Toward a Multisubject Analysis of Neural Connectivity

Directed acyclic graphs (DAGs) and associated probability models are widely used to model neural connectivity and communication channels. In many experiments, data are collected from multiple subjects whose connectivities may differ but are likely to share many features. In such circumstances, it is natural to leverage similarity among subjects to improve statistical efficiency. The first exact algorithm for estimation of multiple related DAGs was recently proposed by Oates, Smith, Mukherjee, and Cussens (2014). In this letter we present examples and discuss implications of the methodology as applied to the analysis of fMRI data from a multisubject experiment. Elicitation of tuning parameters requires care, and we illustrate how this may proceed retrospectively based on technical replicate data. In addition to joint learning of subject-specific connectivity, we allow for heterogeneous collections of subjects and simultaneously estimate relationships between the subjects themselves. This letter aims to highlight the potential for exact estimation in the multisubject setting.

[1]  Jiahua Chen,et al.  Extended Bayesian information criteria for model selection with large model spaces , 2008 .

[2]  N. Meinshausen,et al.  High-dimensional graphs and variable selection with the Lasso , 2006, math/0608017.

[3]  Michael J. Brammer,et al.  Bayesian multi-task learning for decoding multi-subject neuroimaging data , 2014, NeuroImage.

[4]  Christophe Ambroise,et al.  Inferring multiple graphical structures , 2009, Stat. Comput..

[5]  Tom Heskes,et al.  A Bayesian Approach to Constraint Based Causal Inference , 2012, UAI.

[6]  Karl J. Friston,et al.  Effective Connectivity and Intersubject Variability: Using a Multisubject Network to Test Differences and Commonalities , 2002, NeuroImage.

[7]  J. Pearl Causality: Models, Reasoning and Inference , 2000 .

[8]  Mathias Drton,et al.  High-dimensional Ising model selection with Bayesian information criteria , 2014, 1403.3374.

[9]  M. West,et al.  Bayesian forecasting and dynamic models , 1989 .

[10]  Terran Lane,et al.  Bayesian Discovery of Multiple Bayesian Networks via Transfer Learning , 2013, 2013 IEEE 13th International Conference on Data Mining.

[11]  James Cussens,et al.  Advances in Bayesian Network Learning using Integer Programming , 2013, UAI.

[12]  Stephen M. Smith,et al.  Advances and Pitfalls in the Analysis and Interpretation of Resting-State FMRI Data , 2010, Front. Syst. Neurosci..

[13]  Essa Yacoub,et al.  The WU-Minn Human Connectome Project: An overview , 2013, NeuroImage.

[14]  David Maxwell Chickering,et al.  Optimal Structure Identification With Greedy Search , 2002, J. Mach. Learn. Res..

[15]  Constantin F. Aliferis,et al.  The max-min hill-climbing Bayesian network structure learning algorithm , 2006, Machine Learning.

[16]  Russell A. Poldrack,et al.  Six problems for causal inference from fMRI , 2010, NeuroImage.

[17]  Thomas E. Nichols,et al.  Simple group fMRI modeling and inference , 2009, NeuroImage.

[18]  A. Philip Dawid,et al.  Beware of the DAG! , 2008, NIPS Causality: Objectives and Assessment.

[19]  M. Drton,et al.  Bayesian model choice and information criteria in sparse generalized linear models , 2011, 1112.5635.

[20]  Christopher A. Penfold,et al.  Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks , 2012, Bioinform..

[21]  Danielle S. Bassett,et al.  A validated network of effective amygdala connectivity , 2007, NeuroImage.

[22]  W. Wong,et al.  Learning Causal Bayesian Network Structures From Experimental Data , 2008 .

[23]  James Cussens,et al.  Improved maximum likelihood reconstruction of complex multi-generational pedigrees. , 2014, Theoretical population biology.

[24]  Casper J. Albers,et al.  Intervention and Causality: Forecasting Traffic Flows Using a Dynamic Bayesian Network , 2009 .

[25]  Mark W. Woolrich,et al.  Resting-state fMRI in the Human Connectome Project , 2013, NeuroImage.

[26]  Thomas E. Nichols,et al.  Comprar Handbook Of Functional Mri Data Analysis | R. Poldrack | 9780521517669 | Cambridge University Press , 2011 .

