Non-negative matrix factorization of multimodal MRI, fMRI and phenotypic data reveals differential changes in default mode subnetworks in ADHD

NeuroImage

Volumn 102, Issue P1, 2014, Pages 207-219

  Anderson, Ariana ^a   Douglas, Pamela K ^a   Kerr, Wesley T ^a   Haynes, Virginia S ^b   Yuille, Alan L ^a   Xie, Jianwen ^a   Wu, Ying Nian ^a   Brown, Jesse A ^c   Cohen, Mark S ^a,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b ELI LILLY AND COMPANY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d University of California   (United States)

Author keywords

ADHD; Attention deficit; Biomarkers; Default mode; FMRI; Latent variables; Machine learning; MRI; Multimodal data; NMF; Phenotype; Sparsity; Topic modeling

Indexed keywords

ALGORITHM; ATTENTION DEFICIT DISORDER; BEHAVIOR; BRAIN FUNCTION; DEFAULT MODE NETWORK; DISEASE CLASSIFICATION; FUNCTIONAL MAGNETIC RESONANCE IMAGING; HUMAN; MACHINE LEARNING; NEUROIMAGING; NON NEGATIVE MATRIX FACTORIZATION; NUCLEAR MAGNETIC RESONANCE IMAGING; PARAHIPPOCAMPAL GYRUS; PHENOTYPE; POSTERIOR CINGULATE; PRECUNEUS; REVIEW; STATISTICAL ANALYSIS; ADOLESCENT; ATTENTION DEFICIT DISORDER WITH HYPERACTIVITY; CHILD; FEMALE; GENETICS; MALE; MULTIMODAL IMAGING; YOUNG ADULT;

ADOLESCENT; ALGORITHMS; ATTENTION DEFICIT DISORDER WITH HYPERACTIVITY; CHILD; FEMALE; HUMANS; MAGNETIC RESONANCE IMAGING; MALE; MULTIMODAL IMAGING; NEUROIMAGING; PHENOTYPE; YOUNG ADULT;

EID: 84908384066     PISSN: 10538119     EISSN: 10959572     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2013.12.015     Document Type: Review

References (70)

