Partial Least Squares (PLS) methods for neuroimaging: A tutorial and review

NeuroImage

Volumn 56, Issue 2, 2011, Pages 455-475

  Krishnan, Anjali ^a   Williams, Lynne J ^b   McIntosh, Anthony Randal ^b,c   Abdi, Hervé ^a  

^a UNIVERSITY OF TEXAS AT DALLAS   (United States)

^b ROTMAN RESEARCH INSTITUTE   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

Asymmetric PLS; Barycentric discriminant analysis; Behavior PLS; Canonical variate analysis; Co inertia analysis; Common factor analysis; Multi block PLS; Multi table PLS; Multiple factor analysis; Partial least squares correlation; Partial least squares path modeling; Partial least squares regression; PLS; Seed PLS; STATIS; Symmetric PLS; Task PLS

Indexed keywords

ARTICLE; BOOTSTRAPPING; BRAIN FUNCTION; BRAIN SIZE; CORRELATION ANALYSIS; FUNCTIONAL MAGNETIC RESONANCE IMAGING; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; METHODOLOGY; NEUROIMAGING; PARTIAL LEAST SQUARES REGRESSION; PRIORITY JOURNAL; PROCESS OPTIMIZATION;

ALGORITHMS; BRAIN; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; LEAST-SQUARES ANALYSIS;

EID: 79955023796     PISSN: 10538119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2010.07.034     Document Type: Article

References (85)

