Showing papers by "Satrajit S. Ghosh published in 2020"

Natural Language Processing Reveals Vulnerable Mental Health Support Groups and Heightened Health Anxiety on Reddit During COVID-19: Observational Study.

Abstract: Background: The COVID-19 pandemic is impacting mental health, but it is not clear how people with different types of mental health problems were differentially impacted as the initial wave of cases hit. Objective: The aim of this study is to leverage natural language processing (NLP) with the goal of characterizing changes in 15 of the world’s largest mental health support groups (eg, r/schizophrenia, r/SuicideWatch, r/Depression) found on the website Reddit, along with 11 non–mental health groups (eg, r/PersonalFinance, r/conspiracy) during the initial stage of the pandemic. Methods: We created and released the Reddit Mental Health Dataset including posts from 826,961 unique users from 2018 to 2020. Using regression, we analyzed trends from 90 text-derived features such as sentiment analysis, personal pronouns, and semantic categories. Using supervised machine learning, we classified posts into their respective support groups and interpreted important features to understand how different problems manifest in language. We applied unsupervised methods such as topic modeling and unsupervised clustering to uncover concerns throughout Reddit before and during the pandemic. Results: We found that the r/HealthAnxiety forum showed spikes in posts about COVID-19 early on in January, approximately 2 months before other support groups started posting about the pandemic. There were many features that significantly increased during COVID-19 for specific groups including the categories “economic stress,” “isolation,” and “home,” while others such as “motion” significantly decreased. We found that support groups related to attention-deficit/hyperactivity disorder, eating disorders, and anxiety showed the most negative semantic change during the pandemic out of all mental health groups. Health anxiety emerged as a general theme across Reddit through independent supervised and unsupervised machine learning analyses. For instance, we provide evidence that the concerns of a diverse set of individuals are converging in this unique moment of history; we discovered that the more users posted about COVID-19, the more linguistically similar (less distant) the mental health support groups became to r/HealthAnxiety (ρ=–0.96, P<.001). Using unsupervised clustering, we found the suicidality and loneliness clusters more than doubled in the number of posts during the pandemic. Specifically, the support groups for borderline personality disorder and posttraumatic stress disorder became significantly associated with the suicidality cluster. Furthermore, clusters surrounding self-harm and entertainment emerged. Conclusions: By using a broad set of NLP techniques and analyzing a baseline of prepandemic posts, we uncovered patterns of how specific mental health problems manifest in language, identified at-risk users, and revealed the distribution of concerns across Reddit, which could help provide better resources to its millions of users. We then demonstrated that textual analysis is sensitive to uncover mental health complaints as they appear in real time, identifying vulnerable groups and alarming themes during COVID-19, and thus may have utility during the ongoing pandemic and other world-changing events such as elections and protests.

Automated assessment of psychiatric disorders using speech: A systematic review.

Abstract: Objective There are many barriers to accessing mental health assessments including cost and stigma. Even when individuals receive professional care, assessments are intermittent and may be limited partly due to the episodic nature of psychiatric symptoms. Therefore, machine-learning technology using speech samples obtained in the clinic or remotely could one day be a biomarker to improve diagnosis and treatment. To date, reviews have only focused on using acoustic features from speech to detect depression and schizophrenia. Here, we present the first systematic review of studies using speech for automated assessments across a broader range of psychiatric disorders. Methods We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. We included studies from the last 10 years using speech to identify the presence or severity of disorders within the Diagnostic and Statistical Manual of Mental Disorders (DSM-5). For each study, we describe sample size, clinical evaluation method, speech-eliciting tasks, machine learning methodology, performance, and other relevant findings. Results 1395 studies were screened of which 127 studies met the inclusion criteria. The majority of studies were on depression, schizophrenia, and bipolar disorder, and the remaining on post-traumatic stress disorder, anxiety disorders, and eating disorders. 63% of studies built machine learning predictive models, and the remaining 37% performed null-hypothesis testing only. We provide an online database with our search results and synthesize how acoustic features appear in each disorder. Conclusion Speech processing technology could aid mental health assessments, but there are many obstacles to overcome, especially the need for comprehensive transdiagnostic and longitudinal studies. Given the diverse types of data sets, feature extraction, computational methodologies, and evaluation criteria, we provide guidelines for both acquiring data and building machine learning models with a focus on testing hypotheses, open science, reproducibility, and generalizability. Level of evidence 3a.

Analysis of task-based functional MRI data preprocessed with fMRIPrep.

