Data-driven approaches to neuroimaging biomarkers for neurological and psychiatric disorders: emerging approaches and examples

Parallel Multilink Group Joint ICA: Fusion of 3D Structural and 4D Functional Data Across Multiple Resting fMRI Networks

Multimodal neuroimaging research plays a pivotal role in understanding the complexities of the human brain and its disorders. Independent component analysis (ICA) has emerged as a widely used and powerful tool for disentangling mixed independent sources, particularly in the analysis of functional magnetic resonance imaging (fMRI) data. This paper extends the use of ICA as a unifying framework for multimodal fusion, introducing a novel approach termed parallel multilink group joint ICA (pmg-jICA). The method allows for the fusion of gray matter maps from structural MRI (sMRI) data to multiple fMRI intrinsic networks, addressing the limitations of previous models. The effectiveness of pmg-jICA is demonstrated through its application to an Alzheimer's dataset, yielding linked structure-function outputs for 53 brain networks. Our approach leverages the complementary information from various imaging modalities, providing a unique perspective on brain alterations in Alzheimer's disease. The pmg-jICA identifies several components with significant differences between HC and AD groups including thalamus, caudate, putamen with in the subcortical (SC) domain, insula, parahippocampal gyrus within the cognitive control (CC) domain, and the lingual gyrus within the visual (VS) domain, providing localized insights into the links between AD and specific brain regions. In addition, because we link across multiple brain networks, we can also compute functional network connectivity (FNC) from spatial maps and subject loadings, providing a detailed exploration of the relationships between different brain regions and allowing us to visualize spatial patterns and loading parameters in sMRI along with intrinsic networks and FNC from the fMRI data. In essence, developed approach combines concepts from joint ICA and group ICA to provide a rich set of output characterizing data-driven links between covarying gray matter networks, and a (potentially large number of) resting fMRI networks allowing further study in the context of structure/function links. We demonstrate the utility of the approach by highlighting key structure/function disruptions in Alzheimer's individuals.

Multimodal active subspace analysis for computing assessment oriented subspaces from neuroimaging data

BACKGROUND

For successful biomarker discovery, it is essential to develop computational frameworks that summarize high-dimensional neuroimaging data in terms of involved sub-systems of the brain, while also revealing underlying heterogeneous functional and structural changes covarying with specific cognitive and biological traits. However, unsupervised decompositions do not inculcate clinical assessment information, while supervised approaches extract only individual feature importance, thereby impeding qualitative interpretation at the level of subspaces.

NEW METHOD

We present a novel framework to extract robust multimodal brain subspaces associated with changes in a given cognitive or biological trait. Our approach involves active subspace learning on the gradients of a trained machine learning model followed by clustering to extract and summarize the most salient and consistent subspaces associated with the target variable.

RESULTS

Through a rigorous cross-validation procedure on an Alzheimer's disease (AD) dataset, our framework successfully extracts multimodal subspaces specific to a given clinical assessment (e.g., memory and other cognitive skills), and also retains predictive performance in standard machine learning algorithms. We also show that the salient active subspace directions occur consistently across randomly sub-sampled repetitions of the analysis.

COMPARISON WITH EXISTING METHOD(S)

Compared to existing unsupervised decompositions based on principle component analysis, the subspace components in our framework retain higher predictive information.

CONCLUSIONS

As an important step towards biomarker discovery, our framework not only uncovers AD-related brain regions in the associated brain subspaces, but also enables automated identification of multiple underlying structural and functional sub-systems of the brain that collectively characterize changes in memory and proficiency in cognitive skills related to brain disorders like AD.

A Brainwide Risk Score for Psychiatric Disorder Evaluated in a Large Adolescent Population Reveals Increased Divergence Among Higher-Risk Groups Relative to Control Participants

BACKGROUND

Accurate psychiatric risk assessment requires biomarkers that are both stable and adaptable to development. Functional network connectivity (FNC), which steadily reconfigures over time, potentially contains abundant information to assess psychiatric risks. However, the absence of suitable analytical methodologies has constrained this area of investigation.