1. American Psychiatric Association Diagnostic and Statistical Manual of Mental Disorders: DSM-IV-TR 2000, American Psychiatric Publishing, Inc.
2. Biswal Bharat, Yetkin F.Zerrin, Haughton Victor M., Hyde James S. Functional connectivity in the motor cortex of resting human brain using echo-planar MRI. Magn. Reson. Med. 1995, 34(4):537-541.
3. Blei David M., Ng Andrew Y., Jordan Michael I. Latent dirichlet allocation. J. Mach. Learn. Res. 2003, 3:993-1022.
4. Brown Matthew R.G., Sidhu Gagan S., Greiner Russell, Asgarian Nasimeh, Bastani Meysam, Silverstone Peter H., Greenshaw Andrew J., Dursun Serdar M. ADHD-200 global competition: diagnosing ADHD using personal characteristic data can outperform resting state fMRI measurements. Front. Syst. Neurosci. 2012, 6(69).
5. Buckner Randy L., Andrews-Hanna Jessica R., Schacter Daniel L. The brain's default network. Ann. N. Y. Acad. Sci. 2008, 1124(1):1-38.
6. Calhoun Vince D., Liu Jingyu, Adali Tülay A review of group ICA for fMRI data and ICA for joint inference of imaging, genetic, and ERP data. NeuroImage 2009, 45(1 Suppl.):S163.
7. Castellanos F.Xavier, Margulies Daniel S., Kelly A.M.Clare, Uddin Lucina Q., Ghaffari Manely, Kirsch Andrew, Shaw David, Shehzad Zarrar, Di Martino Adriana, Biswal Bharat, et al. Cingulate-precuneus interactions: a new locus of dysfunction in adult attention-deficit/hyperactivity disorder. Biol. Psychiatry 2008, 63(3):332.
8. Cheng Wei, Ji Xiaoxi, Zhang Jie, Feng Jianfeng Individual classification of ADHD patients by integrating multiscale neuroimaging markers and advanced pattern recognition techniques. Front. Syst. Neurosci. 2012, 6.
9. Colby John B., Rudie Jeffrey D., Brown Jesse A., Douglas Pamela K., Cohen Mark S., Shehzad Zarrar Insights into multimodal imaging classification of ADHD. Front. Syst. Neurosci. 2012, 6.
10. Cortese Samuele The neurobiology and genetics of attention-deficit/hyperactivity disorder (ADHD): What every clinician should know. Eur. J. Paediatr. Neurol. 2012, 16(5):422-433.
11. Cortese Samuele, Kelly Clare, Chabernaud Camille, Proal Erika, Di Martino Adriana, Milham Michael P., Castellanos F.Xavier Toward systems neuroscience of ADHD: a meta-analysis of 55 fMRI studies. Am. J. Psychiatr. 2012, 169(10):1038-1055.
12. Dai Dai, Wang Jieqiong, Hua Jing, He Huiguang Frontiers: Classification of ADHD children through multimodal magnetic resonance imaging. Front. Syst. Neurosci. 2012, 6.
13. De Martino Federico, Gentile Francesco, Esposito Fabrizio, Balsi Marco, Di Salle Francesco, Goebel Rainer, Formisano Elia Classification of fMRI independent components using IC-fingerprints and support vector machine classifiers. NeuroImage 2007, 34(1):177-194.
14. Devarajan Karthik Nonnegative matrix factorization: an analytical and interpretive tool in computational biology. PLoS Comput. Biol. 2008, 4(7):e1000029.
15. Duan Kai-Bo, Rajapakse Jagath C., Wang Haiying, Azuaje Francisco Multiple svm-rfe for gene selection in cancer classification with expression data. IEEE Trans. Nanobiosci. 2005, 4(3):228-234.
16. Eichele Tom, Calhoun Vince D., Debener Stefan Mining EEG-fMRI using independent component analysis. Int. J. Psychophysiol. 2009, 73(1):53.
17. Ellison-Wright Ian, Ellison-Wright Zoë, et al. Structural brain change in attention deficit hyperactivity disorder identified by meta-analysis. BMC Psychiatry 2008, 8(1):51.
18. Eloyan A., Muschelli J., Nebel M.B., Liu H., Han F., Zhao T., Barber A.D., Joel S., Pekar J.J., Mostofsky S.H., Caffo B. Automated diagnoses of attention deficit hyperactive disorder using magnetic resonance imaging. Front. Syst. Neurosci. 2012, 6.
19. Fair Damien A., Posner Jonathan, Nagel Bonnie J., Bathula Deepti, Costa Dias Taciana G., Mills Kathryn L., Blythe Michael S., Giwa Aishat, Schmitt Colleen F., Nigg Joel T. Atypical default network connectivity in youth with attention-deficit/hyperactivity disorder. Biol. Psychiatry 2010, 68(12):1084-1091.
20. Fassbender Catherine, Zhang Hao, Buzy Wendy M., Cortes Carlos R., Mizuiri Danielle, Beckett Laurel, Schweitzer Julie B., et al. A lack of default network suppression is linked to increased distractibility in ADHD. Brain Res. 2009, 1273:114.
21. Fischl Bruce Freesurfer. NeuroImage 2012, 62(2):774-781.
22. Freire Luis, Mangin J.-F. Motion correction algorithms may create spurious brain activations in the absence of subject motion. NeuroImage 2001, 14(3):709-722.
23. Friston Karl J., Williams Steven, Howard Robert, SJ Frackowiak Richard, Turner Robert Movement-related effects in fMRI time-series. Magn. Reson. Med. 1996, 35(3):346-355.
