Bio

Professional Education


  • Doctor of Philosophy, Stanford University, BIOM-PHD (2010)

Stanford Advisors


Publications

Journal Articles


  • Brain hyperconnectivity in children with autism and its links to social deficits. Cell reports Supekar, K., Uddin, L. Q., Khouzam, A., Phillips, J., Gaillard, W. D., Kenworthy, L. E., Yerys, B. E., Vaidya, C. J., Menon, V. 2013; 5 (3): 738-747

    Abstract

    Autism spectrum disorder (ASD), a neurodevelopmental disorder affecting nearly 1 in 88 children, is thought to result from aberrant brain connectivity. Remarkably, there have been no systematic attempts to characterize whole-brain connectivity in children with ASD. Here, we use neuroimaging to show that there are more instances of greater functional connectivity in the brains of children with ASD in comparison to those of typically developing children. Hyperconnectivity in ASD was observed at the whole-brain and subsystems levels, across long- and short-range connections, and was associated with higher levels of fluctuations in regional brain signals. Brain hyperconnectivity predicted symptom severity in ASD, such that children with greater functional connectivity exhibited more severe social deficits. We replicated these findings in two additional independent cohorts, demonstrating again that at earlier ages, the brain of children with ASD is largely functionally hyperconnected in ways that contribute to social dysfunction. Our findings provide unique insights into brain mechanisms underlying childhood autism.

    View details for DOI 10.1016/j.celrep.2013.10.001

    View details for PubMedID 24210821

  • Neural predictors of individual differences in response to math tutoring in primary-grade school children. Proceedings of the National Academy of Sciences of the United States of America Supekar, K., Swigart, A. G., Tenison, C., Jolles, D. D., Rosenberg-Lee, M., Fuchs, L., Menon, V. 2013; 110 (20): 8230-8235

    Abstract

    Now, more than ever, the ability to acquire mathematical skills efficiently is critical for academic and professional success, yet little is known about the behavioral and neural mechanisms that drive some children to acquire these skills faster than others. Here we investigate the behavioral and neural predictors of individual differences in arithmetic skill acquisition in response to 8-wk of one-to-one math tutoring. Twenty-four children in grade 3 (ages 8-9 y), a critical period for acquisition of basic mathematical skills, underwent structural and resting-state functional MRI scans pretutoring. A significant shift in arithmetic problem-solving strategies from counting to fact retrieval was observed with tutoring. Notably, the speed and accuracy of arithmetic problem solving increased with tutoring, with some children improving significantly more than others. Next, we examined whether pretutoring behavioral and brain measures could predict individual differences in arithmetic performance improvements with tutoring. No behavioral measures, including intelligence quotient, working memory, or mathematical abilities, predicted performance improvements. In contrast, pretutoring hippocampal volume predicted performance improvements. Furthermore, pretutoring intrinsic functional connectivity of the hippocampus with dorsolateral and ventrolateral prefrontal cortices and the basal ganglia also predicted performance improvements. Our findings provide evidence that individual differences in morphometry and connectivity of brain regions associated with learning and memory, and not regions typically involved in arithmetic processing, are strong predictors of responsiveness to math tutoring in children. More generally, our study suggests that quantitative measures of brain structure and intrinsic brain organization can provide a more sensitive marker of skill acquisition than behavioral measures.

    View details for DOI 10.1073/pnas.1222154110

    View details for PubMedID 23630286

  • Developmental Maturation of Dynamic Causal Control Signals in Higher-Order Cognition: A Neurocognitive Network Model PLOS COMPUTATIONAL BIOLOGY Supekar, K., Menon, V. 2012; 8 (2)

    Abstract

    Cognitive skills undergo protracted developmental changes resulting in proficiencies that are a hallmark of human cognition. One skill that develops over time is the ability to problem solve, which in turn relies on cognitive control and attention abilities. Here we use a novel multimodal neurocognitive network-based approach combining task-related fMRI, resting-state fMRI and diffusion tensor imaging (DTI) to investigate the maturation of control processes underlying problem solving skills in 7-9 year-old children. Our analysis focused on two key neurocognitive networks implicated in a wide range of cognitive tasks including control: the insula-cingulate salience network, anchored in anterior insula (AI), ventrolateral prefrontal cortex and anterior cingulate cortex, and the fronto-parietal central executive network, anchored in dorsolateral prefrontal cortex and posterior parietal cortex (PPC). We found that, by age 9, the AI node of the salience network is a major causal hub initiating control signals during problem solving. Critically, despite stronger AI activation, the strength of causal regulatory influences from AI to the PPC node of the central executive network was significantly weaker and contributed to lower levels of behavioral performance in children compared to adults. These results were validated using two different analytic methods for estimating causal interactions in fMRI data. In parallel, DTI-based tractography revealed weaker AI-PPC structural connectivity in children. Our findings point to a crucial role of AI connectivity, and its causal cross-network influences, in the maturation of dynamic top-down control signals underlying cognitive development. Overall, our study demonstrates how a unified neurocognitive network model when combined with multimodal imaging enhances our ability to generalize beyond individual task-activated foci and provides a common framework for elucidating key features of brain and cognitive development. The quantitative approach developed is likely to be useful in investigating neurodevelopmental disorders, in which control processes are impaired, such as autism and ADHD.