Abstract: Functional magnetic resonance imaging (fMRI) is a standard tool to investigate the neural correlates of cognition. fMRI noninvasively measures brain activity, allowing identification of patterns evoked by tasks performed during scanning. Despite the long history of this technique, the idiosyncrasies of each dataset have led to the use of ad-hoc preprocessing protocols customized for nearly every different study. This approach is time consuming, error prone and unsuitable for combining datasets from many sources. Here we showcase fMRIPrep (http://fmriprep.org), a robust tool to prepare human fMRI data for statistical analysis. This software instrument addresses the reproducibility concerns of the established protocols for fMRI preprocessing. By leveraging the Brain Imaging Data Structure to standardize both the input datasets (MRI data as stored by the scanner) and the outputs (data ready for modeling and analysis), fMRIPrep is capable of preprocessing a diversity of datasets without manual intervention. In support of the growing popularity of fMRIPrep, this protocol describes how to integrate the tool in a task-based fMRI investigation workflow.

Real-time fMRI neurofeedback reduces auditory hallucinations and modulates resting state connectivity of involved brain regions: Part 2: Default mode network -preliminary evidence

Abstract: Auditory hallucinations (AHs) are one of the most distressing symptoms of schizophrenia (SZ) and are often resistant to medication. Imaging studies of individuals with SZ show hyperactivation of the default mode network (DMN) and the superior temporal gyrus (STG). Studies in SZ show DMN hyperconnectivity and reduced anticorrelation between DMN and the central executive network (CEN). DMN hyperconnectivity has been associated with positive symptoms such as AHs while reduced DMN anticorrelations with cognitive impairment. Using real-time fMRI neurofeedback (rt-fMRI-NFB) we trained SZ patients to modulate DMN and CEN networks. Meditation is effective in reducing AHs in SZ and to modulate brain network integration and increase DMN anticorrelations. Consequently, patients were provided with meditation strategies to enhance their abilities to modulate DMN/CEN. Results show a reduction of DMN hyperconnectivity and increase in DMNCEN anticorrelation. Furthermore, the change in individual DMN connectivity significantly correlated with reductions in AHs. This is the first time that meditation enhanced through rt-fMRI-NFB is used to reduce AHs in SZ. Moreover, it provides the first empirical evidence for a direct causal relation between meditation enhanced rt-fMRI-NFB modulation of DMNCEN activity and post-intervention modulation of resting state networks ensuing in reductions in frequency and severity of AHs.

Neurodevelopmental and Psychiatric Symptoms in Patients with a Cyst Compressing the Cerebellum: an Ongoing Enigma.

Abstract: A patient diagnosed with developmental delay, intellectual disability, and autistic and obsessive-compulsive symptoms was found to have a posterior fossa arachnoid cyst (PFAC) compressing the cerebellum. The patient was referred to our Ataxia Unit for consideration of surgical drainage of the cyst to improve his clinical constellation. This scenario led to an in-depth analysis including a literature review, functional resting-state MRI analysis of our patient compared to a group of controls, and genetic testing. While it is reasonable to consider that there may be a causal relationship between PFAC and neurodevelopmental or psychiatric symptoms in some patients, there is also a nontrivial prevalence of PFAC in the asymptomatic population and a significant possibility that many PFAC are incidental findings in the context of primary cognitive or psychiatric symptoms. Our functional MRI analysis is the first to examine brain function, and to report cerebellar dysfunction, in a patient presenting with cognitive/psychiatric symptoms found to have a structural abnormality compressing the cerebellum. These neuroimaging findings are inherently limited due to their correlational nature but provide unprecedented evidence suggesting that cerebellar compression may be associated with cerebellar dysfunction. Exome gene sequencing revealed additional etiological possibilities, highlighting the complexity of this field of cerebellar clinical and scientific practice. Our findings and discussion may guide future investigations addressing an important knowledge gap-namely, is there a link between cerebellar compression (including arachnoid cysts and possibly other forms of cerebellar compression such as Chiari malformation), cerebellar dysfunction (including fMRI abnormalities reported here), and neuropsychiatric symptoms?

Real-time fMRI feedback impacts brain activation, results in auditory hallucinations reduction: Part 1: Superior temporal gyrus -Preliminary evidence.

Abstract: Auditory hallucinations (AH) are one of the core symptoms of schizophrenia (SZ) and constitute a significant source of suffering and disability. One third of SZ patients experience pharmacology-resistant AH, so an alternative/complementary treatment strategy is needed to alleviate this debilitating condition. In this study, real-time functional Magnetic Resonance Imaging neurofeedback (rt-fMRI NFB), a non-invasive technique, was used to teach 10 SZ patients with pharmacology-resistant AH to modulate their brain activity in the superior temporal gyrus (STG), a key area in the neurophysiology of AH. A functional task was designed in order to provide patients with a specific strategy to help them modify their brain activity in the desired direction. Specifically, they received neurofeedback from their own STG and were trained to upregulate it while listening to their own voice recording and downregulate it while ignoring a stranger's voice recording. This guided performance neurofeedback training resulted in a) a significant reduction in STG activation while ignoring a stranger's voice, and b) reductions in AH scores after the neurofeedback session. A single, 21-minute session of rt-fMRI NFB was enough to produce these effects, suggesting that this approach may be an efficient and clinically viable alternative for the treatment of pharmacology-resistant AH.

