Factor-analysis methods for higher-performance neural prostheses

Journal of Neurophysiology

Volumn 102, Issue 2, 2009, Pages 1315-1330

  Santhanam, Gopal ^a   Yu, Byron M ^a,b,c   Gilja, Vikash ^a   Ryu, Stephen I ^a,b   Afshar, Afsheen ^a,b   Sahani, Maneesh ^c   Shenoy, Krishna V ^a,b  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY   (United States)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL EXPERIMENT; ARTICLE; BRAIN COMPUTER INTERFACE; CLASSIFIER; FACTORIAL ANALYSIS; MONKEY; NEUROLOGIC DISEASE; NONHUMAN; POISSON DISTRIBUTION; PREMOTOR CORTEX; PRIORITY JOURNAL; STATISTICAL ANALYSIS; TASK PERFORMANCE;

ACTION POTENTIALS; ALGORITHMS; ANALYSIS OF VARIANCE; ANIMALS; ELECTRODES, IMPLANTED; FACTOR ANALYSIS, STATISTICAL; FRONTAL LOBE; HAPLORHINI; MODELS, NEUROLOGICAL; MOTOR ACTIVITY; NEURONS; NEUROPSYCHOLOGICAL TESTS; POISSON DISTRIBUTION; PROSTHESES AND IMPLANTS;

EID: 68149171499     PISSN: 00223077     EISSN: 15221598     Source Type: Journal    
DOI: 10.1152/jn.00097.2009     Document Type: Article

References (58)