    View details for DOI 10.1371/journal.pcbi.1002374

    View details for Web of Science ID 000300729900018

    View details for PubMedID 22319436

  • Dynamic reconfiguration of structural and functional connectivity across core neurocognitive brain networks with development. Journal of Neuroscience Supekar,, K., Lucina Q., U., Ryali, S., Vinod , M. 2011; 31 (50): 18578-89
  • Development of functional and structural connectivity within the default mode network in young children NEUROIMAGE Supekar, K., Uddin, L. Q., Prater, K., Amin, H., Greicius, M. D., Menon, V. 2010; 52 (1): 290-301

    Abstract

    Functional and structural maturation of networks comprised of discrete regions is an important aspect of brain development. The default-mode network (DMN) is a prominent network which includes the posterior cingulate cortex (PCC), medial prefrontal cortex (mPFC), medial temporal lobes (MTL), and angular gyrus (AG). Despite increasing interest in DMN function, little is known about its maturation from childhood to adulthood. Here we examine developmental changes in DMN connectivity using a multimodal imaging approach by combining resting-state fMRI, voxel-based morphometry and diffusion tensor imaging-based tractography. We found that the DMN undergoes significant developmental changes in functional and structural connectivity, but these changes are not uniform across all DMN nodes. Convergent structural and functional connectivity analyses suggest that PCC-mPFC connectivity along the cingulum bundle is the most immature link in the DMN of children. Both PCC and mPFC also showed gray matter volume differences, as well as prominent macrostructural and microstructural differences in the dorsal cingulum bundle linking these regions. Notably, structural connectivity between PCC and left MTL was either weak or non-existent in children, even though functional connectivity did not differ from that of adults. These results imply that functional connectivity in children can reach adult-like levels despite weak structural connectivity. We propose that maturation of PCC-mPFC structural connectivity plays an important role in the development of self-related and social-cognitive functions that emerge during adolescence. More generally, our study demonstrates how quantitative multimodal analysis of anatomy and connectivity allows us to better characterize the heterogeneous development and maturation of brain networks.

    View details for DOI 10.1016/j.neuroimage.2010.04.009

    View details for Web of Science ID 000278637700029

    View details for PubMedID 20385244

  • Development of Large-Scale Functional Brain Networks in Children PLOS BIOLOGY Supekar, K., Musen, M., Menon, V. 2009; 7 (7)

    Abstract

    The ontogeny of large-scale functional organization of the human brain is not well understood. Here we use network analysis of intrinsic functional connectivity to characterize the organization of brain networks in 23 children (ages 7-9 y) and 22 young-adults (ages 19-22 y). Comparison of network properties, including path-length, clustering-coefficient, hierarchy, and regional connectivity, revealed that although children and young-adults' brains have similar "small-world" organization at the global level, they differ significantly in hierarchical organization and interregional connectivity. We found that subcortical areas were more strongly connected with primary sensory, association, and paralimbic areas in children, whereas young-adults showed stronger cortico-cortical connectivity between paralimbic, limbic, and association areas. Further, combined analysis of functional connectivity with wiring distance measures derived from white-matter fiber tracking revealed that the development of large-scale brain networks is characterized by weakening of short-range functional connectivity and strengthening of long-range functional connectivity. Importantly, our findings show that the dynamic process of over-connectivity followed by pruning, which rewires connectivity at the neuronal level, also operates at the systems level, helping to reconfigure and rebalance subcortical and paralimbic connectivity in the developing brain. Our study demonstrates the usefulness of network analysis of brain connectivity to elucidate key principles underlying functional brain maturation, paving the way for novel studies of disrupted brain connectivity in neurodevelopmental disorders such as autism.

    View details for DOI 10.1371/journal.pbio.1000157

    View details for Web of Science ID 000268405700010

    View details for PubMedID 19621066

  • Network analysis of intrinsic functional brain connectivity in Alzheimer's disease PLOS COMPUTATIONAL BIOLOGY Supekar, K., Menon, V., Rubin, D., Musen, M., Greicius, M. D. 2008; 4 (6)

    Abstract

    Functional brain networks detected in task-free ("resting-state") functional magnetic resonance imaging (fMRI) have a small-world architecture that reflects a robust functional organization of the brain. Here, we examined whether this functional organization is disrupted in Alzheimer's disease (AD). Task-free fMRI data from 21 AD subjects and 18 age-matched controls were obtained. Wavelet analysis was applied to the fMRI data to compute frequency-dependent correlation matrices. Correlation matrices were thresholded to create 90-node undirected-graphs of functional brain networks. Small-world metrics (characteristic path length and clustering coefficient) were computed using graph analytical methods. In the low frequency interval 0.01 to 0.05 Hz, functional brain networks in controls showed small-world organization of brain activity, characterized by a high clustering coefficient and a low characteristic path length. In contrast, functional brain networks in AD showed loss of small-world properties, characterized by a significantly lower clustering coefficient (p<0.01), indicative of disrupted local connectivity. Clustering coefficients for the left and right hippocampus were significantly lower (p<0.01) in the AD group compared to the control group. Furthermore, the clustering coefficient distinguished AD participants from the controls with a sensitivity of 72% and specificity of 78%. Our study provides new evidence that there is disrupted organization of functional brain networks in AD. Small-world metrics can characterize the functional organization of the brain in AD, and our findings further suggest that these network measures may be useful as an imaging-based biomarker to distinguish AD from healthy aging.