Toward Community-Driven Big Open Brain Science: Open Big Data and Tools for Structure, Function, and Genetics

Abstract: As acquiring bigger data becomes easier in experimental brain science, computational and statistical brain science must achieve similar advances to fully capitalize on these data. Tackling these problems will benefit from a more explicit and concerted effort to work together. Specifically, brain science can be further democratized by harnessing the power of community-driven tools, which both are built by and benefit from many different people with different backgrounds and expertise. This perspective can be applied across modalities and scales and enables collaborations across previously siloed communities.

Analysis of task-based functional MRI data preprocessed with fMRIPrep

Abstract: Functional magnetic resonance imaging (fMRI) is a standard tool to investigate the neural correlates of cognition. fMRI noninvasively measures brain activity, allowing identification of patterns evoked by tasks performed during scanning. Despite the long history of this technique, the idiosyncrasies of each dataset have led to the use of ad-hoc preprocessing protocols customized for nearly every different study. This approach is time-consuming, error-prone, and unsuitable for combining datasets from many sources. Here we showcase fMRIPrep (http://fmriprep.org), a robust tool to prepare human fMRI data for statistical analysis. This software instrument addresses the reproducibility concerns of the established protocols for fMRI preprocessing. By leveraging the Brain Imaging Data Structure (BIDS) to standardize both the input datasets -MRI data as stored by the scanner- and the outputs -data ready for modeling and analysis-, fMRIPrep is capable of preprocessing a diversity of datasets without manual intervention. In support of the growing popularity of fMRIPrep, this protocol describes how to integrate the tool in a task-based fMRI investigation workflow.

Pydra - a flexible and lightweight dataflow engine for scientific analyses

Abstract: This paper presents a new lightweight dataflow engine written in Python: Pydra. Pydra is developed as an open-source project in the neuroimaging community, but it is designed as a general-purpose dataflow engine to support any scientific domain. The paper describes the architecture of the software, as well as several useful features, that make Pydra a customizable and powerful dataflow engine. Two examples are presented to demonstrate the syntax and properties of the package.

A multimodal cell census and atlas of the mammalian primary motor cortex

Abstract: We report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Together, our results advance the collective knowledge and understanding of brain cell type organization: First, our study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, cross-modal analysis provides compelling evidence for the epigenomic, transcriptomic, and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types and subtypes. Fourth, in situ single-cell transcriptomics provides a spatially-resolved cell type atlas of the motor cortex. Fifth, integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types. We further present an extensive genetic toolset for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. Together, our results establish a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

Uncovering the important acoustic features for detecting vocal fold paralysis with explainable machine learning

Abstract: Objectives To detect unilateral vocal fold paralysis (UVFP) from voice recordings using an explainable model of machine learning. Study Design Case series - retrospective with a control group. Methods Patients with confirmed UVFP through endoscopic examination (N=77) and controls with normal voices matched for age and sex (N=77) were included. Two tasks were used to elicit voice samples: reading the Rainbow Passage and sustaining phonation of the vowel /a/. The eighty-eight extended Geneva Minimalistic Acoustic Parameter Set (eGeMAPS) features were extracted as inputs for four machine learning models of differing complexity. Training and testing were performed using bootstrapped cross-validation. SHAP was used to identify important features. Results The median Area Under the Receiver Operating Characteristic Curve (ROC AUC) score ranged from 0.79 to 0.87 depending on model and task. After removing redundant features for explainability, the highest median ROC AUC score was 0.84 using only 13 features for the vowel task and 0.87 using 39 features for the reading task. The most important features included intensity measures, mean MFCC1, mean F1 amplitude and frequency, and shimmer variability depending on model and task. Conclusion Using the largest dataset studying UVFP to date, we achieve high performance from just a few seconds of voice recordings while discovering which acoustic features are important across models. Notably, we demonstrate that the models use different combinations of features to achieve similar effect sizes. Overall the categories of features related to vocal fold physiology were conserved across the models. Machine learning thus provides a mechanism to detect UVFP and contextualize the accuracy relative to both model architecture and pathophysiology. Level of Evidence Type 3