1. Abdi H. Singular value decomposition (SVD) and generalized singular value decompositon (GSVD). Encyclopedia of Measurement and Statistics 2007, 907-912. Sage, Thousand Oaks (CA). N. Salkind (Ed.).
2. Abdi H. Partial least square regression, projection on latent structure regression, PLS-Regression. Wiley Interdiscip. Rev. Comput. Stat. 2010, 2:97-106.
3. Abdi H., Valentin D. Multiple factor analysis (MFA). Encyclopedia of Measurement and Statistics 2007, 657-663. Sage, Thousand Oaks (CA). N. Salkind (Ed.).
4. Abdi H., Valentin D. STATIS. Encyclopedia of Measurement and Statistics 2007, 955-962. Sage, Thousand Oaks (CA). N. Salkind (Ed.).
5. Abdi H., Williams L.J. Barycentric discriminant analysis. Encyclopedia of Research Design 2010, 64-75. Sage, Thousand Oaks (CA). N. Salkind, D. Dougherty, B. Frey (Eds.).
6. Abdi H., Williams L.J. The jackknife. Encyclopedia of Research Design 2010, 655-660. Sage, Thousand Oaks (CA). N. Salkind, D. Dougherty, B. Frey (Eds.).
7. Abdi H., Williams L.J. Matrix algebra. Encyclopedia of Research Design 2010, 761-776. Sage, Thousand Oaks (CA). N. Salkind, D. Dougherty, B. Frey (Eds.).
8. Abdi H., Williams L.J. Principal components analysis. Wiley Interdiscip. Rev. Comput. Stat. 2010, 2:433-450.
9. Abdi H., Valentin D., O'Toole A.J., Edelman B. DISTATIS: the analysis of multiple distance matrices. Proceedings of the IEEE Computer Society: International Conference on Computer Vision and Pattern Recognition 2005, 43-47.
10. Abdi H., Dunlop J.P., Williams L.J. How to compute reliability estimates and display confidence and tolerance intervals for pattern classifiers using the Bootstrap and 3-way multidimensional scaling (DISTATIS). Neuroimage 2009, 45:89-95.
11. Abdi H., Edelman B., Valentin D., Dowling W.J. Experimental design and analysis for psychology 2009, Oxford University Press, Oxford.
12. Addis D.R., McIntosh A.R., Moscovitch M., Crawley A.P., McAndrews M.P. Characterizing spatial and temporal features of autobiographical memory retrieval networks: a partial least squares approach. Neuroimage 2004, 23:1460-1471.
13. Bergström Z.M., Velmans M., deFockert J., Richardson-Klavehn A. ERP evidence for successful voluntary avoidance of conscious recollection. Brain Res. 2007, 1151:119-133.
14. Bookstein F. The geometric meaning of soft modeling with some generalizations. System under indirect observation 1982, Volume 2. North-Holland, Amsterdam.
15. Bookstein F.L. Partial least squares: a dose-response model for measurement in the behavioral and brain sciences. Psycoloquy 1994, 5.
16. Bookstein F.L., Steissguth A.P., Sampson P.D., Conner P.D., Barr H.M. Corpus callosum shape and neuropsychological deficits in adult males with heavy fetal alcohol exposure. Neuroimage 2002, 15:233-251.
17. Burnham A., Viveros R., MacGregor J. Frameworks for latent variable multivariate regression. J. Chemometr. 1996, 10:31-45.
18. Caplan J.B., McIntosh A.R., De Rosa E. Two distinct functional networks for successful resolution of proactive interference. Cereb. Cortex 2007, 17:1650-1663.
19. Chessel D., Hanafi M. Analyse de la co-inertie de K nuages de points. Rev. Stat. Appl. 1996, 44:35-60.
20. de Jong S. SIMPLS: an alternative approach to partial least squares regression. Chemom. Intell. Lab. Syst. 1993, 18:251-263.
21. de Jong S., Phatak A. Partial least squares regression. Proceedings of the second international workshop on recent advances in total least squares techniques and error-in-variables modeling. Society for Industrial and Applied Mathematics 1997, 25-36.
22. de Leeuw J. Derivatives of generalized eigen-systems with applications. Department of Statistics Papers 2007, 1-28.
23. Della-Maggiore V., Sekuler A.B., Grady C.L., Benett P.J., Sekuler R., McIntosh A.R. Corticolimbic interactions associated with performance on a short-term memory task are modified by age. J. Neurosci. 2000, 20:8410-8416.
24. Dray S., Chessel D., Thioulouse J. Co-inertia analysis and the linking of ecological data tables. Ecology 2003, 84:3078-3089.
25. Efron B., Tibshirani R. Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy. Stat. Sci. 1986, 1:54-77.
26. Escofier B., Pagès J. Multiple factor analysis. Comput. Stat. Data Anal. 1990, 18:120-140.
27. Handbook of Partial Least Squares: Concepts, Methods and Applications 2010, Springer Verlag, New York. V. Esposito-Vinzi, W. Wynne, W.W. Chin, J. Henseler, H. Wang (Eds.).
28. Folstein M.F., Folstein S.E., McHugh P.R. "Mini-Mental State". A practical method for grading the cognitive state of patients for the clinician. J. Psychiatr. Res. 1975, 12:189-198.
29. Fujiwara E., Schwartz M.L., Gao F., Black S.E., Levine B. Ventral frontal cortex functions and quantified MRI in traumatic brain injury. Neuropsychologia 2008, 46:461-474.