    View details for DOI 10.1371/journal.pcbi.1000100

    View details for Web of Science ID 000259786700013

    View details for PubMedID 18584043

  • Brain Organization Underlying Superior Mathematical Abilities in Children with Autism BIOLOGICAL PSYCHIATRY Iuculano, T., Rosenberg-Lee, M., Supekar, K., Lynch, C. J., Khouzam, A., Phillips, J., Uddin, L. Q., Menon, V. 2014; 75 (3): 223-230

    Abstract

    Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social and communication deficits. While such deficits have been the focus of most research, recent evidence suggests that individuals with ASD may exhibit cognitive strengths in domains such as mathematics.Cognitive assessments and functional brain imaging were used to investigate mathematical abilities in 18 children with ASD and 18 age-, gender-, and IQ-matched typically developing (TD) children. Multivariate classification and regression analyses were used to investigate whether brain activity patterns during numerical problem solving were significantly different between the groups and predictive of individual mathematical abilities.Children with ASD showed better numerical problem solving abilities and relied on sophisticated decomposition strategies for single-digit addition problems more frequently than TD peers. Although children with ASD engaged similar brain areas as TD children, they showed different multivariate activation patterns related to arithmetic problem complexity in ventral temporal-occipital cortex, posterior parietal cortex, and medial temporal lobe. Furthermore, multivariate activation patterns in ventral temporal-occipital cortical areas typically associated with face processing predicted individual numerical problem solving abilities in children with ASD but not in TD children.Our study suggests that superior mathematical information processing in children with ASD is characterized by a unique pattern of brain organization and that cortical regions typically involved in perceptual expertise may be utilized in novel ways in ASD. Our findings of enhanced cognitive and neural resources for mathematics have critical implications for educational, professional, and social outcomes for individuals with this lifelong disorder.

    View details for DOI 10.1016/j.biopsych.2013.06.018

    View details for Web of Science ID 000329130500011

    View details for PubMedID 23954299

  • Reconceptualizing functional brain connectivity in autism from a developmental perspective FRONTIERS IN HUMAN NEUROSCIENCE Uddin, L. Q., Supekar, K., Menon, V. 2013; 7

    Abstract

    While there is almost universal agreement amongst researchers that autism is associated with alterations in brain connectivity, the precise nature of these alterations continues to be debated. Theoretical and empirical work is beginning to reveal that autism is associated with a complex functional phenotype characterized by both hypo- and hyper-connectivity of large-scale brain systems. It is not yet understood why such conflicting patterns of brain connectivity are observed across different studies, and the factors contributing to these heterogeneous findings have not been identified. Developmental changes in functional connectivity have received inadequate attention to date. We propose that discrepancies between findings of autism related hypo-connectivity and hyper-connectivity might be reconciled by taking developmental changes into account. We review neuroimaging studies of autism, with an emphasis on functional magnetic resonance imaging studies of intrinsic functional connectivity in children, adolescents and adults. The consistent pattern emerging across several studies is that while intrinsic functional connectivity in adolescents and adults with autism is generally reduced compared with age-matched controls, functional connectivity in younger children with the disorder appears to be increased. We suggest that by placing recent empirical findings within a developmental framework, and explicitly characterizing age and pubertal stage in future work, it may be possible to resolve conflicting findings of hypo- and hyper-connectivity in the extant literature and arrive at a more comprehensive understanding of the neurobiology of autism.

    View details for DOI 10.3389/fnhum.2013.00458

    View details for Web of Science ID 000322812500001

    View details for PubMedID 23966925

  • Salience Network-Based Classification and Prediction of Symptom Severity in Children With Autism JAMA PSYCHIATRY Uddin, L. Q., Supekar, K., Lynch, C. J., Khouzam, A., Phillips, J., Feinstein, C., Ryali, S., Menon, V. 2013; 70 (8): 869-879

    Abstract

    IMPORTANCE Autism spectrum disorder (ASD) affects 1 in 88 children and is characterized by a complex phenotype, including social, communicative, and sensorimotor deficits. Autism spectrum disorder has been linked with atypical connectivity across multiple brain systems, yet the nature of these differences in young children with the disorder is not well understood. OBJECTIVES To examine connectivity of large-scale brain networks and determine whether specific networks can distinguish children with ASD from typically developing (TD) children and predict symptom severity in children with ASD. DESIGN, SETTING, AND PARTICIPANTS Case-control study performed at Stanford University School of Medicine of 20 children 7 to 12 years old with ASD and 20 age-, sex-, and IQ-matched TD children. MAIN OUTCOMES AND MEASURES Between-group differences in intrinsic functional connectivity of large-scale brain networks, performance of a classifier built to discriminate children with ASD from TD children based on specific brain networks, and correlations between brain networks and core symptoms of ASD. RESULTS We observed stronger functional connectivity within several large-scale brain networks in children with ASD compared with TD children. This hyperconnectivity in ASD encompassed salience, default mode, frontotemporal, motor, and visual networks. This hyperconnectivity result was replicated in an independent cohort obtained from publicly available databases. Using maps of each individual's salience network, children with ASD could be discriminated from TD children with a classification accuracy of 78%, with 75% sensitivity and 80% specificity. The salience network showed the highest classification accuracy among all networks examined, and the blood oxygen-level dependent signal in this network predicted restricted and repetitive behavior scores. The classifier discriminated ASD from TD in the independent sample with 83% accuracy, 67% sensitivity, and 100% specificity. CONCLUSIONS AND RELEVANCE Salience network hyperconnectivity may be a distinguishing feature in children with ASD. Quantification of brain network connectivity is a step toward developing biomarkers for objectively identifying children with ASD.