METHODS

We investigated the brainwide risk score (BRS), a novel FNC-based metric that contrasts the relative distances of an individual's FNC to that of psychiatric disorders versus healthy control references. To generate group-level disorder and healthy control references, we utilized a large brain imaging dataset containing 5231 total individuals diagnosed with schizophrenia, autism spectrum disorder, major depressive disorder, and bipolar disorder and their corresponding healthy control individuals. The BRS metric was employed to assess the psychiatric risk in 2 new datasets: Adolescent Brain Cognitive Development (ABCD) Study (n = 8191) and Human Connectome Project Early Psychosis (n = 170).

RESULTS

The BRS revealed a clear, reproducible gradient of FNC patterns from low to high risk for each psychiatric disorder in unaffected adolescents. We found that low-risk ABCD Study adolescent FNC patterns for each disorder were strongly present in over 25% of the ABCD Study participants and homogeneous, whereas high-risk patterns of each psychiatric disorder were strongly present in about 1% of ABCD Study participants and heterogeneous. The BRS also showed its effectiveness in predicting psychosis scores and distinguishing individuals with early psychosis from healthy control individuals.

CONCLUSIONS

The BRS could be a new image-based tool for assessing psychiatric vulnerability over time and in unaffected individuals, and it could also serve as a potential biomarker, facilitating early screening and monitoring interventions.

The role of perfusion, grey matter volume and behavioural phenotypes in the data-driven classification of cognitive syndromes

BACKGROUND

The use of structural and perfusion brain imaging in combination with behavioural information in the prediction of cognitive syndromes using a data-driven approach remains to be explored. Here, we thus examined the contribution of brain structural and perfusion imaging and behavioural features to the existing classification of cognitive syndromes using a data-driven approach.

METHODS

Study participants belonged to the community-based Biomarker and Cognition Cohort Study in Singapore who underwent neuropsychological assessments, structural-functional MRI and blood biomarkers. Participants had a diagnosis of cognitively normal (CN), subjective cognitive impairment (SCI), mild cognitive impairment (MCI) and dementia. Cross-sectional structural and cerebral perfusion imaging, behavioural scale data including mild behaviour impairment checklist, Pittsburgh Sleep Quality Index and Depression, Anxiety and Stress scale data were obtained.

RESULTS

Three hundred seventy-three participants (mean age 60.7 years; 56% female sex) with complete data were included. Principal component analyses demonstrated that no single modality was informative for the classification of cognitive syndromes. However, multivariate glmnet analyses revealed a specific combination of frontal perfusion and temporo-frontal grey matter volume were key protective factors while the severity of mild behaviour impairment interest sub-domain and poor sleep quality were key at-risk factors contributing to the classification of CN, SCI, MCI and dementia (p < 0.0001). Moreover, the glmnet model showed best classification accuracy in differentiating between CN and MCI cognitive syndromes (AUC = 0.704; sensitivity = 0.698; specificity = 0.637).

CONCLUSIONS

Brain structure, perfusion and behavioural features are important in the classification of cognitive syndromes and should be incorporated by clinicians and researchers. These findings illustrate the value of using multimodal data when examining syndrome severity and provide new insights into how cerebral perfusion and behavioural impairment influence classification of cognitive syndromes.

Performance reserves in brain-imaging-based phenotype prediction

This study examines the impact of sample size on predicting cognitive and mental health phenotypes from brain imaging via machine learning. Our analysis shows a 3- to 9-fold improvement in prediction performance when sample size increases from 1,000 to 1 M participants. However, despite this increase, the data suggest that prediction accuracy remains worryingly low and far from fully exploiting the predictive potential of brain imaging data. Additionally, we find that integrating multiple imaging modalities boosts prediction accuracy, often equivalent to doubling the sample size. Interestingly, the most informative imaging modality often varied with increasing sample size, emphasizing the need to consider multiple modalities. Despite significant performance reserves for phenotype prediction, achieving substantial improvements may necessitate prohibitively large sample sizes, thus casting doubt on the practical or clinical utility of machine learning in some areas of neuroimaging.