[27]  Michael A. West,et al.  Bayesian Forecasting and Dynamic Models (2nd edn) , 1997, J. Oper. Res. Soc..

[28]  杉原 玄一 Interindividual uniformity and variety of the "writing center" : a functional MRI study , 2007 .

[29]  A. Dawid,et al.  Hyper Markov Laws in the Statistical Analysis of Decomposable Graphical Models , 1993 .

[30]  Laurence A. Wolsey,et al.  Integer and Combinatorial Optimization , 1988 .

[31]  James G. Scott,et al.  Bayes and empirical-Bayes multiplicity adjustment in the variable-selection problem , 2010, 1011.2333.

[32]  Karl J. Friston,et al.  Effective connectivity: Influence, causality and biophysical modeling , 2011, NeuroImage.

[33]  Po-Ling Loh,et al.  Structure estimation for discrete graphical models: Generalized covariance matrices and their inverses , 2012, NIPS.

[34]  Dario L Ringach,et al.  Spontaneous and driven cortical activity: implications for computation , 2009, Current Opinion in Neurobiology.

[35]  Dirk Husmeier,et al.  Gene Regulatory Network Reconstruction by Bayesian Integration of Prior Knowledge and/or Different Experimental Conditions , 2008, J. Bioinform. Comput. Biol..

[36]  Mark W. Woolrich,et al.  Network modelling methods for FMRI , 2011, NeuroImage.

[37]  Jim Q. Smith,et al.  Exact estimation of multiple directed acyclic graphs , 2014, Stat. Comput..

[38]  Martin J. McKeown,et al.  Dynamic Bayesian network modeling of fMRI: A comparison of group-analysis methods , 2008, NeuroImage.

[39]  Guido Consonni,et al.  Moment priors for Bayesian model choice with applications to directed acyclic graphs , 2011 .

[40]  Nir Friedman,et al.  Being Bayesian About Network Structure. A Bayesian Approach to Structure Discovery in Bayesian Networks , 2004, Machine Learning.

[41]  Catriona M. Queen,et al.  Multiregression dynamic models , 1993 .

[42]  Thomas Vincent,et al.  Group-level impacts of within- and between-subject hemodynamic variability in fMRI , 2013, NeuroImage.

[43]  Bin Yu,et al.  Reversible MCMC on Markov equivalence classes of sparse directed acyclic graphs , 2012, ArXiv.

[44]  Karl J. Friston Functional and Effective Connectivity: A Review , 2011, Brain Connect..

[45]  Lourens J. Waldorp,et al.  Effective connectivity of fMRI data using ancestral graph theory: Dealing with missing regions , 2011, NeuroImage.

[46]  A. Willsky,et al.  Latent variable graphical model selection via convex optimization , 2010, 1008.1290.

[47]  Takashi Washio,et al.  Learning a common substructure of multiple graphical Gaussian models , 2012, Neural Networks.

[48]  Thomas E. Nichols,et al.  Handbook of Functional MRI Data Analysis: Index , 2011 .

[49]  Patrick Danaher,et al.  The joint graphical lasso for inverse covariance estimation across multiple classes , 2011, Journal of the Royal Statistical Society. Series B, Statistical methodology.

[50]  Casey Diekman,et al.  Discovering Functional Neuronal Connectivity from Serial Patterns in Spike Train Data , 2014, Neural Computation.

[51]  Marco A. R. Ferreira,et al.  Bayesian hierarchical multi-subject multiscale analysis of functional MRI data , 2012, NeuroImage.

[52]  Terence P. Speed,et al.  Bayesian Inference of Signaling Network Topology in a Cancer Cell Line , 2012, Bioinform..

[53]  Stephen M. Smith,et al.  Probabilistic independent component analysis for functional magnetic resonance imaging , 2004, IEEE Transactions on Medical Imaging.

[54]  Russell A. Poldrack,et al.  Handbook of Functional MRI Data Analysis: Bibliography , 2011 .

[55]  R. Tibshirani,et al.  Sparse inverse covariance estimation with the graphical lasso. , 2008, Biostatistics.

[56]  Thomas E. Nichols,et al.  Searching Multiregression Dynamic Models of Resting-State fMRI Networks Using Integer Programming , 2015, 1505.06832.