24. Gaussier Eric, Goutte Cyril Relation between PLSA and NMF and implications. Proceedings of the 28th annual international ACM SIGIR conference on Research and development in information retrieval 2005, 601-602. ACM.
25. Girolami Mark, Kabán Ata On an equivalence between PLSI and LDA. Proceedings of the 26th annual international ACM SIGIR conference on Research and development in informaion retrieval 2003, 433-434. ACM.
26. Greicius Michael D., Srivastava Gaurav, Reiss Allan L., Menon Vinod Default-mode network activity distinguishes Alzheimer's disease from healthy aging: evidence from functional MRI. Proc. Natl. Acad. Sci. U. S. A. 2004, 101(13):4637-4642.
27. Guillamet David, Vitria Jordi, Schiele Bernt Introducing a weighted non-negative matrix factorization for image classification. Pattern Recogn. Lett. 2003, 24(14):2447-2454.
28. Hall Mark, Frank Eibe, Holmes Geoffrey, Pfahringer Bernhard, Reutemann Peter, Witten Ian H. The WEKA data mining software: an update. ACM SIGKDD Explor. Newsl. 2009, 11(1):10-18.
29. Højen-Sørensen Pedro A.D.F.R., Winther Ole, Hansen Lars Kai Mean-field approaches to independent component analysis. Neural Comput. 2002, 14(4):889-918.
30. Hyvärinen Aapo, Oja Erkki Independent component analysis: algorithms and applications. Neural Netw. 2000, 13(4):411-430.
31. Kerr Welsey T., Anderson A., Douglas P.K., Cohen M.S. How to Cheat: Parameter Optimization Using Cross-Validation Accuracy 2013, (submitted for publication).
32. Kim Hyunsoo, Park Haesun Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis. Bioinformatics 2007, 23(12):1495-1502.
33. Laird Angela R., Eickhoff Simon B., Li Karl, Robin Donald A., Glahn David C., Fox Peter T. Investigating the functional heterogeneity of the default mode network using coordinate-based meta-analytic modeling. J. Neurosci. 2009, 29(46):14496-14505.
34. Lee Daniel D., Seung H.Sebastian, et al. Learning the parts of objects by non-negative matrix factorization. Nature 1999, 401(6755):788-791.
35. Lei Xu., Qiu Chuan, Peng Xu., Yao Dezhong A parallel framework for simultaneous EEG/fMRI analysis: methodology and simulation. NeuroImage 2010, 52(3):1123-1134.
36. Lin Chih-Jen Projected gradient methods for nonnegative matrix factorization. Neural Comput. 2007, 19(10):2756-2779.
37. Liu Suhai NMFN: Non-negative Matrix Factorization. R package version 2.0 2012.
38. Liu Jingyu, Calhoun Vince Parallel independent component analysis for multimodal analysis: application to fMRI and EEG data. Biomedical Imaging: From Nano to Macro, 2007. ISBI 2007. 4th IEEE International Symposium on 2007, 1028-1031. IEEE.
39. Liu Weixiang, Zheng Nanning Non-negative matrix factorization based methods for object recognition. Pattern Recogn. Lett. 2004, 25(8):893-897.
40. Mahoney Michael W., Drineas Petros CUR matrix decompositions for improved data analysis. PNAS 2009, 106:697-702.
41. Mantini Dante, Marzetti L., Corbetta M., Romani G.L., Del Gratta C. Multimodal integration of fMRI and EEG data for high spatial and temporal resolution analysis of brain networks. Brain Topogr. 2010, 23(2):150-158.
42. Martinez-Montes Eduardo, Valdés-Sosa Pedro A., Miwakeichi Fumikazu, Goldman Robin I., Cohen Mark S. Concurrent EEG/fMRI analysis by multiway partial least squares. NeuroImage 2004, 22(3):1023-1034.
43. McGough James J. Attention deficit hyperactivity disorder pharmacogenetics: the dopamine transporter and d4 receptor. Pharmacogenomics 2012, 13(4):365-368.
44. Mennes Maarten, Biswal Bharat, Castellanos F.Xavier, Milham Michael P. Making data sharing work: the FCP/INDI experience. NeuroImage 2013, 82:683-691. (15 November).
45. Mills Kathryn L., Bathula Deepti, Costa Dias Taciana G., Iyer Swathi P., Fenesy Michelle C., Musser Erica D., Stevens Corinne A., Thurlow Bria L., Carpenter Samuel D., Nagel Bonnie J., et al. Altered cortico-striatal-thalamic connectivity in relation to spatial working memory capacity in children with ADHD. Front. Psychiatry 2012, 3.
46. Molgaard L.L., Jorgensen K.W., Hansen Lars Kai Castsearch-context based spoken document retrieval. Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on 2007, vol. 4:IV-93. IEEE.
47. Oakes T.R., Johnstone T., Ores Walsh K.S., Greischar L.L., Alexander A.L., Fox A.S., Davidson R.J., et al. Comparison of fMRI motion correction software tools. NeuroImage 2005, 28(3):529-543.
48. Olivetti Emanuele, Greiner Susanne, Avesani Paolo ADHD diagnosis from multiple data sources with batch effects. Front. Syst. Neurosci. 2012, 6:70.
49. Qi Qihao, Zhao Yingdong, Li MingChung, Simon Richard Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-arraytools. Bioinformatics 2009, 25(4):545-547.
50. Quinlan John Ross C4. 5: programs for machine learning 1993, vol. 1. Morgan kaufmann.
