Model-based feature construction for multivariate decoding

NeuroImage

Volumn 56, Issue 2, 2011, Pages 601-615

  Brodersen, Kay H ^a,b   Haiss, Florent ^b   Ong, Cheng Soon ^a   Jung, Fabienne ^c   Tittgemeyer, Marc ^c   Buhmann, Joachim M ^a   Weber, Bruno ^b   Stephan, Klaas E ^b,d  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c MAX PLANCK INSTITUTE FOR NEUROLOGICAL RESEARCH   (Germany)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Bayesian model selection; Classification; DCM; Dynamic causal modelling; Feature extraction; Feature selection; Multivariate decoding; Structural model selection

Indexed keywords

ANIMAL EXPERIMENT; ARTICLE; BAYES THEOREM; BRAIN ELECTROPHYSIOLOGY; CAUSAL MODELING; CLASSIFICATION ALGORITHM; CLASSIFIER; CONTROLLED STUDY; DATA ANALYSIS; DYNAMIC CAUSAL MODELING; EVIDENCE BASED PRACTICE; MALE; MULTIVARIATE ANALYSIS; MULTIVARIATE DECODING; NEUROANATOMY; NEUROBIOLOGY; NEUROPHYSIOLOGY; NONHUMAN; PRIORITY JOURNAL; RAT; STIMULUS RESPONSE; STRUCTURE ANALYSIS; TASK PERFORMANCE;

ANIMALS; BRAIN; COMPUTER SIMULATION; MODELS, NEUROLOGICAL; RATS;

EID: 79955047327     PISSN: 10538119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2010.04.036     Document Type: Article

References (69)