1. Batista AP, Santhanam G, Yu BM, Ryu SI, Afshar A, Shenoy KV. Reference frames for reach planning in macaque dorsal premotor cortex. J Neurophysiol 98: 966-983, 2007.
2. Brockwell AE, Rojas AL, Kass RE. Recursive Bayesian decoding of motor cortical signals by particle filtering. J Neurophysiol 91: 1899-1907, 2004.
3. Brown EN, Frank LM, Tang D, Quirk MC, Wilson MA. A statistical paradigm for neural spike train decoding applied to position prediction from the ensemble firing patterns of rat hippocampal place cells. J Neurosci 18: 7411-7425, 1998.
4. Brown TA. Confirmatory Factor Analysis for Applied Research (Methodology in the Social Sciences Series). New York: Guilford, 2006.
5. 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.
6. Chestek CA, Batista AP, Santhanam G, Yu BM, Afshar A, Cunningham JP, Gilja V, Ryu SI, Churchland MM, Shenoy KV. Single-neuron stability during repeated reaching in macaque premotor cortex. J Neurosci 27: 10742-10750, 2007.
7. Churchland MM, Santhanam G, Shenoy KV. Preparatory activity in premotor and motor cortex reflects the speed of the upcoming reach. J Neurophysiol 96: 3130-3146, 2006a.
8. Churchland MM, Yu BM, Ryu SI, Santhanam G, Shenoy KV. Neural variability in premotor cortex provides a signature of motor preparation. J Neurosci 26: 3697-3712, 2006b.
9. Cisek P, Kalaska JF. Modest gaze-related discharge modulation in monkey dorsal premotor cortex during a reaching task performed with free fixation. J Neurophysiol 88: 1064-1072, 2002.
10. Cisek P, Kalaska JF. Neural correlates of mental rehearsal in dorsal premotor cortex. Nature 431: 993-996, 2004.
11. Cunningham JP, Yu BM, Gilja V, Ryu SI, Shenoy KV. Toward optimal target placement for neural prosthetic devices. J Neurophysiol 100: 3445-3457, 2008.
12. Dayan P, Abbott LF. Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems. Cambridge, MA: MIT Press, 2001.
13. Dempster AP, Laird NM, Rubin DB. Maximum likelihood from incomplete data via the EM algorithm (with discussion). J R Stat Soc Ser B 39: 1-38, 1977.
14. Everitt BS. An Introduction to Latent Variable Models. London: Chapman & Hall, 1984.
15. Faisal AA, Selen LPJ, Wolpert DM. Noise in the nervous system. Nat Rev Neurosci 9: 292-303, 2008.
16. Georgopoulos AP, Kalaska JF, Caminiti R, Massey JT. On the relations between the direction of two-dimensional arm movements and cell discharge in primate motor cortex. J Neurosci 2: 1527-1537, 1982.
17. Ghahramani Z, Hinton G. The EM algorithm for mixtures of factor analyzers. Technical Report CRG-TR-96-1. Toronto: Department of Computer Science, Univ. of Toronto, 1997.
18. Gilja V, Kalmar RS, Santhanam G, Ryu SI, Yu BM, Afshar A, Shenoy KV. Trial-by-trial mean normalization improves plan period reach target decoding. Soc Neurosci Abstr 519.18, 2005.
19. Godschalk M, Lemon RN, Kuypers HG, van der Steen J. The involvement of monkey premotor cortex neurones in preparation of visually cued arm movements. Behav Brain Res 18: 143-157, 1985.
20. Gomez JE, Fu Q, Flament D, Ebner TJ. Representation of accuracy in the dorsal premotor cortex. Eur J Neurosci 12: 3748-3760, 2000.
21. Hastie T, Tibshirani R, Friedman JH. The Elements of Statistical Leaning (2nd ed.). New York: Springer, 2003.
22. Hatsopoulos N, Joshi J, O'Leary JG. Decoding continuous and discrete motor behaviors using motor and premotor cortical ensembles. J Neurophysiol 92: 1165-1174, 2004.
23. Hochberg LR, Serruya MD, Friehs GM, Mukand JA, Saleh M, Caplan AH, Branner A, Chen D, Penn RD, Donoghue JP. Neuronal ensemble control of prosthetic devices by a human with tetraplegia. Nature 442: 164-171, 2006.
24. Hocherman S, Wise SP. Effects of hand movement path on motor cortical activity in awake, behaving rhesus monkeys. Exp Brain Res 83: 285-302, 1991.
25. Kalmar RS, Gilja V, Santhanam G, Ryu SI, Yu BM, Afshar A, Shenoy KV. PMd delay activity during rapid sequential movement plans. Soc Neurosci Abstr 519.17, 2005.
26. Kemere C, Santhanam G, Yu BM, Afshar A, Ryu SI, Meng TH, Shenoy KV. Detecting neural state transitions using hidden Markov models for motor cortical prostheses. J Neurophysiol 100: 2441-2452, 2008.
27. Kennedy PR, Bakay RAE, Moore MM, Adams K, Goldwaithe J. Direct control of a computer from the human central nervous system. IEEE Trans Rehabil Eng 8: 198-202, 2000.
28. Kihlberg JK, Herson JH, Schotz WE. Square root transformation revisited. Appl Statist 21: 76-81, 1972.
29. Kulkarni J, Paninski L. Common-input models for multiple neural spike-train data. Network Comput Neural Syst 18: 375-407, 2007.
30. Leuthardt EC, Schalk G, Wolpaw JR, Ojemann JG, Morann DW. A brain- computer interface using electrocorticographic signals in humans. J Neural Eng 1: 63-71, 2004.
31. Maynard EM, Hatsopoulos NG, Ojakangas CL, Acuna BD, Sanes JN, Normann RA, Donoghue JP. Neuronal interactions improve cortical population coding of movement direction. J Neurosci 19: 8083-8093, 1999.