    View details for DOI 10.1001/jamapsychiatry.2013.104

    View details for Web of Science ID 000322833600013

    View details for PubMedID 23803651

  • Default Mode Network in Childhood Autism: Posteromedial Cortex Heterogeneity and Relationship with Social Deficits BIOLOGICAL PSYCHIATRY Lynch, C. J., Uddin, L. Q., Supekar, K., Khouzam, A., Phillips, J., Menon, V. 2013; 74 (3): 212-219

    Abstract

    BACKGROUND: The default mode network (DMN), a brain system anchored in the posteromedial cortex, has been identified as underconnected in adults with autism spectrum disorder (ASD). However, to date there have been no attempts to characterize this network and its involvement in mediating social deficits in children with ASD. Furthermore, the functionally heterogeneous profile of the posteromedial cortex raises questions regarding how altered connectivity manifests in specific functional modules within this brain region in children with ASD. METHODS: Resting-state functional magnetic resonance imaging and an anatomically informed approach were used to investigate the functional connectivity of the DMN in 20 children with ASD and 19 age-, gender-, and IQ-matched typically developing (TD) children. Multivariate regression analyses were used to test whether altered patterns of connectivity are predictive of social impairment severity. RESULTS: Compared with TD children, children with ASD demonstrated hyperconnectivity of the posterior cingulate and retrosplenial cortices with predominately medial and anterolateral temporal cortex. In contrast, the precuneus in ASD children demonstrated hypoconnectivity with visual cortex, basal ganglia, and locally within the posteromedial cortex. Aberrant posterior cingulate cortex hyperconnectivity was linked with severity of social impairments in ASD, whereas precuneus hypoconnectivity was unrelated to social deficits. Consistent with previous work in healthy adults, a functionally heterogeneous profile of connectivity within the posteromedial cortex in both TD and ASD children was observed. CONCLUSIONS: This work links hyperconnectivity of DMN-related circuits to the core social deficits in young children with ASD and highlights fundamental aspects of posteromedial cortex heterogeneity.

    View details for DOI 10.1016/j.biopsych.2012.12.013

    View details for Web of Science ID 000321443100012

    View details for PubMedID 23375976

  • Underconnectivity between voice-selective cortex and reward circuitry in children with autism PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Abrams, D. A., Lynch, C. J., Cheng, K. M., Phillips, J., Supekar, K., Ryali, S., Uddin, L. Q., Menon, V. 2013; 110 (29): 12060-12065

    Abstract

    Individuals with autism spectrum disorders (ASDs) often show insensitivity to the human voice, a deficit that is thought to play a key role in communication deficits in this population. The social motivation theory of ASD predicts that impaired function of reward and emotional systems impedes children with ASD from actively engaging with speech. Here we explore this theory by investigating distributed brain systems underlying human voice perception in children with ASD. Using resting-state functional MRI data acquired from 20 children with ASD and 19 age- and intelligence quotient-matched typically developing children, we examined intrinsic functional connectivity of voice-selective bilateral posterior superior temporal sulcus (pSTS). Children with ASD showed a striking pattern of underconnectivity between left-hemisphere pSTS and distributed nodes of the dopaminergic reward pathway, including bilateral ventral tegmental areas and nucleus accumbens, left-hemisphere insula, orbitofrontal cortex, and ventromedial prefrontal cortex. Children with ASD also showed underconnectivity between right-hemisphere pSTS, a region known for processing speech prosody, and the orbitofrontal cortex and amygdala, brain regions critical for emotion-related associative learning. The degree of underconnectivity between voice-selective cortex and reward pathways predicted symptom severity for communication deficits in children with ASD. Our results suggest that weak connectivity of voice-selective cortex and brain structures involved in reward and emotion may impair the ability of children with ASD to experience speech as a pleasurable stimulus, thereby impacting language and social skill development in this population. Our study provides support for the social motivation theory of ASD.

    View details for DOI 10.1073/pnas.1302982110

    View details for Web of Science ID 000322086100085

    View details for PubMedID 23776244

  • A parcellation scheme based on von Mises-Fisher distributions and Markov random fields for segmenting brain regions using resting-state fMRI NEUROIMAGE Ryali, S., Chen, T., Supekar, K., Menon, V. 2013; 65: 83-96

    Abstract

    Understanding the organization of the human brain requires identification of its functional subdivisions. Clustering schemes based on resting-state functional magnetic resonance imaging (fMRI) data are rapidly emerging as non-invasive alternatives to cytoarchitectonic mapping in postmortem brains. Here, we propose a novel spatio-temporal probabilistic parcellation scheme that overcomes major weaknesses of existing approaches by (i) modeling the fMRI time series of a voxel as a von Mises-Fisher distribution, which is widely used for clustering high dimensional data; (ii) modeling the latent cluster labels as a Markov random field, which provides spatial regularization on the cluster labels by penalizing neighboring voxels having different cluster labels; and (iii) introducing a prior on the number of labels, which helps in uncovering the number of clusters automatically from the data. Cluster labels and model parameters are estimated by an iterative expectation maximization procedure wherein, given the data and current estimates of model parameters, the latent cluster labels, are computed using ?-expansion, a state of the art graph cut, method. In turn, given the current estimates of cluster labels, model parameters are estimated by maximizing the pseudo log-likelihood. The performance of the proposed method is validated using extensive computer simulations. Using novel stability analysis we examine the sensitivity of our methods to parameter initialization and demonstrate that the method is robust to a wide range of initial parameter values. We demonstrate the application of our methods by parcellating spatially contiguous as well as non-contiguous brain regions at both the individual participant and group levels. Notably, our analyses yield new data on the posterior boundaries of the supplementary motor area and provide new insights into functional organization of the insular cortex. Taken together, our findings suggest that our method is a powerful tool for investigating functional subdivisions in the human brain.

