Randomized Structural Sparsity-Based Support Identification with Applications to Locating Activated or Discriminative Brain Areas: A Multicenter Reproducibility Study

In this paper, we focus on how to locate the relevant or discriminative brain regions related with external stimulus or certain mental decease, which is also called support identification, based on the neuroimaging data. The main difficulty lies in the extremely high dimensional voxel space and relatively few training samples, easily resulting in an unstable brain region discovery (or called feature selection in context of pattern recognition). When the training samples are from different centers and have between-center variations, it will be even harder to obtain a reliable and consistent result. Corresponding, we revisit our recently proposed algorithm based on stability selection and structural sparsity. It is applied to the multicenter MRI data analysis for the first time. A consistent and stable result is achieved across different centers despite the between-center data variation while many other state-of-the-art methods such as two sample t-test fail. Moreover, we have empirically showed that the performance of this algorithm is robust and insensitive to several of its key parameters. In addition, the support identification results on both functional MRI and structural MRI are interpretable and can be the potential biomarkers.

[1]  Jieping Ye,et al.  Efficient nonconvex sparse group feature selection via continuous and discrete optimization , 2015, Artif. Intell..

[2]  Vince D. Calhoun,et al.  Sparse representation based biomarker selection for schizophrenia with integrated analysis of fMRI and SNPs , 2014, NeuroImage.

[3]  Krzysztof J. Gorgolewski,et al.  Making big data open: data sharing in neuroimaging , 2014, Nature Neuroscience.

[4]  Yilun Wang,et al.  Randomized structural sparsity via constrained block subsampling for improved sensitivity of discriminative voxel identification , 2014, NeuroImage.

[5]  秀俊 松井,et al.  Statistics for High-Dimensional Data: Methods, Theory and Applications , 2014 .

[6]  Jing Liu,et al.  Clustering-Guided Sparse Structural Learning for Unsupervised Feature Selection , 2014, IEEE Transactions on Knowledge and Data Engineering.

[7]  J. S. Guntupalli,et al.  Decoding neural representational spaces using multivariate pattern analysis. , 2014, Annual review of neuroscience.

[8]  Kerstin Dautenhahn,et al.  Using the Humanoid Robot KASPAR to Autonomously Play Triadic Games and Facilitate Collaborative Play Among Children With Autism , 2014, IEEE Transactions on Autonomous Mental Development.

[9]  Sébastien Serres,et al.  Structural and functional effects of metastases in rat brain determined by multimodal MRI , 2014, International journal of cancer.

[10]  John Shawe-Taylor,et al.  SCoRS—A Method Based on Stability for Feature Selection and Mapping in Neuroimaging , 2014, IEEE Transactions on Medical Imaging.

[11]  Peter Bühlmann,et al.  Controlling false positive selections in high-dimensional regression and causal inference , 2013, Statistical methods in medical research.

[12]  Gaël Varoquaux,et al.  Identifying Predictive Regions from fMRI with TV-L1 Prior , 2013, 2013 International Workshop on Pattern Recognition in Neuroimaging.

[13]  Daniel P. Kennedy,et al.  The Autism Brain Imaging Data Exchange: Towards Large-Scale Evaluation of the Intrinsic Brain Architecture in Autism , 2013, Molecular Psychiatry.

[14]  Z. Gu,et al.  A Sparse Representation-Based Algorithm for Pattern Localization in Brain Imaging Data Analysis , 2012, PloS one.

[15]  Gilles Blanchard,et al.  A Simple Extension of Stability Feature Selection , 2012, DAGM/OAGM Symposium.

[16]  Luca Baldassarre,et al.  Structured Sparsity Models for Brain Decoding from fMRI Data , 2012, 2012 Second International Workshop on Pattern Recognition in NeuroImaging.

[17]  Gaël Varoquaux,et al.  Small-sample brain mapping: sparse recovery on spatially correlated designs with randomization and clustering , 2012, ICML.

[18]  Jieping Ye,et al.  Sparse learning and stability selection for predicting MCI to AD conversion using baseline ADNI data , 2012, BMC Neurology.

[19]  Lars Kai Hansen,et al.  Model sparsity and brain pattern interpretation of classification models in neuroimaging , 2012, Pattern Recognit..