30. Gidskehaug L., Stødkilde-Jørgensen H., Martens M., Martens H. Bridge-PLS regression: two-block bilinear regression without deflation. J. Chemometr. 2004, 18:208-215.
31. Giessing C., Fink G., Rosler F., Thiel C. fMRI data predict individual differences of behavioral effects of nicotine: a partial least squares analysis. J. Cogn. Neurosci. 2007, 19:658-670.
32. Gittins R. Canonical Analysis 1985, Springer-Verlag, New York.
33. Gottfries J., Blennow K., Wallin A., Gottfries C.G. Diagnosis of dementias using partial least squares discriminant analysis. Dementia 1995, 6:83-88.
34. Grady C.L., McIntosh A.R., Beig S., Keightley M.L., Burian H., Black S.E. Evidence from functional neuroimaging of a compensatory prefrontal network in Alzheimer's disease. J. Neurosci. 2003, 23:986-993.
35. Greenacre M. Theory and applications of correspondence analysis 1984, Academic Press, London.
36. Iidaka T., Anderson N.D., Kapur S., Cabeza R., Craik F.I.M. The effect of divided attention on encoding and retrieval in episodic memory revealed by positron emission tomography. J. Cogn. Neurosci. 2000, 12:267-280.
37. Keightley M.L., Seminowicz D.A., Bagby R.M., Costa P.T., Fossati P., Mayberg H.S. Personality influences limbic-cortical interactions during sad mood induction. Neuroimage 2003, 20:2031-2039.
38. Keightley M.L., Winocur G., Graham S.J., Mayberg H.S., Hevenor S.J., Grady C.L. An fMRI study investigating cognitive modulation of brain regions associated with emotional processing of visual stimuli. Neuropsychologia 2003, 41:585-596.
39. Kherif F., Poline J.-B., Mériaux S., Benali H., Flandin G., Brett M. Group analysis in functional neuroimaging: selecting subjects using similarity measures. Neuroimage 2003, 20:2197-2208.
40. Köhler S., Moscovitch M., Wincour G., Houle S., McIntosh A.R. Networks of domain-specific and general regions involved in episodic memory for spatial location and object identity. Neuropsychologia 1998, 36:129-142.
41. Lehmann C., Koenig T., Jelic V., Prichep L., John R.E., Wahlund L.-O., Dodge Y., Dierks T. Application and comparison of classification algorithms for recognition of Alzheimer's disease in electrical brain activity. J. Neurosci. Meth. 2007, 161:342-350.
42. Mardia K.V., Kent J.T., Bibby J.M. Multivariate analysis 1979, Academic Press, London.
43. Martens H., Martens M. Multivariate analysis of quality: an introduction 2001, Wiley, London.
44. Martens H., Naes T. Multivariate calibration 1989, Wiley, London.
45. Martinez-Montes E., Valdés-Sosa P.A., Miwakeichi F., Goldman R.I., Cohen M.S. Concurrent EEG/fMRI analysis by partial least squares. Neuroimage 2004, 22:1023-1034.
46. Mazerolles G., Hanafi M., Dufour E., Bertrand D., Qannari E. Common components and specific weights analysis: a chemometric method for dealing with complexity of food products. Chemometr. Intell. Lab. Syst. 2006, 81:41-49.
47. McIntosh A., Gonzalez-Lima F. Structural modeling of functional neural pathways mapped with 2-deoxyglucose: effects of acoustic startle habituation on the auditory system. Brain Res. 1991, 547:295-302.
48. McIntosh A.R., Lobaugh N.J. Partial least squares analysis of neuroimaging data: applications and advances. Neuroimage 2004, 23:S250-S263.
49. McIntosh A.R., Bookstein F., Haxby J., Grady C. Spatial pattern analysis of functional brain images using partial least squares. Neuroimage 1996, 3:143-157.
50. McIntosh A., Nyberg L., Bookstein F.L., Tulving E. Differential functional connectivity of prefrontal and medial temporal cortices during episodic memory retrieval. Hum. Brain Mapp. 1997, 5:323-327.
51. McIntosh A.R., Lobaugh N.J., Cabeza R., Bookstein F.L., Houle S. Convergence of neural systems processing stimulus associations and coordinating motor responses. Cereb. Cortex 1998, 8:648-659.
52. McIntosh A.R., Chau W., Protzner A. Spatiotemporal analysis of event-related fMRI data using partial least squares. Neuroimage 2004, 23:764-775.
53. Mentis M.J., Dhawan V., Feigin A., Delalot D., Zgaljardic D., Edwards C., Eidelberg D. Early stage Parkinson's disease patients and normal volunteers: comparative mechanisms of sequence learning. Hum. Brain Mapp. 2003, 20:246-258.
54. Menzies L., Achard S., Chamberlain S.R., Fineberg N., Chen C.-H., delCampo N., Sahakian B.J., Robbins T.W., Bullmore E. Neurocognitive endophenotypes of obsessive-compulsive disorder. Brain 2007, 130:3223-3236.
55. Mevik B.-H., Wehrens R. The PLS package: principal component and partial least squares regression in R. J. Stat. Softw. 2007, 18:1-24.
56. Nestor P.G., O'Donnell B.F., Mccarley R.W., Niznikeiwicz M., Barnard J., Shen Z.J., Bookstein F.L., Shenton M.E. A new statistical method for testing hypotheses of neuropsychological/MRI relationships in schizophrenia: partial least squares analysis. Schizophr. Res. 2002, 53:57-66.
57. Nyberg L., McIntosh A.R., Cabeza R., Habib R., Houle S., Tulving E. General and specific brain regions involved in encoding and retrieval of events: what, where and when. Proc. Natl. Acad. Sci. USA 1996, 93:11280-11285.