32. Messier J, Kalaska JF. Covariation of primate dorsal premotor cell activity with direction and amplitude during a memorized-delay reaching task. J Neurophysiol 84: 152-165, 2000.
33. Musallam S, Corneil BD, Greger B, Scherberger H, Andersen RA. Cognitive control signals for neural prosthetics. Science 305: 258-262, 2004.
34. Ng AY, Jordan MI. On discriminative vs. generative classifiers: a comparison of logistic regression and naive Bayes. In: Advances in Neural Information Processing Systems 14, edited by Dietterich TG, Becker S, Ghahramani Z. Cambridge, MA: MIT Press, 2002, vol. 2, p. 841-848.
35. Okatan M, Wilson MA, Brown EN. Analyzing functional connectivity using a network likelihood model of ensemble neural spiking activity. Neural Comput 17: 1927-1961, 2005.
36. Raina R, Shen Y, Ng AY, McCallum A. Classification with hybrid generative/discriminative models. In: Advances in Neural Information Processing Systems 16, edited by Thrun S, Saul LK, Schölkopf B. Cambridge, MA: MIT Press, 2004, p. 545-552.
37. Riehle A, MacKay WA, Requin J. Are extent and force independent movement parameters? Preparation- and movement-related neuronal activity in the monkey cortex. Exp Brain Res 99: 56-74, 1994.
38. Roweis S, Ghahramani Z. A unifying review of linear Gaussian models. Neural Comput 11: 305-345, 1999.
39. Roweis ST. EM algorithms for PCA and SPCA. In: Advances in Neural Information Processing Systems 10, edited by Jordan MI, Kearns MJ, Solla SA. Cambridge, MA: MIT Press, 1998, p. 626-632.
40. Santhanam G, Ryu SI, Yu BM, Afshar A, Shenoy KV. A high-performance brain-computer interface. Nature 442: 195-198, 2006a.
41. Santhanam G, Yu BM, Shenoy KV, Sahani M. Factor analysis with Poisson output. Technical Report NPSL-TR-06-1. Stanford, CA: Stanford Univ., 2006b.
42. Schalk G, Miller KJ, Anderson NR, Wilson JA, Smyth MD, Ojemann JG, Moran DW, Wolpaw JR, Leuthardt EC. Two-dimensional movement control using electrocorticographic signals in humans. J Neural Eng 5: 75-84, 2008.
43. Serruya MD, Hatsopoulos NG, Paninski L, Fellows MR, Donoghue JP. Instant neural control of a movement signal. Nature 416: 141-142, 2002.
44. Shadlen MN, Newsome WT. The variable discharge of cortical neurons: implications for connectivity, computation, and information coding. J Neurosci 18: 3870-3896, 1998.
45. Shenoy KV, Meeker D, Cao S, Kureshi SA, Pesaran B, Mitra P, Buneo CA, Batista AP, Burdick JW, Andersen RA. Neural prosthetic control signals from plan activity. Neuroreport 14: 591-596, 2003.
46. Shmulewitz D, Auerbach SB, Lehner T, Blundell ML, Winick JD, Youngman LD, Skilling V, Heath SC, Ott J, Stoffel M, Breslow JL, Friedman JM. Epidemiology and factor analysis of obesity, type II diabetes, hypertension, and dyslipidemia (syndrome X) on the Island of Kosrae, Federated States of Micronesia. Hum Hered 51: 8-19, 2001.
47. Smith AC, Brown EN. Estimating a state-space model from point process observations. Neural Comput 15: 965-991, 2003.
48. Taylor DM, Helms Tillery SI, Schwartz AB. Direct cortical control of 3D neuroprosthetic devices. Science 296: 1829-1832, 2002.
49. Thacker NA, Bromiley PA. The effects of a square root transform on a Poisson distributed quantity. Technical Report 2001-010. Manchester, UK: Univ. of Manchester, 2001.
50. Tipping ME, Bishop CM. Probabilistic principal component analysis. J R Stat Soc B 61: 611-622, 1999.
51. Truccolo W, Eden UT, Fellows MR, Donoghue JP, Brown EN. A point process framework for relating neural spiking activity to spiking history, neural ensemble and extrinsic covariate effects. J Neurophysiol 93: 1074-1089, 2005.
52. Velliste M, Perel S, Spalding MC, Whitford AS, Schwartz AB. Cortical control of a prosthetic arm for self-feeding. Nature 453: 1098 -1101, 2008.
53. Wolpaw JR, McFarland DJ. Control of a two-dimensional movement signal by a noninvasive brain-computer interface in humans. Proc Natl Acad Sci USA 101: 17849-17854, 2004.
54. 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.
55. Wu W, Kulkarni JE, Hatsopoulos NG, Paninski L. Neural decoding of goal-directed movements using a linear statespace. In: Computational and Systems Neuroscience (COSYNE) 2008 Workshops, Salt Lake City, UT. New York: Nova Science, 2008, p. 155.
56. Yu BM, Afshar A, Santhanam G, Ryu SI, Shenoy KV, Sahani M. Extracting dynamical structure embedded in neural activity. In: Advances in Neural Information Processing Systems 18, edited by Weiss Y, Schölkopf B, Platt J. Cambridge, MA: MIT Press, 2006, p. 1545-1552.
57. Yu BM, Kemere C, Santhanam G, Afshar A, Ryu SI, Meng TH, Sahani M, Shenoy KV. Mixture of trajectory models for neural decoding of goaldirected movements. J Neurophysiol 97: 3763-3780, 2007.
58. Zhang K, Ginzburg I, McNaughton B, Sejnowski TJ. Interpreting neuronal population activity by reconstruction: unified framework with application to hippocampal place cells. J Neurophysiol 79: 1017-1044, 1998.