    View details for DOI 10.1016/j.neuroimage.2012.09.067

    View details for Web of Science ID 000312283900008

    View details for PubMedID 23041530

  • NDAR: A Model Federal System for Secondary Analysis in Developmental Disabilities Research USING SECONDARY DATASETS TO UNDERSTAND PERSONS WITH DEVELOPMENTAL DISABILITIES AND THEIR FAMILIES Novikova, S. I., RICHMAN, D. M., Supekar, K., Barnard-Brak, L., Hall, D. 2013; 45: 123-153
  • Immature integration and segregation of emotion-related brain circuitry in young children PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Qin, S., Young, C. B., Supekar, K., Uddin, L. Q., Menon, V. 2012; 109 (20): 7941-7946

    Abstract

    The human brain undergoes protracted development, with dramatic changes in expression and regulation of emotion from childhood to adulthood. The amygdala is a brain structure that plays a pivotal role in emotion-related functions. Investigating developmental characteristics of the amygdala and associated functional circuits in children is important for understanding how emotion processing matures in the developing brain. The basolateral amygdala (BLA) and centromedial amygdala (CMA) are two major amygdalar nuclei that contribute to distinct functions via their unique pattern of interactions with cortical and subcortical regions. Almost nothing is currently known about the maturation of functional circuits associated with these amygdala nuclei in the developing brain. Using intrinsic connectivity analysis of functional magnetic resonance imaging data, we investigated developmental changes in functional connectivity of the BLA and CMA in twenty-four 7- to 9-y-old typically developing children compared with twenty-four 19- to 22-y-old healthy adults. Children showed significantly weaker intrinsic functional connectivity of the amygdala with subcortical, paralimbic, and limbic structures, polymodal association, and ventromedial prefrontal cortex. Importantly, target networks associated with the BLA and CMA exhibited greater overlap and weaker dissociation in children. In line with this finding, children showed greater intraamygdala connectivity between the BLA and CMA. Critically, these developmental differences were reproducibly identified in a second independent cohort of adults and children. Taken together, our findings point toward weak integration and segregation of amygdala circuits in young children. These immature patterns of amygdala connectivity have important implications for understanding typical and atypical development of emotion-related brain circuitry.

    View details for DOI 10.1073/pnas.1120408109

    View details for Web of Science ID 000304369800076

    View details for PubMedID 22547826

  • Estimation of functional connectivity in fMRI data using stability selection-based sparse partial correlation with elastic net penalty NEUROIMAGE Ryali, S., Chen, T., Supekar, K., Menon, V. 2012; 59 (4): 3852-3861

    Abstract

    Characterizing interactions between multiple brain regions is important for understanding brain function. Functional connectivity measures based on partial correlation provide an estimate of the linear conditional dependence between brain regions after removing the linear influence of other regions. Estimation of partial correlations is, however, difficult when the number of regions is large, as is now increasingly the case with a growing number of large-scale brain connectivity studies. To address this problem, we develop novel methods for estimating sparse partial correlations between multiple regions in fMRI data using elastic net penalty (SPC-EN), which combines L1- and L2-norm regularization We show that L1-norm regularization in SPC-EN provides sparse interpretable solutions while L2-norm regularization improves the sensitivity of the method when the number of possible connections between regions is larger than the number of time points, and when pair-wise correlations between brain regions are high. An issue with regularization-based methods is choosing the regularization parameters which in turn determine the selection of connections between brain regions. To address this problem, we deploy novel stability selection methods to infer significant connections between brain regions. We also compare the performance of SPC-EN with existing methods which use only L1-norm regularization (SPC-L1) on simulated and experimental datasets. Detailed simulations show that the performance of SPC-EN, measured in terms of sensitivity and accuracy is superior to SPC-L1, especially at higher rates of feature prevalence. Application of our methods to resting-state fMRI data obtained from 22 healthy adults shows that SPC-EN reveals a modular architecture characterized by strong inter-hemispheric links, distinct ventral and dorsal stream pathways, and a major hub in the posterior medial cortex - features that were missed by conventional methods. Taken together, our findings suggest that SPC-EN provides a powerful tool for characterizing connectivity involving a large number of correlated regions that span the entire brain.