[20]  Jieping Ye,et al.  Efficient Sparse Group Feature Selection via Nonconvex Optimization , 2012, ICML.

[21]  Julien Mairal,et al.  Supervised feature selection in graphs with path coding penalties and network flows , 2012, J. Mach. Learn. Res..

[22]  Robert Leech,et al.  Salience network integrity predicts default mode network function after traumatic brain injury , 2012, Proceedings of the National Academy of Sciences.

[23]  Peter A. Bandettini,et al.  Does feature selection improve classification accuracy? Impact of sample size and feature selection on classification using anatomical magnetic resonance images , 2012, NeuroImage.

[24]  Kaustubh Supekar,et al.  Estimation of functional connectivity in fMRI data using stability selection-based sparse partial correlation with elastic net penalty , 2012, NeuroImage.

[25]  Joseph V. Hajnal,et al.  Identification and characterisation of midbrain nuclei using optimised functional magnetic resonance imaging , 2012, NeuroImage.

[26]  Jieping Ye,et al.  Efficient Methods for Overlapping Group Lasso , 2011, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[27]  Julien Mairal,et al.  Structured sparsity through convex optimization , 2011, ArXiv.

[28]  Julien Mairal,et al.  Optimization with Sparsity-Inducing Penalties , 2011, Found. Trends Mach. Learn..

[29]  Bernard Ng,et al.  Generalized group sparse classifiers with application in fMRI brain decoding , 2011, CVPR 2011.

[30]  Sara van de Geer,et al.  Statistics for High-Dimensional Data: Methods, Theory and Applications , 2011 .

[31]  Rajen Dinesh Shah,et al.  Variable selection with error control: another look at stability selection , 2011, 1105.5578.

[32]  Bertrand Thirion,et al.  Multi-scale Mining of fMRI Data with Hierarchical Structured Sparsity , 2011, 2011 International Workshop on Pattern Recognition in NeuroImaging.

[33]  Gaël Varoquaux,et al.  A supervised clustering approach for fMRI-based inference of brain states , 2011, Pattern Recognit..

[34]  Gaël Varoquaux,et al.  Total Variation Regularization for fMRI-Based Prediction of Behavior , 2011, IEEE Transactions on Medical Imaging.

[35]  Jieping Ye,et al.  Moreau-Yosida Regularization for Grouped Tree Structure Learning , 2010, NIPS.

[36]  Tso-Jung Yen,et al.  Discussion on "Stability Selection" by Meinshausen and Buhlmann , 2010 .

[37]  Kaustubh Supekar,et al.  Sparse logistic regression for whole-brain classification of fMRI data , 2010, NeuroImage.

[38]  Nikolaus Kriegeskorte,et al.  Pattern‐information fMRI: New questions which it opens up and challenges which face it , 2010, Int. J. Imaging Syst. Technol..

[39]  Michael B. Miller,et al.  How reliable are the results from functional magnetic resonance imaging? , 2010, Annals of the New York Academy of Sciences.

[40]  Zengyou He,et al.  Stable Feature Selection for Biomarker Discovery , 2010, Comput. Biol. Chem..

[41]  Peter J. Ramadge,et al.  Boosting with Spatial Regularization , 2009, NIPS.

[42]  Wotao Yin,et al.  Sparse Signal Reconstruction via Iterative Support Detection , 2009, SIAM J. Imaging Sci..

[43]  Jianfeng Feng,et al.  Voxel Selection in fMRI Data Analysis Based on Sparse Representation , 2009, IEEE Transactions on Biomedical Engineering.

[44]  Jieping Ye,et al.  Multi-Task Feature Learning Via Efficient l2, 1-Norm Minimization , 2009, UAI.

[45]  Jean-Philippe Vert,et al.  Group lasso with overlap and graph lasso , 2009, ICML '09.

[46]  Masa-aki Sato,et al.  Sparse estimation automatically selects voxels relevant for the decoding of fMRI activity patterns , 2008, NeuroImage.

[47]  N. Meinshausen,et al.  Stability selection , 2008, 0809.2932.

[48]  V. Menon,et al.  A critical role for the right fronto-insular cortex in switching between central-executive and default-mode networks , 2008, Proceedings of the National Academy of Sciences.

[49]  Chris H. Q. Ding,et al.  Stable feature selection via dense feature groups , 2008, KDD.

