Any-way and Sparse Analyses for Multimodal Fusion and Imaging Genomics

This dissertation aims to develop new algorithms that leverage sparsity and mutual information across data modalities built upon the independent component analysis (ICA) framework to improve the performance of current ICA-based multimodal fusion approaches. These algorithms are further applied to both simulated data and real neuroimaging and genomic data to examine their performance. The identified neuroimaging and genomic patterns can help better delineate the pathology of mental disorders or brain development. To alleviate the signal-background separation difficulties in infomax-decomposed sources for genomic data, we propose a sparse infomax by enhancing a robust sparsity measure, the Hoyer index. Hoyer index is scale-invariant and well suited for ICA frameworks since the scale of decomposed sources is arbitrary. Simulation results demonstrate that sparse infomax increases the component detection accuracy for situations where the source signal-to-background (SBR) ratio is low, particularly for single nucleotide polymorphism (SNP) data. The proposed sparse infomax is further extended into two data modalities as a sparse parallel ICA for applications to imaging genomics in order to investigate the associations between brain imaging and genomics. Simulation results show that sparse parallel ICA outperforms parallel ICA with improved accuracy for structural magnetic resonance imaging (sMRI)-SNP association detection and component spatial map recovery, as well as with enhanced sparsity for sMRI and SNP components under noisy cases. Applying the proposed sparse parallel ICA to fuse the whole-brain sMRI and whole-genome SNP data of 24985 participants in the UK biobank, we identify three stable and replicable sMRI-SNP pairs. The identified sMRI components highlight frontal, parietal, and temporal regions and associate with multiple cognitive measures (with different association strengths in different age groups for the temporal component). Top SNPs in the identified SNP factor are enriched in inflammatory disease and inflammatory response pathways, which also regulate gene expression, isoform percentage, transcription expression, or methylation level in the frontal region, and the regulation effects are significantly enriched. Applying the proposed sparse parallel ICA to imaging genomics in attention-deficit/hyperactivity disorder (ADHD), we identify and replicate one SNP component related to gray matter volume (GMV) alterations in superior and middle frontal gyri underlying working memory deficit in adults and adolescents with ADHD. The association is more significant in ADHD families than controls and stronger in adults and older adolescents than younger ones. The identified SNP component highlights SNPs in long non-coding RNAs (lncRNAs) in chromosome 5 and in several protein-coding genes that are involved in ADHD, such as MEF2C, CADM2, and CADPS2. Top SNPs are enriched in human brain neuron cells and regulate gene expression, isoform percentage, transcription expression, or methylation level in the frontal region. Moreover, to increase the flexibility and robustness in mining multimodal data, we propose aNy-way ICA, which optimizes the entire correlation structure of linked components across any number of modalities via the Gaussian independent vector analysis and simultaneously optimizes independence via separate (parallel) ICAs. Simulation results demonstrate that aNy-way ICA recover sources and loadings, as well as the true covariance patterns with improved accuracy compared to existing multimodal fusion approaches, especially under noisy conditions. Applying the proposed aNy-way ICA to integrate structural MRI, fractal n-back, and emotion identification task functional MRIs collected in the Philadelphia Neurodevelopmental Cohort (PNC), we identify and replicate one linked GMV-threat-2-back component, and the threat and 2-back components are related to intelligence quotient (IQ) score in both discovery and replication samples. Lastly, we extend the proposed aNy-way ICA with a reference constraint to enable prior-guided multimodal fusion. Simulation results show that aNy-way ICA with reference recovers the designed linkages between reference and modalities, cross-modality correlations, as well as loading and component matrices with improved accuracy compared to multi-site canonical correlation analysis with reference (MCCAR)+joint ICA under noisy conditions. Applying aNy-way ICA with reference to supervise structural MRI, fractal n-back, and emotion identification task functional MRIs fusion in PNC with IQ as the reference, we identify and replicate one IQ-related GMV-threat-2-back component, and this component is significantly correlated across modalities in both discovery and replication samples.Ph.D

Alpha Event-Related Decreases During Encoding in Adults with ADHD - An Investigation of Sustained Attention and Working Memory Processes.