Asymmetric Functional Gradients in the Human Subcortex

Abstract: A central principle in our understanding of cerebral cortical organization is that homotopic left and right areas are functionally linked to each other, and also connected with structures that share similar functions within each cerebral cortical hemisphere. Here we refer to this concept as interhemispheric functional symmetry (IHFS). While multiple studies have described the distribution and variations of IHFS in the cerebral cortex, descriptions of IHFS in the subcortex are largely absent in the neuroscientific literature. Further, the proposed anatomical basis of IHFS is centered on callosal and other commissural tracts. These commissural fibers are present in virtually all cerebral cortical areas, but almost absent in the subcortex. There is thus an important knowledge gap in our understanding of subcortical IHFS. What is the distribution and variations of subcortical IHFS, and what are the anatomical correlates and physiological implications of this important property in the subcortex? Using fMRI functional gradient analyses in a large dataset (Human Connectome Project, n=1003), here we explored IHFS in human thalamus, lenticular nucleus, cerebellar cortex, and caudate nucleus. Our detailed descriptions provide an empirical foundation upon which to build hypotheses for the anatomical and physiological basis of subcortical IHFS. Our results indicate that direct or driver cerebral cortical afferent connectivity, as opposed to indirect or modulatory cerebral cortical afferent connectivity, is associated with stronger subcortical IHFS in thalamus and lenticular nucleus. In cerebellar cortex and caudate, where there is no variability in terms of either direct vs. indirect or driver vs. modulatory cerebral cortical afferent connections, connectivity to cerebral cortical areas with stronger cerebral cortical IHFS is associated with stronger IHFS in the subcortex. These two observations support a close relationship between subcortical IHFS and connectivity between subcortex and cortex, and generate new testable hypotheses that advance our understanding of subcortical organization.

Remote Digital Psychiatry: MindLogger for Mobile Mental Health Assessment and Therapy

Abstract: Background: Universal access to assessment and treatment of mental health and learning disorders remains a significant and unmet need. There is a vast number of people without access to care because of economic, geographic, and cultural barriers as well as limited availability of clinical experts who could help advance our understanding of mental health. Objective: To create an open, configurable software platform to build clinical measures, mobile assessments, tasks, and interventions without programming expertise. Specifically, our primary requirements include: an administrator interface for creating and scheduling recurring and customized questionnaires where end users receive and respond to scheduled notifications via an iOS or Android app on a mobile device. Such a platform would help relieve overwhelmed health systems, and empower remote and disadvantaged subgroups in need of accurate and effective information, assessment, and care. This platform has potential to advance scientific research by supporting the collection of data with instruments tailored to specific scientific questions from large, distributed, and diverse populations. Methods: We conducted a search for tools that satisfy the above requirements. We designed and developed a new software platform called "MindLogger" that exceeds the above requirements. To demonstrate the tool9s configurability, we built multiple "applets" (collections of activities) within the MindLogger mobile application and deployed several, including a comprehensive set of assessments underway in a large-scale, longitudinal, mental health study. Results: Of the hundreds of products we researched, we found 10 that met our primary requirements above with 4 that support end-to-end encryption, 2 that enable restricted access to individual users9 data, 1 that provides open source software, and none that satisfy all three. We compared features related to information presentation and data capture capabilities, privacy and security, and access to the product, code, and data. We successfully built MindLogger mobile and web applications, as well as web browser-based tools for building and editing new applets and for administering them to end users. MindLogger has end-to-end encryption, enables restricted access, is open source, and supports a variety of data collection features. One applet is currently collecting data from children and adolescents in our mental health study, and other applets are in different stages of testing and deployment for use in clinical and research settings. Conclusions: We have demonstrated the flexibility and applicability of the MindLogger platform through its deployment in a large-scale, longitudinal, mobile mental health study, and by building a variety of other mental health-related applets. With this release, we encourage a broad range of users to apply the MindLogger platform to create and test applets to advance health care and scientific research. We hope that increasing availability of applets designed to assess and administer interventions will facilitate access to health care in the general population.

Software Tool to Read, Represent, Manipulate, and Apply N-Dimensional Spatial Transforms

Abstract: Spatial transforms formalize mappings between coordinates of objects in biomedical images. Transforms typically are the outcome of image registration methodologies, which estimate the alignment between two images. Image registration is a prominent task present in nearly all standard image processing and analysis pipelines. The proliferation of software implementations of image registration methodologies has resulted in a spread of data structures and file formats used to preserve and communicate transforms. This segregation of formats hinders the compatibility between tools and endangers the reproducibility of results. We propose a software tool capable of converting between formats and resampling images to apply transforms generated by the most popular neuroimaging packages and libraries (AFNI, FSL, FreeSurfer, ITK, and SPM). The proposed software is subject to continuous integration tests to check the compatibility with each supported tool after every change to the code base (https://github.com/poldracklab/nitransforms). Compatibility between software tools and imaging formats is a necessary bridge to ensure the reproducibility of results and enable the optimization and evaluation of current image processing and analysis workflows.