Template-based spike pattern identification with linear convolution and dynamic time warping

Journal of Neurophysiology

Volumn 97, Issue 2, 2007, Pages 1221-1235

  Chi, Zhiyi ^a,c,d   Wu, Wei ^b   Haga, Zach ^c   Hatsopoulos, Nicholas G ^c   Margoliash, Daniel ^c  

^a UNIVERSITY OF CONNECTICUT   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

^d NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; DYNAMICS; ELECTROPHYSIOLOGY; FINCH; LINEAR SYSTEM; MACACA; MALE; MONKEY; MOTOR CORTEX; NEUROPHYSIOLOGY; NONHUMAN; PRIORITY JOURNAL; RELIABILITY; SCORING SYSTEM; SPIKE WAVE; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; ELECTROPHYSIOLOGY; FINCHES; MACACA MULATTA; MALE; MEMBRANE POTENTIALS; MICROELECTRODES; MODELS, NEUROLOGICAL; MODELS, STATISTICAL; NEURONS; SOFTWARE;

EID: 33846939250     PISSN: 00223077     EISSN: 15221598     Source Type: Journal    
DOI: 10.1152/jn.00448.2006     Document Type: Article

References (51)

1. Aach J, Church GM. Aligning gene expression time series with time warping algorithms. Bioinformatics 17: 495-508, 2001.
2. Abeles M, Bergman H, Margalit E, Vaadia E. Spatiotemporal firing patterns in the frontal cortex of behaving monkeys. J Neurophysiol 70: 1629-1638, 1993.
3. Abeles M, Gerstein GM. Detecting spatiotemporal firing patterns among simultaneously recorded single neurons. J Neurophysiol 60: 909-924, 1988.
4. Anderson SE, Dave AS, Margoliash D. Template-based automatic recognition of birdsong syllables from continuous recordings. J Acoust Soc Am 100: 1209-1219, 1996.
5. Bishop MJ, Thompson E. Maximum likelihood alignment of DNA sequences. J Mol Biol 190: 159-165, 1986.
6. Brenowitz EA, Margoliash D, Nordeen KW. An introduction to birdsong and the avian song system. J Neurobiol 33: 495-500, 1997.
7. Brockwell AE, Rojas AL, Kass RE. Recursive Bayesian decoding of motor cortical signals by particle filtering. J Neurophysiol 91: 1899-1907, 2004.
8. Buzsáki G. Two-stage model of memory trace formation: a role for "noisy" brain states. Neuroscience 31: 551-570, 1989.
9. Buzsáki G. Memory consolidation during sleep: a neurophysiological perspective. J Sleep Res 7, Suppl. 1: 17-23, 1998.
10. Carmena JM, Lebedev MA, Crist RE, O'Doherty JE, Santucci DM, Dimitrov DF, Patil PG, Henriquez CS, Nicolelis MAL. Learning to control a brain-machine interface for reaching and grasping by primates. PLoS Biol 1: 193-208, 2003.
11. Chi Z, Margoliash D. Temporal precision and temporal drift in brain and behavior of zebra finch song. Neuron 32: 899-910, 2001.
12. Chi Z, Rauske PL, Margoliash D. Pattern filtering for detection of neural activity, with examples from HVc activity during sleep in zebra finches. Neural Comput 15: 2307-2338, 2003.
13. Dave AS, Margoliash D. Song replay during sleep and computational rules for sensorimotor vocal learning. Science 290: 812-816, 2000.
14. Georgopoulos AP, Schwartz AB, Kettner RE. Neuronal population coding for movement direction. Science 233: 1416-1419, 1986.
15. Hahnloser RHR, Kozhevnikov AA, Fee MS. An ultra-sparse code underlies the generation of neural sequences in a songbird. Nature 419: 65-70, 2002.
16. Hahnloser RHR, Kozhevnikov AA, Fee MS. Sleep-related neural activity in a premotor and a basal-ganglia pathway of the songbird. J Neurophysiol 96: 794-812, 2006.
17. Hatsopoulos NG, Joshi L, O'Leary JG. Decoding continuous and discrete motor behavior from motor and premotor cortical ensembles. J Neurophysiol 92: 1165-1174, 2004.
18. Hoffman KL, McNaughton BL. Coordinated reactivation of distributed memory traces in primate neocortex. Science 297: 2070-2073, 2002.
19. Huang S-S, Gray RM. Spellmode recognition based on vector quantization. Speech Recogn 7: 41-53, 1988.
20. Ito K, Mori K. Dynamic programming matching as a simulation of budgerigar contact-call discrimination. J Acoust Soc Am 105: 552-559, 1999.
21. Kogan JA, Margoliash D. Automated recognition of bird song elements from continuous recordings using dynamic time warping and hidden Markov models: a comparison study. J Acoust Soc Am 103: 2185-2196, 1998.
22. Lee AK, Wilson MA. Memory of sequential experience in the hippocampus during slow wave sleep. Neuron 36: 1183-1194, 2002.