1. Allen P., Stephan K.E., Mechelli A., Day F., Ward N., Dalton J., Williams S.C., et al. Cingulate activity and fronto-temporal connectivity in people with prodromal signs of psychosis. NeuroImage 2010, 49(1):947-955. 10.1016/j.neuroimage.2009.08.038.
2. Baldeweg T. Repetition effects to sounds: evidence for predictive coding in the auditory system. Trends Cogn. Sci. 2006, 10(3):93-94. 10.1016/j.tics.2006.01.010.
3. Ben-Hur A., Ong C.S., Sonnenburg S., Schölkopf B., Rätsch G. Support vector machines and kernels for computational biology. PLoS Comput. Biol. 2008, 4(10):e1000173. 10.1371/journal.pcbi.1000173.
4. Blankertz B., Lemm S., Treder M., Haufe S., Müller K. Single-trial analysis and classification of ERP components-a tutorial. NeuroImage 2011, 56:814-825.
5. Bles M., Haynes J. Detecting concealed information using brain-imaging technology. Neurocase 2008, 14(1):82-92. 10.1080/13554790801992784.
6. Bode S., Haynes J. Decoding sequential stages of task preparation in the human brain. NeuroImage 2009, 45(2):606-613. 10.1016/j.neuroimage.2008.11.031.
7. Brodersen K.H., Penny W.D., Harrison L.M., Daunizeau J., Ruff C.C., Duzel E., Friston K.J., et al. Integrated Bayesian models of learning and decision making for saccadic eye movements. Neural Netw. 2008, 21(9):1247-1260. 10.1016/j.neunet.2008.08.007.
8. Brodersen K.H., Ong C.S., Stephan K.E., Buhmann J.M. The balanced accuracy and its posterior distribution 2010, Proceedings of the 20th International Conference on Pattern Recognition (ICPR).
9. Caron F., Doucet A. Sparse Bayesian nonparametric regression. Proceedings of the 25th International Conference on Machine Learning 2008, 88-95. ACM, Helsinki, Finland. 10.1145/1390156.1390168.
10. Chang, C., and Lin, C. (n.d.). LIBSVM: a library for support vector machines. Retrieved from http://www.csie.ntu.edu.tw/%20cjlin/libsvm/.
11. Cox D.D., Savoy R.L. Functional magnetic resonance imaging (fMRI) "brain reading": detecting and classifying distributed patterns of fMRI activity in human visual cortex. NeuroImage 2003, 19(2):261-270. 10.1016/S1053-8119(03)00049-1.
12. Davatzikos C., Ruparel K., Fan Y., Shen D., Acharyya M., Loughead J., Gur R., et al. Classifying spatial patterns of brain activity with machine learning methods: application to lie detection. NeuroImage 2005, 28(3):663-668. 10.1016/j.neuroimage.2005.08.009.
13. David O., Friston K.J. A neural mass model for MEG/EEG: coupling and neuronal dynamics. NeuroImage 2003, 20(3):1743-1755. 10.1016/j.neuroimage.2003.07.015.
14. David O., Kiebel S.J., Harrison L.M., Mattout J., Kilner J.M., Friston K.J. Dynamic causal modeling of evoked responses in EEG and MEG. NeuroImage 2006, 30(4):1255-1272. 10.1016/j.neuroimage.2005.10.045.
15. Felleman D.J., Van Essen D.C. Distributed hierarchical processing in the primate cerebral cortex. Cerebral Cortex (New York, N.Y.: 1991) 1991, 1(1):1-47.
16. Ford J., Farid H., Makedon F., Flashman L.A., McAllister T.W., Megalooikonomou V., Saykin A.J. Patient classification of fMRI activation maps. Medical Image Computing and Computer-Assisted Intervention 2003, 58-65. MICCAI, Retrieved from http://www.springerlink.com/content/b1fgfpu9reyxw1pu.
17. Formisano E., De Martino F., Bonte M., Goebel R. "Who" is saying "what"? brain-based decoding of human voice and speech. Science 2009, 322(5903):970-973. 10.1126/science.1164318.
18. Friston, K., in press. Dynamic causal modeling and Granger causality Comments on: The identification of interacting networks in the brain using fMRI: model selection, causality and deconvolution. NeuroImage, Corrected Proof. doi:10.1016/j.neuroimage.2009.09.031.
19. Friston K.J., Harrison L., Penny W. Dynamic causal modelling. NeuroImage 2003, 19(4):1273-1302. 10.1016/S1053-8119(03)00202-7.
20. Friston K., Mattout J., Trujillo-Barreto N., Ashburner J., Penny W. Variational free energy and the Laplace approximation. NeuroImage 2007, 34(1):220-234. 10.1016/j.neuroimage.2006.08.035.
21. Friston K., Chu C., Mourao-Miranda J., Hulme O., Rees G., Penny W., Ashburner J. Bayesian decoding of brain images. NeuroImage 2008, 39(1):181-205. 10.1016/j.neuroimage.2007.08.013.
22. Garrido M.I., Friston K.J., Kiebel S.J., Stephan K.E., Baldeweg T., Kilner J.M. The functional anatomy of the MMN: a DCM study of the roving paradigm. NeuroImage 2008, 42(2):936-944. 10.1016/j.neuroimage.2008.05.018.