51. R Development Core Team R: A Language and Environment for Statistical Computing 2012, R Foundation for Statistical Computing, Vienna, Austria.
52. Rabiner Lawrence R. A tutorial on hidden markov models and selected applications in speech recognition. Proc. IEEE 1989, 77(2):257-286.
53. Raichle Marcus E., MacLeod Ann Mary, Snyder Abraham Z., Powers William J., Gusnard Debra A., Shulman Gordon L. A default mode of brain function. Proc. Natl. Acad. Sci. 2001, 98(2):676-682.
54. Rubinov Mikail, Sporns Olaf Weight-conserving characterization of complex functional brain networks. NeuroImage 2011, 56(4):2068-2079.
55. Sheline Yvette I., Barch Deanna M., Price Joseph L., Rundle Melissa M., Vaishnavi S.Neil, Snyder Abraham Z., Mintun Mark A., Wang Suzhi, Coalson Rebecca S., Raichle Marcus E. The default mode network and self-referential processes in depression. Proc. Natl. Acad. Sci. 2009, 106(6):1942-1947.
56. Shirer W.R., Ryali S., Rykhlevskaia E., Menon V., Greicius M.D. Decoding subject-driven cognitive states with whole-brain connectivity patterns. Cereb. Cortex 2012, 22(1):158-165.
57. Smith Stephen M., Fox Peter T., Miller Karla L., Glahn David C., Fox P.Mickle, Mackay Clare E., Filippini Nicola, Watkins Kate E., Toro Roberto, Laird Angela R., Beckmann Christian F. Correspondence of the brain's functional architecture during activation and rest. Proc. Natl. Acad. Sci. U. S. A. 2009, 106(31):13040-13045. (August).
58. Smolensky Paul Information processing in dynamical systems: Foundations of harmony theory 1986.
59. Sonuga-Barke Edmund J.S., Castellanos F.Xavier Spontaneous attentional fluctuations in impaired states and pathological conditions: a neurobiological hypothesis. Neurosci. Biobehav. Rev. 2007, 31(7):977-986.
60. Sui Jing, Pearlson Godfrey, Caprihan Arvind, Adali Tülay, Kiehl Kent A., Liu Jingyu, Yamamoto Jeremy, Calhoun Vince D. Discriminating schizophrenia and bipolar disorder by fusing fMRI and DTI in a multimodal CCA+joint ICA model. NeuroImage 2011, 57(3):839-855.
61. Sun Li, Cao Qingjiu, Long Xiangyu, Sui Manqiu, Cao Xiaohua, Zhu Chaozhe, Zuo Xinian, An Li, Song Yan, Zang Yufeng, et al. Abnormal functional connectivity between the anterior cingulate and the default mode network in drug-naïve boys with attention deficit hyperactivity disorder. Psychiatry Res. Neuroimaging 2012, 201(2):120-127.
62. Swanson J.M., Sunohara G.A., Kennedy J.L., Regino R., Fineberg E., Wigal T., Lerner M., Williams L., LaHoste G.J., Wigal S., et al. Association of the dopamine receptor d4 (drd4) gene with a refined phenotype of attention deficit hyperactivity disorder (ADHD): a family-based approach. Mol. Psychiatry 1998, 3(1):38.
63. Teicher Martin H., Ito Yutaka, Glod Carol A., Barber Natacha I. Objective measurement of hyperactivity and attentional problems in ADHD. J. Am. Acad. Child Adolesc. Psychiatry 1996, 35(3):334-342.
64. Tomasi Dardo, Volkow Nora D. Abnormal functional connectivity in children with attention-deficit/hyperactivity disorder. Biol. Psychiatry 2012, 71(5):443-450.
65. Tomasi Dardo, Volkow Nora D. Functional connectivity of substantia nigra and ventral tegmental area: Maturation during adolescence and effects of ADHD. Cereb. Cortex 2012, (Epub ahead of print).
66. Uddin Lucina Q., Kelly A.M., Biswal Bharat B., Margulies Daniel S., Shehzad Zarrar, Shaw David, Ghaffari Manely, Rotrosen John, Adler Lenard A., Castellanos F.Xavier, et al. Network homogeneity reveals decreased integrity of default-mode network in ADHD. J. Neurosci. Methods 2008, 169(1):249-254.
67. Van De Ville Dimitri, Jhooti Permi, Haas Tanja, Kopel Rotem, Lovblad Karl-Olof, Scheffler Klaus, Haller Sven Recovery of the default mode network after demanding neurofeedback training occurs in spatio-temporally segregated subnetworks. NeuroImage 2012, 63(4):1775-1781. (December).
68. Xu Wei, Liu Xin, Gong Yihong Document clustering based on non-negative matrix factorization. Proceedings of the 26th annual international ACM SIGIR conference on Research and development in informaion retrieval 2003, 267-273. ACM.
69. Yu-Feng Zang, Yong He, Chao-Zhe Zh.u., Qing-Jiu Cao, Man-Qiu Sui, Meng Liang, Li-Xia Tian, Tian-Zi Jiang, Yu-Feng Wang Altered baseline brain activity in children with ADHD revealed by resting-state functional MRI. Brain Dev. 2007, 29(2):83-91.
70. Zhu C.Z., Zang Y.F., Liang M., Tian L.X., He Y., Li X.B., Sui M.Q., Wang Y.F., Jiang T.Z. Discriminative analysis of brain function at resting-state for attention-deficit/hyperactivity disorder. Medical Image Computing and Computer-Assisted Intervention-MICCAI 2005 2005, 468-475. Springer.