23. Lee AK, Wilson MA. A combinatorial method for analyzing sequential firing patterns involving an arbitrary number of neurons based on relative time order. J Neurophysiol 92: 2555-2573, 2004.
24. Louie K, Wilson MA. Temporally structured replay of awake hippocampal ensemble activity during rapid eye movement sleep. Neuron 29: 145-156, 2001.
25. Margoliash D. Preference for autogenous song by auditory neurons in a song system nucleus of the white-crowned sparrow. J Neurosci 6: 1643-1661, 1986.
26. Margoliash D. Evaluating theories of bird song learning: implications for future directions. J Comp Physiol A Sens Neural Behav Physiol 188: 851-866, 2002.
27. Margoliash D, Staicer CA, Inoue SA. Stereotyped and plastic song in adult indigo buntings, passerina cyanea. Anim Behav 42: 367-388, 1991.
28. Nádasdy Z. Spike sequences and their consequences. J Physiol (Paris) 94: 505-524, 2000.
29. Nádasdy Z, Hirase H, Czurkó A, Csicsvari J, Buzsáki G. Replay and time compression of recurring spike sequences in the hippocampus. J Neurosci 19: 9497-9507, 1999.
30. Needleman S, Wunsch C. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-453, 1970.
31. Nordeen KW, Nordeen EJ. Auditory feedback is necessary for the maintenance of stereotyped song in adult zebra finches. Behav Neural Biol 57: 58-66, 1992.
32. O'Shaughnessy D. Speech Communication: Human and Machine (2nd ed.). New York: Wiley-IEEE Press, 1999.
33. Rabiner L, Juang BH. Fundamentals of Speech Recognition. Lebanon, IN: Prentice Hall, 1993.
34. Reich DS, Mechler F, Purpura KP, Victor JD. Interspike intervals, receptive fields, and information encoding in primary visual cortex. J Neurosci 20: 1964-1974, 2000.
35. Reich DS, Mechler F, Victor JD. Independent and redundant information in nearby cortical neurons. Science 294: 2566-2568, 2001.
36. Riehle A, Grün S, Diesmann M, Aertsen A. Spike synchronization and rate modulation differentially involved in motor cortical function. Science 278: 1950-1953, 1997.
37. Sankoff D, Kruskal JB. Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. Reading, MA: Addison-Wesley, 1983.
38. Scott SH. Apparatus for measuring and perturbing shoulder and elbow joint positions and torques during reaching. J Neurosci Methods 89: 119-127, 1999.
39. Serruya MD, Hatsopoulos NG, Paninski L, Fellows MR, Donoghue JP. Brain-machine interface: instant neural control of a movement signal. Nature 416: 141-142, 2002.
40. Skaggs WE, McNaughton BL. Replay of neuronal firing sequences in rat hippocampus during sleep following spatial experience. Science 271: 1870-1873, 1996.
41. Smith AC, Brown EN. Estimating a state-space model from point process observations. Neural Comput 15: 965-991, 2003.
42. Smith AC, Smith P. A set probability technique for detecting relative time order across multiple neurons. Neural Comput 18: 1197-1214, 2006.
43. Sossinka R, Böhner J. Song types in the zebra finch (poephila guttata castanotis). Z Tierpsychol 53: 123-132, 1980.
44. Victor JD, Purpura KP. Nature and precision of temporal coding in visual cortex: a metric-space analysis. J Neurophysiol 76: 1310-1326, 1996.
45. Wagner RA, Fischer MJ. The string-to-string correction problem. J Assoc Comput Mach 21: 168-173, 1974.
46. Waterman MS, Gordon L, Arratia R. Phase transitions in sequence matches and nucleic acid structure. Proc Natl Acad Sci USA 84: 1239-1243, 1987.
47. Wilson MA, McNaughton BL. Reactivation of hippocampal ensemble memories during sleep. Science 265: 676-679, 1994.
48. Wu W, Black MJ, Mumford D, Gao Y, Bienenstock E, Donoghue JP. Modeling and decoding motor cortical activity using a switching Kalman filter. IEEE Trans Biomed Eng 51: 933-942, 2004.
49. Wu W, Gao Y, Bienenstock E, Donoghue JP, Black MJ. Bayesian population decoding of motor cortical activity using a Kalman filter. Neural Comput 18: 80-118, 2006.
50. Yu AC, Margoliash D. Temporal hierarchical control of singing in birds. Science 273: 1871-1875, 1996.
51. Zugaro MB, Monconduit L, Buzsáki G. Spike phase precession persists after transient intrahippocampal perturbation. Nat Neurosci 8: 67-71, 2005.