in multi-motion scenes and in close interaction
M. Mancas, F. Pirri, M. Pizzoli
Proceeding of the 9th International Gesture Workshop on Gesture in Embodied Communication and Human-Computer Interaction, Athens, Greece, May 2011
http://tcts.fpms.ac.be/publications/regpapers/2011/mmfpmp_isvc_LNCS.pdf

13) Hardware Accelerated Visual Attention Algorithm
P. Akselrod, F. Zhao, I. Derekli, C. Farabet, B. Martini, Y. LeCun and Eugenio Culurciello
Proc. Conference on Information Sciences and Systems (CISS), IEEE, Baltimore, 2011
http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=05766191

12) Towards guiding principles in workflow design to facilitate collaborative projects involving massively parallel electrophysiological data
Michael Denker, Andrew Davison, Markus Diesmann, Sonja Grün
Twentieth Annual Computational Neuroscience Meeting: CNS*2011
BMC Neuroscience 2011, 12 (Suppl 1):P131
http://www.biomedcentral.com/1471-2202/12/S1/P131

11) Hardware Accelerated Visual Attention Algorithm
P. Akselrod, F. Zhao, I. Derekli, C. Farabet, B. Martini, Y. LeCun and Eugenio Culurciello
Proc. Conference on Information Sciences and Systems (CISS’11), IEEE, Baltimore, 2011
http://data.clement.farabet.net/pubs/ciss11.pdf

10) Re-testing the energy model: identifying features and nonlinearities of complex cells
COSYNE 2010, Poster
Timm Lochmann, Joseph N. Stember,  Tim Blanche, Daniel A. Butts
http://www.clfs.umd.edu/biology/ntlab/NTlab/Cosyne2010_files/Cosyne2010_V1_small.pdf

9) A dataset and evaluation methodology for visual saliency in videos
J. Li, Y. Tiang, T. Huang, W. Gao
ICME'09 Proceedings of the 2009 IEEE international conference on Multimedia and Expo, IEEE Press
http://dl.acm.org/citation.cfm?id=1699033

8) Cepstrum of Bispectrum Spike Detection applied to Extracellular Signals with Concurrent Intracellular Signals
BMC Neuroscience Vol. 10, Supplement 1, P59, DOI 10.1186/1471-2202-10-S1-P59
Eighteenth Annual Computational Neuroscience Meeting: CNS*2009
Shahjahan Shahid and Leslie S. Smith
http://www.springerlink.com/content/86163265j5323p25/

7) Assessing the effectiveness of Cepstrum of Bispectrum based spike detection on simultaneously recorded intra- and extra- cellularly recorded data
Poster presentation, SfN09.
Leslie S. Smith and Shahjahan Shahid
Dept. of Computing Science and Mathematics University of Stirling, Stirling,
Scotland, UK.
http://www.carmen.org.uk/publications/SFN09-poster-final-ls.pdf

6) Real-time estimation of human visual attention with dynamic Bayesian network and MCMC-based particle filter.
Kouji Miyazato, Akisato Kimura, Shigeru Takagi and Junji Yamato
2009 IEEE International Conference on Multimedia and Expo (ICME 2009)
http://www.brl.ntt.co.jp/people/akisato/pdf/icme2009miyazato.pdf

5) Real time estimation of human visual attention with MCMC-based particle filter
MIRU2009
The 12th International Conference on Image Recognition
Meeting on Image Recognition and Understanding
Kouji Miyazato, Akisato Kimura, Shigeru Takagi, Junji Yamato, and Kunio
Kashino
NTT Communication Science Laboratories, NTT Corporation, Japan.
Department of Information and Communication Systems Engineering, Okinawa
National College of Technology, Japan.
www.brl.ntt.co.jp/people/akisato/pdf/miru2009Miyazato.pdf

4) Dependent Dirichlet Process Spike Sorting
2009 Neural Information Processing Systems conference (NIPS 2009)
Jan Gasthaus, Frank Wood, Dilan Go ru r, Yee Whye Teh
Gatsby Computational Neuroscience Unit University College London.
http://books.nips.cc/papers/files/nips21/NIPS2008_0998.pdf

3) Spike-train communities: Finding groups of similar spike trains
M.D. Humphries, Univ. Sheffield, Sheffield, United Kingdom.
Program No. 322.11. 2009 Neuroscience Meeting Planner. Chicago, IL: Society
for Neuroscience, 2009. Online

2) Accurate spike sorting of multiunit recording data based on the robust variational Bayesian clustering
SfN 2008
Takashi Takekawa, Yoshikazu Isomura and Tomoki Fukai Lab. for Neural Circuit
Theory, RIKEN Brain Science Institute
http://nct.brain.riken.jp/~takekawa/SfN2008.pdf

1) Introduction of an automatic spike sorter, Clust016; its features and performance evaluation.
2008 abstract.
Hidekazu Kaneko & Hiroshi Tamura
Institute for Human Science and Biomedical Engineering, National Institute
of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan.
Laboratory for Cognitive Neuroscience, Graduate School of Frontier Biosciences,
Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
http://www2.bpe.es.osaka-u.ac.jp/multineuron/multineuron2008/abstract/Kaneko.pdf

C.  Masters Thesis

Spike Sorting Using Time-Varying Dirichlet Process Mixture Models
Jan A. Gasthaus
MSc in Intelligent Systems
University College London submitted September 5th, 2008
supervised by Frank Wood and Yee Whye Teh
http://www.gatsby.ucl.ac.uk/~ucabjga/papers/Gasthaus_2008_MScThesis.pdf

D.  Online resources

http://code.google.com/p/caton/
Spike sorting software which uses data hosted at CRCNS.org to test spike sorting algorithms.

http://xcorr.wordpress.com/2009/10/22/crcns-data-set-pvc-1-by-ringach-lab-getting-something-to-work/
Description of an analysis that was developed and tested using a data set hosted at CRCNS.org.

E.  Courses referencing data

CS/CNS/EE 253: Advanced Topics in Machine Learning
Taught at CalTech, Spring 2010.
http://www.cs.caltech.edu/courses/cs253/projects.html

Statistical analysis of neural data
Spring 2009, Columbia University
Instructor: Liam Paninski
http://www.stat.columbia.edu/~liam/teaching/neurostat-spr09/