    View details for DOI 10.1016/j.neuroimage.2011.11.054

    View details for Web of Science ID 000301090100078

    View details for PubMedID 22155039

  • Multivariate dynamical systems models for estimating causal interactions in fMRI NEUROIMAGE Ryali, S., Supekar, K., Chen, T., Menon, V. 2011; 54 (2): 807-823

    Abstract

    Analysis of dynamical interactions between distributed brain areas is of fundamental importance for understanding cognitive information processing. However, estimating dynamic causal interactions between brain regions using functional magnetic resonance imaging (fMRI) poses several unique challenges. For one, fMRI measures Blood Oxygenation Level Dependent (BOLD) signals, rather than the underlying latent neuronal activity. Second, regional variations in the hemodynamic response function (HRF) can significantly influence estimation of causal interactions between them. Third, causal interactions between brain regions can change with experimental context over time. To overcome these problems, we developed a novel state-space Multivariate Dynamical Systems (MDS) model to estimate intrinsic and experimentally-induced modulatory causal interactions between multiple brain regions. A probabilistic graphical framework is then used to estimate the parameters of MDS as applied to fMRI data. We show that MDS accurately takes into account regional variations in the HRF and estimates dynamic causal interactions at the level of latent signals. We develop and compare two estimation procedures using maximum likelihood estimation (MLE) and variational Bayesian (VB) approaches for inferring model parameters. Using extensive computer simulations, we demonstrate that, compared to Granger causal analysis (GCA), MDS exhibits superior performance for a wide range of signal to noise ratios (SNRs), sample length and network size. Our simulations also suggest that GCA fails to uncover causal interactions when there is a conflict between the direction of intrinsic and modulatory influences. Furthermore, we show that MDS estimation using VB methods is more robust and performs significantly better at low SNRs and shorter time series than MDS with MLE. Our study suggests that VB estimation of MDS provides a robust method for estimating and interpreting causal network interactions in fMRI data.

    View details for DOI 10.1016/j.neuroimage.2010.09.052

    View details for Web of Science ID 000285486000009

    View details for PubMedID 20884354

  • Dissociable Connectivity within Human Angular Gyrus and Intraparietal Sulcus: Evidence from Functional and Structural Connectivity CEREBRAL CORTEX Uddin, L. Q., Supekar, K., Amin, H., Rykhlevskaia, E., Nguyen, D. A., Greicius, M. D., Menon, V. 2010; 20 (11): 2636-2646

    Abstract

    The inferior parietal lobule (IPL) of the human brain is a heterogeneous region involved in visuospatial attention, memory, and mathematical cognition. Detailed description of connectivity profiles of subdivisions within the IPL is critical for accurate interpretation of functional neuroimaging studies involving this region. We separately examined functional and structural connectivity of the angular gyrus (AG) and the intraparietal sulcus (IPS) using probabilistic cytoarchitectonic maps. Regions-of-interest (ROIs) included anterior and posterior AG subregions (PGa, PGp) and 3 IPS subregions (hIP2, hIP1, and hIP3). Resting-state functional connectivity analyses showed that PGa was more strongly linked to basal ganglia, ventral premotor areas, and ventrolateral prefrontal cortex, while PGp was more strongly connected with ventromedial prefrontal cortex, posterior cingulate, and hippocampus-regions comprising the default mode network. The anterior-most IPS ROIs, hIP2 and hIP1, were linked with ventral premotor and middle frontal gyrus, while the posterior-most IPS ROI, hIP3, showed connectivity with extrastriate visual areas. In addition, hIP1 was connected with the insula. Tractography using diffusion tensor imaging revealed structural connectivity between most of these functionally connected regions. Our findings provide evidence for functional heterogeneity of cytoarchitectonically defined subdivisions within IPL and offer a novel framework for synthesis and interpretation of the task-related activations and deactivations involving the IPL during cognition.

    View details for DOI 10.1093/cercor/bhq011

    View details for Web of Science ID 000282750600013

    View details for PubMedID 20154013

  • Sparse logistic regression for whole-brain classification of fMRI data NEUROIMAGE Ryali, S., Supekar, K., Abrams, D. A., Menon, V. 2010; 51 (2): 752-764

    Abstract

    Multivariate pattern recognition methods are increasingly being used to identify multiregional brain activity patterns that collectively discriminate one cognitive condition or experimental group from another, using fMRI data. The performance of these methods is often limited because the number of regions considered in the analysis of fMRI data is large compared to the number of observations (trials or participants). Existing methods that aim to tackle this dimensionality problem are less than optimal because they either over-fit the data or are computationally intractable. Here, we describe a novel method based on logistic regression using a combination of L1 and L2 norm regularization that more accurately estimates discriminative brain regions across multiple conditions or groups. The L1 norm, computed using a fast estimation procedure, ensures a fast, sparse and generalizable solution; the L2 norm ensures that correlated brain regions are included in the resulting solution, a critical aspect of fMRI data analysis often overlooked by existing methods. We first evaluate the performance of our method on simulated data and then examine its effectiveness in discriminating between well-matched music and speech stimuli. We also compared our procedures with other methods which use either L1-norm regularization alone or support vector machine-based feature elimination. On simulated data, our methods performed significantly better than existing methods across a wide range of contrast-to-noise ratios and feature prevalence rates. On experimental fMRI data, our methods were more effective in selectively isolating a distributed fronto-temporal network that distinguished between brain regions known to be involved in speech and music processing. These findings suggest that our method is not only computationally efficient, but it also achieves the twin objectives of identifying relevant discriminative brain regions and accurately classifying fMRI data.

    View details for DOI 10.1016/j.neuroimage.2010.02.040

    View details for Web of Science ID 000277141200026

    View details for PubMedID 20188193

  • Typical and atypical development of functional human brain networks: insights from resting-state FMRI. Frontiers in systems neuroscience Uddin, L. Q., Supekar, K., Menon, V. 2010; 4: 21-?