23. Garrido M.I., Kilner J.M., Stephan K.E., Friston K.J. The mismatch negativity: a review of underlying mechanisms. Clin. Neurophysiol. 2009, 120(3):453-463. 10.1016/j.clinph.2008.11.029.
24. Grosenick L., Greer S., Knutson B. Interpretable classifiers for fMRI improve prediction of purchases. IEEE Transactions on Neural Systems and Rehabilitation Engineering 2008, Retrieved from http://www-psych.stanford.edu/~span/Publications/lg08tnsre_proof.pdf.
25. Grosenick L., Klingenberg B., Greer S., Taylor J., Knutson B. Whole-brain sparse penalized discriminant analysis for predicting choice. NeuroImage 2009, 47(Supplement 1):S58. 10.1016/S1053-8119(09)70232-0.
26. Hampton A.N., O'Doherty J.P. Decoding the neural substrates of reward-related decision making with functional MRI. Proc. Natl. Acad. Sci. 2007, 104(4):1377-1382. 10.1073/pnas.0606297104.
27. Harrison S.A., Tong F. Decoding reveals the contents of visual working memory in early visual areas. Nature 2009, 458:632-635. 10.1038/nature07832.
28. Hassabis D., Chu C., Rees G., Weiskopf N., Molyneux P.D., Maguire E.A. Decoding neuronal ensembles in the human hippocampus. Curr. Biol. 2009, 19(7):546-554. 10.1016/j.cub.2009.02.033.
29. Haynes J., Rees G. Predicting the orientation of invisible stimuli from activity in human primary visual cortex. Nat. Neurosci. 2005, 8(5):686-691.
30. Haynes J., Sakai K., Rees G., Gilbert S., Frith C., Passingham R.E. Reading hidden intentions in the human brain. Curr. Biol. 2007, 17(4):323-328. 10.1016/j.cub.2006.11.072.
31. Howard J.D., Plailly J., Grueschow M., Haynes J.-D., Gottfried J.A. Odor quality coding and categorization in human posterior piriform cortex. Nat. Neurosci. 2009, 12:932-938. 10.1038/nn.2324.
32. Jansen B.H., Rit V.G. Electroencephalogram and visual evoked potential generation in a mathematical model of coupled cortical columns. Biol. Cybern. 1995, 73(4):357-366.
33. Jung, F., Tittgemeyer, M., Kumagai, T., Moran, R., Stephan, K. E., Endepols, H., and Graf, R. (2009). Detection of auditory evoked potentials and mismatch negativity-like responses in the awake and unrestrained rat. Presented at the Society for Neuroscience.
34. Kamitani Y., Tong F. Decoding the visual and subjective contents of the human brain. Nat. Neurosci. 2005, 8(5):679-685. 10.1038/nn1444.
35. Kamitani Y., Tong F. Decoding seen and attended motion directions from activity in the human visual cortex. Curr. Biol. 2006, 16(11):1096-1102. 10.1016/j.cub.2006.04.003.
36. Kay K.N., Naselaris T., Prenger R.J., Gallant J.L. Identifying natural images from human brain activity. Nature 2008, 452(7185):352-355. 10.1038/nature06713.
37. Kiebel S.J., Garrido M.I., Friston K.J. Dynamic causal modelling of evoked responses: the role of intrinsic connections. NeuroImage 2007, 36(2):332-345. 10.1016/j.neuroimage.2007.02.046.
38. Kiebel S.J., Garrido M.I., Moran R., Chen C., Friston K.J. Dynamic causal modeling for EEG and MEG. Hum. Brain Mapp. 2009, 30(6):1866-1876. 10.1002/hbm.20775.
39. Kozel F.A., Johnson K.A., Mu Q., Grenesko E.L., Laken S.J., George M.S. Detecting deception using functional magnetic resonance imaging. Biol. Psychiatry 2005, 58(8):605-613. 10.1016/j.biopsych.2005.07.040.
40. Krajbich I., Camerer C., Ledyard J., Rangel A. Using neural measures of economic value to solve the public goods free-rider problem. Science (New York, N.Y.) 2009, 326(5952):596-599. 10.1126/science.1177302.
41. Kriegeskorte N., Goebel R., Bandettini P. Information-based functional brain mapping. PNAS 2006, 103(10):3863-3868. 10.1073/pnas.0600244103.
42. Kriegeskorte N., Formisano E., Sorger B., Goebel R. Individual faces elicit distinct response patterns in human anterior temporal cortex. PNAS 2007, 104(51):20600-20605. 10.1073/pnas.0705654104.
43. MacKay D.J.C. Bayesian interpolation. Neural Comput. 1992, 4:415-447.
44. Mitchell T.M., Hutchinson R., Just M.A., Niculescu R.S., Pereira F., Wang X. Classifying instantaneous cognitive states from fMRI data. Annual Symposium Proceedings 2003, 2003:465-469.
45. Mitchell T.M., Shinkareva S.V., Carlson A., Chang K., Malave V.L., Mason R.A., Just M.A. Predicting human brain activity associated with the meanings of nouns. Science 2008, 320(5880):1191-1195. 10.1126/science.1152876.
46. Miyawaki Y., Uchida H., Yamashita O., Sato M., Morito Y., Tanabe H.C., Sadato N., et al. Visual image reconstruction from human brain activity using a combination of multiscale local image decoders. Neuron 2008, 60(5):915-929. 10.1016/j.neuron.2008.11.004.