Revolutionizing stress-related disorder regulation through neuroinformatics and data analysis: An editorial

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Network models to enhance the translational impact of cross-species studies

Neuroscience studies are often carried out in animal models for the purpose of understanding specific aspects of the human condition. However, the translation of findings across species remains a substantial challenge. Network science approaches can enhance the translational impact of cross-species studies by providing a means of mapping small-scale cellular processes identified in animal model studies to larger-scale inter-regional circuits observed in humans. In this Review, we highlight the contributions of network science approaches to the development of cross-species translational research in neuroscience. We lay the foundation for our discussion by exploring the objectives of cross-species translational models. We then discuss how the development of new tools that enable the acquisition of whole-brain data in animal models with cellular resolution provides unprecedented opportunity for cross-species applications of network science approaches for understanding large-scale brain networks. We describe how these tools may support the translation of findings across species and imaging modalities and highlight future opportunities. Our overarching goal is to illustrate how the application of network science tools across human and animal model studies could deepen insight into the neurobiology that underlies phenomena observed with non-invasive neuroimaging methods and could simultaneously further our ability to translate findings across species.

Deep Learning for Brain MRI Confirms Patterned Pathological Progression in Alzheimer's Disease

Deep learning (DL) on brain magnetic resonance imaging (MRI) data has shown excellent performance in differentiating individuals with Alzheimer's disease (AD). However, the value of DL in detecting progressive structural MRI (sMRI) abnormalities linked to AD pathology has yet to be established. In this study, an interpretable DL algorithm named the Ensemble of 3-dimensional convolutional neural network (Ensemble 3DCNN) with enhanced parsing techniques is proposed to investigate the longitudinal trajectories of whole-brain sMRI changes denoting AD onset and progression. A set of 2369 T1-weighted images from the multi-centre Alzheimer's Disease Neuroimaging Initiative and Open Access Series of Imaging Studies cohorts are applied to model derivation, validation, testing, and pattern analysis. An Ensemble-3DCNN-based P-score is generated, based on which multiple brain regions, including amygdala, insular, parahippocampal, and temporal gyrus, exhibit early and connected progressive neurodegeneration. Complex individual variability in the sMRI is also observed. This study combining non-invasive sMRI and interpretable DL in detecting patterned sMRI changes confirmed AD pathological progression, shedding new light on predicting AD progression using whole-brain sMRI.

MRI data quality assessment for the RIN - Neuroimaging Network using the ACR phantoms

PURPOSE

Generating big-data is becoming imperative with the advent of machine learning. RIN-Neuroimaging Network addresses this need by developing harmonized protocols for multisite studies to identify quantitative MRI (qMRI) biomarkers for neurological diseases. In this context, image quality control (QC) is essential. Here, we present methods and results of how the RIN performs intra- and inter-site reproducibility of geometrical and image contrast parameters, demonstrating the relevance of such QC practice.

METHODS

American College of Radiology (ACR) large and small phantoms were selected. Eighteen sites were equipped with a 3T scanner that differed by vendor, hardware/software versions, and receiver coils. The standard ACR protocol was optimized (in-plane voxel, post-processing filters, receiver bandwidth) and repeated monthly. Uniformity, ghosting, geometric accuracy, ellipse's ratio, slice thickness, and high-contrast detectability tests were performed using an automatic QC script.

RESULTS

Measures were mostly within the ACR tolerance ranges for both T1- and T2-weighted acquisitions, for all scanners, regardless of vendor, coil, and signal transmission chain type. All measurements showed good reproducibility over time. Uniformity and slice thickness failed at some sites. Scanners that upgraded the signal transmission chain showed a decrease in geometric distortion along the slice encoding direction. Inter-vendor differences were observed in uniformity and geometric measurements along the slice encoding direction (i.e. ellipse's ratio).