58. Nyberg L., Persson J., Habib R., Tulving E., McIntosh A.R., Cabeza R., Houle S. Large scale neurocognitive networks underlying episodic memory. J. Cogn. Neurosci. 2000, 12:163-173.
59. Nyberg L., Forkstam C., Petersson K.M., Cabeza R., Ingvar M. Brain imaging of human memory systems: between-systems similarities and within-system differences. Brain Res. Interact. 2002, 13:281-292.
60. Price J., Ziolko S., Weissfeld L., Klunk W., Lu X., Hoge J., Meltzer C., Davis S., Lopresti B., Holt D., DeKosky S., Mathis C. Quantitative and statistical analyses of PET imaging studies of amyloid deposition in humans. 2004 IEEE 2004, 5:3161-3164.
61. Protzner A.B., McIntosh A.R. The interplay of stimulus modality and response latency in neural network organization for simple working memory tasks. J. Neurosci. 2007, 27:3187-3197.
62. Rajah M.N., McIntosh A.R. Overlap in the functional neural systems involved in semantic and episodic memory retrieval. J. Cogn. Neurosci. 2005, 17:470-482.
63. Rao C. The use and interpretation of principal component analysis in applied research. Sankhya 1964, 26:329-359.
64. Rao A., Aljabar P., Rueckert D. Hierarchical statistical shape analysis and prediction of sub-cortical brain structures. Med. Image Anal. 2008, 12:55-68.
65. Shinkareva S., Ombao H., Sutton B., Mohanty A., Miller G. Classification of functional brain images with a spatio-temporal dissimilarity map. Neuroimage 2006, 33:63-71.
66. Shinkareva S.V., Mason R.A., Malave V.L., Wang W., Mitchell T.M., Just M.A. Using fMRI brain activation to identify cognitive states associated with perception of tools and dwellings. PLoS ONE 2008, 3.
67. Sidtis J.J., Strother S.C., Rottenberg D.A. Predicting performance from functional imaging data: methods matter. Neuroimage 2003, 20:615-624.
68. Stone M., Brooks R.J. Continuum regression: cross-validated sequentially constructed prediction embracing ordinary least squares, partial least squares and principal components regression. J. R. Stat. Soc. B Methodol. 1990, 52:237-269.
69. Streissguth A., Bookstein F., Sampson P., Barr H. Methods of latent variable modeling by partial least squares. The Enduring Effects of Prenatal Alcohol Exposure on Child Development 1993, University of Michigan Press.
70. Takane Y. Relationships among various kinds of eigenvalue and singular value decompositions. New developments in psychometrics 2002, 45-46. Springer Verlag, Tokyo. H. Yanai, A. Okada, K. Shigemasu, Y. Kano, J. Meulman (Eds.).
71. Talairach J., Tournoux P. Co-planar Stereotaxic Atlas of the Human Brain 1988, Thieme.
72. Tenenhaus M. La regression PLS 1998, Technip, Paris.
73. Tenenhaus, M., Tenenhaus, A., in press, Regularized generalized canonical correlation analysis. Psychometrika.
74. Thioulouse J., Simier M., Chessel D. Simultaneous analysis of a sequence of paired ecological tables. Ecology 2003, 20:2197-2208.
75. Tippett W., Black S. Regional cerebral blood flow correlates of visuospatial tasks in Alzheimer's disease. J. Int. Neuropsychol. Soc. 2008, 14:1034-1045.
76. Tucker L. An inter-battery method of factor analysis. Psychometrika 1958, 23:111-136.
77. Tyler D.E. On the optimality of the simultaneous redundancy transformations. Psychometrika 1982, 47:77-86.
78. Vallesi A., McIntosh A.R., Alexander M.P., Stuss D.T. fMRI evidence of a functional network setting the criteria for withholding a response. Neuroimage 2009, 45:537-548.
79. van den Wollenberg A. Redundancy analysis: an alternative to canonical correlation. Psychometrika 1977, 42:207-219.
80. Wang J.Y., Bakhadirov K., Devous M.D., Abdi H., McColl R., Moore C., de la Plata C.D.M., Ding K., Whittemore A., Babcock E., Rickbeil T., Dobervich J., Kroll D., Dao B., Mohindra N., Madden C.J., Diaz-Arrastia R. Diffusion tensor tractography of traumatic diffuse axonal injury. Arch. Neurol. 2008, 65:619-626.
81. West R., Krompinger J. Neural correlates of prospective and retrospective memory. Neuropsychologia 2005, 43:418-433.
82. West R., Wymbs N. Is detecting prospective cues the same as selecting targets? An ERP study. Cogn. Affect. Behav. Neurosci. 2004, 4:354-363.
83. Williams L.J., Abdi H., French R., Orange J.B. A tutorial on Multi-Block Discriminant Correspondence Analysis (MUDICA): A new method for analyzing discourse data from clinical populations. Journal of Speech Language and Hearing Research 2010, 53:1372-1393.
84. Wold H. Soft modelling, the basic design and some extensions. Systems Under Indirect Observation: Causality-Structure-Prediction. Part II 1982, 1-54. North-Holland Publishing Company, Amsterdam. H. Wold, K.-G. Jöreskog (Eds.).
85. Wold S., Sjöström M., Eriksson L. PLS-regression: a basic tool of chemometrics. Chemom. Intell. Lab. Syst. 2001, 58:109-130.