47. Moran R., Stephan K., Kiebel S., Rombach N., O'Connor W., Murphy K., Reilly R., et al. Bayesian estimation of synaptic physiology from the spectral responses of neural masses. NeuroImage 2008, 42(1):272-284. 10.1016/j.neuroimage.2008.01.025.
48. Moran R.J., Stephan K.E., Seidenbecher T., Pape H., Dolan R.J., Friston K.J. Dynamic causal models of steady-state responses. NeuroImage 2009, 44(3):796-811. 10.1016/j.neuroimage.2008.09.048.
49. Mourao-Miranda J., Bokde A., Born C., Hampel H., Stetter M. Classifying brain states and determining the discriminating activation patterns: support vector machine on functional MRI data. NeuroImage 2005, 28(4):980-995. 10.1016/j.neuroimage.2005.06.070.
50. Näätänen R., Tervaniemi M., Sussman E., Paavilainen P., Winkler I. "Primitive intelligence" in the auditory cortex. Trends Neurosci. 2001, 24(5):283-288.
51. Naselaris T., Prenger R.J., Kay K.N., Oliver M., Gallant J.L. Bayesian reconstruction of natural images from human brain activity. Neuron 2009, 63(6):902-915. 10.1016/j.neuron.2009.09.006.
52. Paninski L., Pillow J., Lewi J. Statistical models for neural encoding, decoding, and optimal stimulus design. Prog. Brain Res. 2007, 165:493-507. 10.1016/S0079-6123(06)65031-0.
53. Penny W.D., Stephan K.E., Mechelli A., Friston K.J. Comparing dynamic causal models. Neuroimage 2004, 22(3):1157-1172.
54. Pillow J.W., Shlens J., Paninski L., Sher A., Litke A.M., Chichilnisky E.J., Simoncelli E.P. Spatio-temporal correlations and visual signalling in a complete neuronal population. Nature 2008, 454(7207):995-999. 10.1038/nature07140.
55. Polyn S.M., Natu V.S., Cohen J.D., Norman K.A. Category-specific cortical activity precedes retrieval during memory search. Science 2005, 310(5756):1963-1966. 10.1126/science.1117645.
56. Ryali S., Supekar K., Abrams D.A., Menon V. Sparse logistic regression for whole-brain classification of fMRI data. NeuroImage 2010, 51(2):752-764. 10.1016/j.neuroimage.2010.02.040.
57. Schölkopf B., Smola A.J. Learning with kernels: support vector machines, regularization, optimization, and beyond 2002, MIT Press.
58. Serences J.T., Boynton G.M. The representation of behavioral choice for motion in human visual cortex. J. Neurosci. 2007, 27(47):12893-12899. 10.1523/JNEUROSCI.4021-07.2007.
59. Shawe-Taylor J., Cristianini N. Kernel Methods for Pattern Analysis 2004, Cambridge University Press.
60. Sitaram R., Caria A., Veit R., Gaber T., Rota G., Kuebler A., Birbaumer N. fMRI brain-computer interface: a tool for neuroscientific research and treatment. Comput. Intell. Neurosci. 2007, Retrieved from http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2007/25487.
61. Soon C., Namburi P., Goh C., Chee M., Haynes J. Surface-based information detection from cortical activity. NeuroImage 2009, 47(Supplement 1):S79. 10.1016/S1053-8119(09)70551-8.
62. Stephan K.E., Harrison L.M., Kiebel S.J., David O., Penny W.D., Friston K.J. Dynamic causal models of neural system dynamics: current state and future extensions. J. Biosci. 2007, 32(1):129-144.
63. Stephan K.E., Weiskopf N., Drysdale P.M., Robinson P.A., Friston K.J. Comparing hemodynamic models with DCM. NeuroImage 2007, 38(3):387-401. 10.1016/j.neuroimage.2007.07.040.
64. Stephan K.E., Kasper L., Harrison L.M., Daunizeau J., den Ouden H.E., Breakspear M., Friston K.J. Nonlinear dynamic causal models for fMRI. NeuroImage 2008, 42(2):649-662. 10.1016/j.neuroimage.2008.04.262.
65. Stephan K.E., Friston K.J., Frith C.D. Dysconnection in schizophrenia: from abnormal synaptic plasticity to failures of self-monitoring. Schizophr. Bull. 2009, 35(3):509-527. 10.1093/schbul/sbn176.
66. Stephan K.E., Penny W.D., Daunizeau J., Moran R.J., Friston K.J. Bayesian model selection for group studies. NeuroImage 2009, 46(4):1004-1017. 10.1016/j.neuroimage.2009.03.025.
67. van Gerven M., Hesse C., Jensen O., Heskes T. Interpreting single trial data using groupwise regularisation. NeuroImage 2009, 46(3):665-676. 10.1016/j.neuroimage.2009.02.041.
68. von der Behrens W., Bäuerle P., Kössl M., Gaese B.H. Correlating stimulus-specific adaptation of cortical neurons and local field potentials in the awake rat. J. Neurosci. 2009, 29(44):13837-13849. 10.1523/JNEUROSCI.3475-09.2009.
69. Yamashita O., Sato M., Yoshioka T., Tong F., Kamitani Y. Sparse estimation automatically selects voxels relevant for the decoding of fMRI activity patterns. NeuroImage 2008, 42(4):1414-1429. 10.1016/j.neuroimage.2008.05.050.