    Abstract

    Over the past several decades, structural MRI studies have provided remarkable insights into human brain development by revealing the trajectory of gray and white matter maturation from childhood to adolescence and adulthood. In parallel, functional MRI studies have demonstrated changes in brain activation patterns accompanying cognitive development. Despite these advances, studying the maturation of functional brain networks underlying brain development continues to present unique scientific and methodological challenges. Resting-state fMRI (rsfMRI) has emerged as a novel method for investigating the development of large-scale functional brain networks in infants and young children. We review existing rsfMRI developmental studies and discuss how this method has begun to make significant contributions to our understanding of maturing brain organization. In particular, rsfMRI has been used to complement studies in other modalities investigating the emergence of functional segregation and integration across short and long-range connections spanning the entire brain. We show that rsfMRI studies help to clarify and reveal important principles of functional brain development, including a shift from diffuse to focal activation patterns, and simultaneous pruning of local connectivity and strengthening of long-range connectivity with age. The insights gained from these studies also shed light on potentially disrupted functional networks underlying atypical cognitive development associated with neurodevelopmental disorders. We conclude by identifying critical gaps in the current literature, discussing methodological issues, and suggesting avenues for future research.

    View details for DOI 10.3389/fnsys.2010.00021

    View details for PubMedID 20577585

  • Annotation and Image Markup: Accessing and Interoperating with the Semantic Content in Medical Imaging IEEE INTELLIGENT SYSTEMS Rubin, D. L., Supekar, K., Mongkolwat, P., Kleper, V., Channin, D. S. 2009; 24 (1): 57-65
  • Resting-State Functional Connectivity Reflects Structural Connectivity in the Default Mode Network CEREBRAL CORTEX Greicius, M. D., Supekar, K., Menon, V., Dougherty, R. F. 2009; 19 (1): 72-78

    Abstract

    Resting-state functional connectivity magnetic resonance imaging (fcMRI) studies constitute a growing proportion of functional brain imaging publications. This approach detects temporal correlations in spontaneous blood oxygen level-dependent (BOLD) signal oscillations while subjects rest quietly in the scanner. Although distinct resting-state networks related to vision, language, executive processing, and other sensory and cognitive domains have been identified, considerable skepticism remains as to whether resting-state functional connectivity maps reflect neural connectivity or simply track BOLD signal correlations driven by nonneural artifact. Here we combine diffusion tensor imaging (DTI) tractography with resting-state fcMRI to test the hypothesis that resting-state functional connectivity reflects structural connectivity. These 2 modalities were used to investigate connectivity within the default mode network, a set of brain regions--including medial prefrontal cortex (MPFC), medial temporal lobes (MTLs), and posterior cingulate cortex (PCC)/retropslenial cortex (RSC)--implicated in episodic memory processing. Using seed regions from the functional connectivity maps, the DTI analysis revealed robust structural connections between the MTLs and the retrosplenial cortex whereas tracts from the MPFC contacted the PCC (just rostral to the RSC). The results demonstrate that resting-state functional connectivity reflects structural connectivity and that combining modalities can enrich our understanding of these canonical brain networks.

    View details for DOI 10.1093/cercor/bhn059

    View details for Web of Science ID 000261679400007

    View details for PubMedID 18403396

  • Unsupervised method for automatic construction of a disease dictionary from a large free text collection. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium Xu, R., Supekar, K., Morgan, A., Das, A., Garber, A. 2008: 820-824

    Abstract

    Concept specific lexicons (e.g. diseases, drugs, anatomy) are a critical source of background knowledge for many medical language-processing systems. However, the rapid pace of biomedical research and the lack of constraints on usage ensure that such dictionaries are incomplete. Focusing on disease terminology, we have developed an automated, unsupervised, iterative pattern learning approach for constructing a comprehensive medical dictionary of disease terms from randomized clinical trial (RCT) abstracts, and we compared different ranking methods for automatically extracting con-textual patterns and concept terms. When used to identify disease concepts from 100 randomly chosen, manually annotated clinical abstracts, our disease dictionary shows significant performance improvement (F1 increased by 35-88%) over available, manually created disease terminologies.

    View details for PubMedID 18999169

  • Knowledge Zone: A Public Repository of Peer-Reviewed Biomedical Ontologies MEDINFO 2007: PROCEEDINGS OF THE 12TH WORLD CONGRESS ON HEALTH (MEDICAL) INFORMATICS, PTS 1 AND 2 Supekar, K., Rubin, D., Noy, N., Musen, M. 2007; 129: 812-816

    Abstract

    Reuse of ontologies is important for achieving better interoperability among health systems and relieving knowledge engineers from the burden of developing ontologies from scratch. Most of the work that aims to facilitate ontology reuse has focused on building ontology libraries that are simple repositories of ontologies or has led to keyword-based search tools that search among ontologies. To our knowledge, there are no operational methodologies that allow users to evaluate ontologies and to compare them in order to choose the most appropriate ontology for their task. In this paper, we present, Knowledge Zone - a Web-based portal that allows users to submit their ontologies, to associate metadata with their ontologies, to search for existing ontologies, to find ontology rankings based on user reviews, to post their own reviews, and to rate reviews.