CONCLUSIONS

Use of the ACR phantoms highlighted issues that triggered interventions to correct performance at some sites and to improve the longitudinal stability of the scanners. This is relevant for establishing precision levels for future multisite studies of qMRI biomarkers.

A training program for researchers in population neuroimaging: Early experiences

Recent advances in neuroimaging create groundbreaking opportunities to better understand human neurological and psychiatric diseases, but also bring new challenges. With the advent of more and more sophisticated and efficient multimodal image processing software, we can now study much larger populations and integrate information from multiple modalities. In consequence, investigators that use neuroimaging techniques must also understand and apply principles of population sampling and contemporary data analytic techniques. The next generation of neuroimaging researchers must be skilled in numerous previously distinct disciplines and so a new integrated model of training is needed. This tutorial presents the rationale for such a new training model and presents the results from the first years of the training program focused on population neuroimaging of Alzheimer's Disease. This approach is applicable to other areas of population neuroimaging.

SVR-based Multimodal Active Subspace Analysis for the Brain using Neuroimaging Data.. [DOI: 10.1101/2022.07.28.501879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Understanding the patterns of changes in brain function and structure due to various disorders and diseases is of utmost importance. There have been numerous efforts toward successful biomarker discovery for complex brain disorders by evaluating neuroimaging datasets with novel analytical frameworks. However, due to the multi-faceted nature of the disorders involving a wide and overlapping range of symptoms as well as complex changes in structural and functional brain networks, it is increasingly important to devise computational frameworks that can consider the underlying patterns of heterogeneous changes with specific target assessments, at the same time producing a summarizing output from the high-dimensional neuroimaging data. While various machine learning approaches focus on diagnostic prediction, many learning frameworks analyze important features at the level of brain regions involved in prediction using supervised methods. Unsupervised learning methods have also been utilized to break down the neuroimaging features into lower dimensional components. However, most learning frameworks either do not consider the target assessment information while extracting brain subspaces, or can extract only higher dimensional importance associations as an ordered list of involved features, making manual interpretation at the level of subspaces difficult. We present a novel multimodal active subspace learning framework to understand various subspaces within the brain that are associated with changes in particular biological and cognitive traits. For a given cognitive or biological trait, our framework performs a decomposition of the feature importances to extract robust multimodal subspaces that define the most significant change in the given trait. Through a rigorous cross-validation procedure on an Alzheimer’s disease (AD) dataset, we show that our framework can extract subspaces covering both functional and structural modalities, which are specific to a given clinical assessment (like memory and other cognitive skills) and also retain predictive performance in standard machine learning algorithms. We show that our framework not only uncovers AD-related brain regions (e.g., hippocampus, entorhinal cortex) in the associated brain subspaces, but also enables an automated identification of multiple underlying structural and functional sub-systems of the brain that collectively characterize changes in memory and cognitive skill proficiency related to brain disorders like AD.

How Machine Learning is Powering Neuroimaging to Improve Brain Health

This report presents an overview of how machine learning is rapidly advancing clinical translational imaging in ways that will aid in the early detection, prediction, and treatment of diseases that threaten brain health. Towards this goal, we aresharing the information presented at a symposium, "Neuroimaging Indicators of Brain Structure and Function - Closing the Gap Between Research and Clinical Application", co-hosted by the McCance Center for Brain Health at Mass General Hospital and the MIT HST Neuroimaging Training Program on February 12, 2021. The symposium focused on the potential for machine learning approaches, applied to increasingly large-scale neuroimaging datasets, to transform healthcare delivery and change the trajectory of brain health by addressing brain care earlier in the lifespan. While not exhaustive, this overview uniquely addresses many of the technical challenges from image formation, to analysis and visualization, to synthesis and incorporation into the clinical workflow. Some of the ethical challenges inherent to this work are also explored, as are some of the regulatory requirements for implementation. We seek to educate, motivate, and inspire graduate students, postdoctoral fellows, and early career investigators to contribute to a future where neuroimaging meaningfully contributes to the maintenance of brain health.