BACKGROUND: Executive functioning deficits are central to established neuropsychological models of ADHD. Oscillatory activity, particularly the alpha rhythm (8-12Hz) has been associated with cognitive impairments in ADHD. However, most studies to date examined such neural mechanisms underlying executive dysfunction in children and adolescents with ADHD, raising the question of whether and to what extent those ADHD-related working memory impairments are still present in adults. To this end, the current study aimed to investigate the role of alpha event-related decreases (ERD) during working memory processes in adults with and without ADHD. METHODS: We collected electroencephalographic (EEG) data from 85 adults with a lifetime diagnosis of ADHD and 105 controls (aged 32-64), while they performed a continuous performance (CPT) and a Sternberg working memory task (SDRT). Time-frequency and independent component analysis (ICA) was used to identify alpha (8-12Hz) clusters to examine group and condition effects during the temporal profile of sustained attention and working memory processes (encoding, maintenance, retrieval), loads (low and high) and trial type (go and nogo). RESULTS: Individuals with ADHD exhibited higher reaction time-variability in SDRT, and slower response times in SDRT and CPT, despite no differences in task accuracy. Although working memory load was associated with stronger alpha ERD in both tasks and both groups (ADHD, controls), we found no evidence for attenuated alpha ERD in adults with ADHD, failing to replicate effects reported in children. In contrast, when looking at the whole sample, the correlations of alpha power during encoding with inattention and hyperactivity-impulsivity symptoms were significant, replicating prior findings in children with ADHD, but suggesting an alternate source for these effects in adults. CONCLUSIONS: Our results corroborate the robustness of alpha as a marker of visual attention and suggest that occipital alpha ERD normalizes in adulthood, but with unique contributions of centro-occipital alpha ERD, suggesting a secondary source. This implies that deviations in processes other than previously reported visuospatial cortex engagement account for the persistent symptoms and cognitive deficits in adults with a history of ADHD

A benchmark for prediction of psychiatric multimorbidity from resting EEG data in a large pediatric sample

Psychiatric disorders are among the most common and debilitating illnesses across the lifespan and begin usually during childhood and adolescence, which emphasizes the importance of studying the developing brain. Most of the previous pediatric neuroimaging studies employed traditional univariate statistics on relatively small samples. Multivariate machine learning approaches have a great potential to overcome the limitations of these approaches. On the other hand, the vast majority of existing multivariate machine learning studies have focused on differentiating between children with an isolated psychiatric disorder and typically developing children. However, this line of research does not reflect the real-life situation as the majority of children with a clinical diagnosis have multiple psychiatric disorders (multimorbidity), and consequently, a clinician has the task to choose between different diagnoses and/or the combination of multiple diagnoses. Thus, the goal of the present benchmark is to predict psychiatric multimorbidity in children and adolescents. For this purpose, we implemented two kinds of machine learning benchmark challenges: The first challenge targets the prediction of the seven most prevalent DSM-V psychiatric diagnoses for the available data set, of which each individual can exhibit multiple ones concurrently (i.e. multi-task multi-label classification). Based on behavioral and cognitive measures, a second challenge focuses on predicting psychiatric symptom severity on a dimensional level (i.e. multiple regression task). For the present benchmark challenges, we will leverage existing and future data from the biobank of the Healthy Brain Network (HBN) initiative, which offers a unique large-sample dataset (N = 2042) that provides a wide array of different psychiatric developmental disorders and true hidden data sets. Due to limited real-world practicability and economic viability of MRI measurements, the present challenge will permit only resting state EEG data and demographic information to derive predictive models. We believe that a community driven effort to derive predictive markers from these data using advanced machine learning algorithms can help to improve the diagnosis of psychiatric developmental disorders

Oscillatory neural networks underlying resting-state, attentional control and social cognition task conditions in children with ASD, ADHD and ASD+ADHD

Autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD) are common and impairing neurodevelopmental disorders that frequently co-occur. The neurobiological mechanisms involved in ASD and ADHD are not fully understood. However, alterations in large-scale neural networks have been proposed as core deficits in both ASD and ADHD and may help to disentangle the neurobiological basis of these disorders and their co-occurrence. In this study, we examined similarities and differences in large-scale oscillatory neural networks between boys aged 8-13 years with ASD (n = 19), ADHD (n = 18), ASD + ADHD (n = 29) and typical development (Controls, n = 26). Oscillatory neural networks were computed using graph-theoretical methods from electroencephalographic (EEG) data collected during an eyes-open resting-state and attentional control and social cognition tasks in which we previously reported disorder-specific atypicalities in oscillatory power and event-related potentials (ERPs). We found that children with ASD showed significant hypoconnectivity in large-scale networks during all three task conditions compared to children without ASD. In contrast, children with ADHD showed significant hyperconnectivity in large-scale networks during the attentional control and social cognition tasks, but not during the resting-state, compared to children without ADHD. Children with co-occurring ASD + ADHD did not differ from children with ASD when paired with this group and vice versa when paired with the ADHD group, indicating that these children showed both ASD-like hypoconnectivity and ADHD-like hyperconnectivity. Our findings suggest that ASD and ADHD are associated with distinct alterations in large-scale oscillatory networks, and these atypicalities present together in children with both disorders. These alterations appear to be task-independent in ASD but task-related in ADHD, and may underlie other neurocognitive atypicalities in these disorders. [Abstract copyright: Copyright © 2019 Elsevier Ltd. All rights reserved.

Recent Applications in Graph Theory

Graph theory, being a rigorously investigated field of combinatorial mathematics, is adopted by a wide variety of disciplines addressing a plethora of real-world applications. Advances in graph algorithms and software implementations have made graph theory accessible to a larger community of interest. Ever-increasing interest in machine learning and model deployments for network data demands a coherent selection of topics rewarding a fresh, up-to-date summary of the theory and fruitful applications to probe further. This volume is a small yet unique contribution to graph theory applications and modeling with graphs. The subjects discussed include information hiding using graphs, dynamic graph-based systems to model and control cyber-physical systems, graph reconstruction, average distance neighborhood graphs, and pure and mixed-integer linear programming formulations to cluster networks

Brain-Computer Interface

Brain-computer interfacing (BCI) with the use of advanced artificial intelligence identification is a rapidly growing new technology that allows a silently commanding brain to manipulate devices ranging from smartphones to advanced articulated robotic arms when physical control is not possible. BCI can be viewed as a collaboration between the brain and a device via the direct passage of electrical signals from neurons to an external system. The book provides a comprehensive summary of conventional and novel methods for processing brain signals. The chapters cover a range of topics including noninvasive and invasive signal acquisition, signal processing methods, deep learning approaches, and implementation of BCI in experimental problems

Dynamic Configuration of Large-Scale Cortical Networks: A Useful Framework for Clarifying the Heterogeneity Found in Attention-Deficit/Hyperactivity Disorder

The heterogeneity of attention-deficit/hyperactivity disorder(ADHD) traits (inattention vs. hyperactivity/impulsivity) complicates diagnosis and intervention. Identifying how the configuration of large-scale functional brain networks during cognitive processing correlate with this heterogeneity could help us understand the neural mechanisms altered across ADHD presentations. Here, we recorded high-density EEG while 62 non-clinical participants (ages 18-24; 32 male) underwent an inhibitory control task (Go/No-Go). Functional EEG networks were created using sensors as nodes and across-trial phase-lag index values as edges. Using cross-validated LASSO regression, we examined whether graph-theory metrics applied to both static networks (averaged across time-windows: -500–0ms, 0–500ms) and dynamic networks (temporally layered with 2ms intervals), were associated with hyperactive/impulsive and inattentive traits. Network configuration during response execution/inhibition was associated with hyperactive/impulsive (mean R2across test sets = .20, SE = .02), but not inattentive traits. Post-stimulus results at higher frequencies (Beta, 14-29Hz; Gamma, 30-90Hz) showed the strongest association with hyperactive/impulsive traits, and predominantly reflected less burst-like integration between modules in oscillatory beta networks during execution, and increased integration/small-worldness in oscillatory gamma networks during inhibition. We interpret the beta network results as reflecting weaker integration between specialized pre-frontal and motor systems during motor response preparation, and the gamma results as reflecting a compensatory mechanism used to integrate processing between less functionally specialized networks. This research demonstrates that the neural network mechanisms underlying response execution/inhibition might be associated with hyperactive/impulsive traits, and that dynamic, task-related changes in EEG functional networks may be useful in disentangling ADHD heterogeneity