    View details for Web of Science ID 000272064000163

    View details for PubMedID 17911829

  • Extracting Subject Demographic Information From Abstracts of Randomized Clinical Trial Reports MEDINFO 2007: PROCEEDINGS OF THE 12TH WORLD CONGRESS ON HEALTH (MEDICAL) INFORMATICS, PTS 1 AND 2 xu, r., Garten, Y., Supekar, K. S., Das, A. K., Altman, R. B., Garber, A. M. 2007; 129: 550-554

    Abstract

    In order to make more informed healthcare decisions, consumers need information systems that deliver accurate and reliable information about their illnesses and potential treatments. Reports of randomized clinical trials (RCTs) provide reliable medical evidence about the efficacy of treatments. Current methods to access, search for, and retrieve RCTs are keyword-based, time-consuming, and suffer from poor precision. Personalized semantic search and medical evidence summarization aim to solve this problem. The performance of these approaches may improve if they have access to study subject descriptors (e.g. age, gender, and ethnicity), trial sizes, and diseases/symptoms studied. We have developed a novel method to automatically extract such subject demographic information from RCT abstracts. We used text classification augmented with a Hidden Markov Model to identify sentences containing subject demographics, and subsequently these sentences were parsed using Natural Language Processing techniques to extract relevant information. Our results show accuracy levels of 82.5%, 92.5%, and 92.0% for extraction of subject descriptors, trial sizes, and diseases/symptoms descriptors respectively.

    View details for Web of Science ID 000272064000111

    View details for PubMedID 17911777

  • Ontology integration: Experience with medical terminologies COMPUTERS IN BIOLOGY AND MEDICINE Lee, Y., Supekar, K., Geller, J. 2006; 36 (7-8): 893-919

    Abstract

    To build a common controlled vocabulary is a formidable challenge in medical informatics. Due to vast scale and multiplicity in interpretation of medical data, it is natural to face overlapping terminologies in the process of practicing medical informatics [A. Rector, Clinical terminology: why is it so hard? Methods Inf. Med. 38 (1999) 239-252]. A major concern lies in the integration of seemingly overlapping terminologies in the medical domain and this issue has not been well addressed. In this paper, we describe a novel approach for medical ontology integration that relies on the theory of Algorithmic Semantic Refinement we previously developed. Our approach simplifies the task of matching pairs of corresponding concepts derived from a pair of ontologies, which is vital to terminology mapping. A formal theory and algorithm for our approach have been devised and the application of this method to two medical terminologies has been developed. The result of our work is an integrated medical terminology and a methodology and implementation ready to use for other ontology integration tasks.

    View details for DOI 10.1016/j.compbiomed.2005.04.013

    View details for Web of Science ID 000238735300014

    View details for PubMedID 16157328

  • Ontology-based annotation and query of tissue microarray data. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium Shah, N. H., Rubin, D. L., Supekar, K. S., Musen, M. A. 2006: 709-713

    Abstract

    The Stanford Tissue Microarray Database (TMAD) is a repository of data amassed by a consortium of pathologists and biomedical researchers. The TMAD data are annotated with multiple free-text fields, specifying the pathological diagnoses for each tissue sample. These annotations are spread out over multiple text fields and are not structured according to any ontology, making it difficult to integrate this resource with other biological and clinical data. We developed methods to map these annotations to the NCI thesaurus and the SNOMED-CT ontologies. Using these two ontologies we can effectively represent about 80% of the annotations in a structured manner. This mapping offers the ability to perform ontology driven querying of the TMAD data. We also found that 40% of annotations can be mapped to terms from both ontologies, providing the potential to align the two ontologies based on experimental data. Our approach provides the basis for a data-driven ontology alignment by mapping annotations of experimental data.

    View details for PubMedID 17238433

  • Combining text classification and Hidden Markov Modeling techniques for categorizing sentences in randomized clinical trial abstracts. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium xu, r., Supekar, K., Huang, Y., Das, A., Garber, A. 2006: 824-828

    Abstract

    Randomized clinical trials (RCT) papers provide reliable information about efficacy of medical interventions. Current keyword based search methods to retrieve medical evidence,overload users with irrelevant information as these methods often do not take in to consideration semantics encoded within abstracts and the search query. Personalized semantic search, intelligent clinical question answering and medical evidence summarization aim to solve this information overload problem. Most of these approaches will significantly benefit if the information available in the abstracts is structured into meaningful categories (e.g., background, objective, method, result and conclusion). While many journals use structured abstract format, majority of RCT abstracts still remain unstructured.We have developed a novel automated approach to structure RCT abstracts by combining text classification and Hidden Markov Modeling(HMM) techniques. Results (precision: 0.98, recall: 0.99) of our approach significantly outperform previously reported work on automated categorization of sentences in RCT abstracts.

    View details for PubMedID 17238456

  • Representing lexical components of medical terminologies in OWL. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium Supekar, K., Chute, C. G., Solbrig, H. 2005: 719-723

    Abstract

    Medical Terminologies play a vital role in clinical data capture, reporting, information integration, indexing and retrieval. The Web Ontology language (OWL) provides an opportunity for the medical community to leverage the capabilities of OWL semantics and tools to build formal, sound and consistent medical terminologies, and to provide a standard web accessible medium for inter-operability,access and reuse. One of the tasks facing the medical community today is to represent the extensive terminology content that already exists into this new medium. This paper addresses one aspect of this challenge - how to incorporate multilingual, structured lexical information such as definitions, synonyms, usage notes, etc. into the OWL ontology model in a standardized, consistent and useful fashion.

    View details for PubMedID 16779134

  • Ontology metadata to support the building of a library of biomedical ontologies. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium Supekar, K., Musen, M. 2005: 1126-?

    View details for PubMedID 16779413

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