[50]  Gregory G. Brown,et al.  r Human Brain Mapping 29:958–972 (2008) r Test–Retest and Between-Site Reliability in a Multicenter fMRI Study , 2022 .

[51]  Chih-Jen Lin,et al.  LIBLINEAR: A Library for Large Linear Classification , 2008, J. Mach. Learn. Res..

[52]  Melanie Hilario,et al.  Approaches to dimensionality reduction in proteomic biomarker studies , 2007, Briefings Bioinform..

[53]  Trevor Hastie,et al.  Averaged gene expressions for regression. , 2007, Biostatistics.

[54]  Yong He,et al.  Altered baseline brain activity in children with ADHD revealed by resting-state functional MRI. , 2007, Brain & development.

[55]  Gary H. Glover,et al.  Reducing inter-scanner variability of activation in a multicenter fMRI study: Role of smoothness equalization , 2006, NeuroImage.

[56]  Lee Friedman,et al.  Report on a multicenter fMRI quality assurance protocol , 2006, Journal of magnetic resonance imaging : JMRI.

[57]  R. Poldrack Can cognitive processes be inferred from neuroimaging data? , 2006, Trends in Cognitive Sciences.

[58]  H. Zou,et al.  Regularization and variable selection via the elastic net , 2005 .

[59]  Tom M. Mitchell,et al.  Learning to Decode Cognitive States from Brain Images , 2004, Machine Learning.

[60]  D. Amaral,et al.  The Amygdala Is Enlarged in Children But Not Adolescents with Autism; the Hippocampus Is Enlarged at All Ages , 2004, The Journal of Neuroscience.

[61]  Isabelle Guyon,et al.  An Introduction to Variable and Feature Selection , 2003, J. Mach. Learn. Res..

[62]  C. Frith,et al.  Autism, Asperger syndrome and brain mechanisms for the attribution of mental states to animated shapes. , 2002, Brain : a journal of neurology.

[63]  N. Tzourio-Mazoyer,et al.  Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain , 2002, NeuroImage.

[64]  A. Ishai,et al.  Distributed and Overlapping Representations of Faces and Objects in Ventral Temporal Cortex , 2001, Science.

[65]  G. Shulman,et al.  Medial prefrontal cortex and self-referential mental activity: Relation to a default mode of brain function , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[66]  H. Critchley,et al.  The functional neuroanatomy of social behaviour: changes in cerebral blood flow when people with autistic disorder process facial expressions. , 2000, Brain : a journal of neurology.

[67]  Nikunj C. Oza,et al.  Online Ensemble Learning , 2000, AAAI/IAAI.

[68]  Karl J. Friston,et al.  Voxel-Based Morphometry—The Methods , 2000, NeuroImage.

[69]  M. Posner,et al.  Cognitive and emotional influences in anterior cingulate cortex , 2000, Trends in Cognitive Sciences.

[70]  S. Lahiri Theoretical comparisons of block bootstrap methods , 1999 .

[71]  Pat Langley,et al.  Selection of Relevant Features and Examples in Machine Learning , 1997, Artif. Intell..

[72]  G. Edelman,et al.  A measure for brain complexity: relating functional segregation and integration in the nervous system. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[73]  Elie Bienenstock,et al.  Neural Networks and the Bias/Variance Dilemma , 1992, Neural Computation.

[74]  Thomas M. Cover,et al.  Geometrical and Statistical Properties of Systems of Linear Inequalities with Applications in Pattern Recognition , 1965, IEEE Trans. Electron. Comput..

[75]  Ben Taskar,et al.  Generative-Discriminative Basis Learning for Medical Imaging , 2012, IEEE Transactions on Medical Imaging.

[76]  Sara van de Geer,et al.  Statistics for High-Dimensional Data , 2011 .

[77]  Tim Oates,et al.  A critique of multi-voxel pattern analysis , 2010 .

[78]  R. Buyya,et al.  Ensemble Learning , 2021, Machine Learning for Cloud Management.

[79]  Bryon Mueller,et al.  How to do a Functional Multi-Center Neuroimaging Study , 2010 .

[80]  R. Tibshirani Regression Shrinkage and Selection via the Lasso , 1996 .

[81]  P. G. D. Vries,et al.  Stratified Random Sampling , 1986 .