Modern Views of Machine Learning for Precision Psychiatry

In light of the NIMH's Research Domain Criteria (RDoC), the advent of functional neuroimaging, novel technologies and methods provide new opportunities to develop precise and personalized prognosis and diagnosis of mental disorders. Machine learning (ML) and artificial intelligence (AI) technologies are playing an increasingly critical role in the new era of precision psychiatry. Combining ML/AI with neuromodulation technologies can potentially provide explainable solutions in clinical practice and effective therapeutic treatment. Advanced wearable and mobile technologies also call for the new role of ML/AI for digital phenotyping in mobile mental health. In this review, we provide a comprehensive review of the ML methodologies and applications by combining neuroimaging, neuromodulation, and advanced mobile technologies in psychiatry practice. Additionally, we review the role of ML in molecular phenotyping and cross-species biomarker identification in precision psychiatry. We further discuss explainable AI (XAI) and causality testing in a closed-human-in-the-loop manner, and highlight the ML potential in multimedia information extraction and multimodal data fusion. Finally, we discuss conceptual and practical challenges in precision psychiatry and highlight ML opportunities in future research

AI-based dimensional neuroimaging system for characterizing heterogeneity in brain structure and function in major depressive disorder:COORDINATE-MDD consortium design and rationale

BACKGROUND: Efforts to develop neuroimaging-based biomarkers in major depressive disorder (MDD), at the individual level, have been limited to date. As diagnostic criteria are currently symptom-based, MDD is conceptualized as a disorder rather than a disease with a known etiology; further, neural measures are often confounded by medication status and heterogeneous symptom states. METHODS: We describe a consortium to quantify neuroanatomical and neurofunctional heterogeneity via the dimensions of novel multivariate coordinate system (COORDINATE-MDD). Utilizing imaging harmonization and machine learning methods in a large cohort of medication-free, deeply phenotyped MDD participants, patterns of brain alteration are defined in replicable and neurobiologically-based dimensions and offer the potential to predict treatment response at the individual level. International datasets are being shared from multi-ethnic community populations, first episode and recurrent MDD, which are medication-free, in a current depressive episode with prospective longitudinal treatment outcomes and in remission. Neuroimaging data consist of de-identified, individual, structural MRI and resting-state functional MRI with additional positron emission tomography (PET) data at specific sites. State-of-the-art analytic methods include automated image processing for extraction of anatomical and functional imaging variables, statistical harmonization of imaging variables to account for site and scanner variations, and semi-supervised machine learning methods that identify dominant patterns associated with MDD from neural structure and function in healthy participants. RESULTS: We are applying an iterative process by defining the neural dimensions that characterise deeply phenotyped samples and then testing the dimensions in novel samples to assess specificity and reliability. Crucially, we aim to use machine learning methods to identify novel predictors of treatment response based on prospective longitudinal treatment outcome data, and we can externally validate the dimensions in fully independent sites. CONCLUSION: We describe the consortium, imaging protocols and analytics using preliminary results. Our findings thus far demonstrate how datasets across many sites can be harmonized and constructively pooled to enable execution of this large-scale project

Towards literature-based feature selection for diagnostic classification: A meta-analysis of resting-state fMRI in depression

Information derived from functional magnetic resonance imaging (fMRI) during wakeful rest has been introduced as a candidate diagnostic biomarker in unipolar major depressive disorder (MDD). Multiple reports of resting state fMRI in MDD describe group effects. Such prior knowledge can be adopted to pre-select potentially discriminating features for diagnostic classification models with the aim to improve diagnostic accuracy. Purpose of this analysis was to consolidate spatial information about alterations of spontaneous brain activity in MDD, primarily to serve as feature selection for multivariate pattern analysis techniques (MVPA). Thirty two studies were included in final analyses. Coordinates extracted from the original reports were assigned to two categories based on directionality of findings. Meta-analyses were calculated using the non-additive activation likelihood estimation approach with coordinates organized by subject group to account for non-independent samples. Converging evidence revealed a distributed pattern of brain regions with increased or decreased spontaneous activity in MDD. The most distinct finding was hyperactivity/hyperconnectivity presumably reflecting the interaction of cortical midline structures (posterior default mode network components including the precuneus and neighboring posterior cingulate cortices associated with self-referential processing and the subgenual anterior cingulate and neighboring medial frontal cortices) with lateral prefrontal areas related to externally-directed cognition. Other areas of hyperactivity/hyperconnectivity include the left lateral parietal cortex, right hippocampus and right cerebellum whereas hypoactivity/hypoconnectivity was observed mainly in the left temporal cortex, the insula, precuneus, superior frontal gyrus, lentiform nucleus and thalamus. Results are made available in two different data formats to be used as spatial hypotheses in future studies, particularly for diagnostic classification by MVPA

Predicting the future:Clinical outcome prediction with machine learning in neuropsychiatry

Treatment of psychiatric disorders relies on subjective measures of symptoms to establish diagnoses and lacks an objective way to determine which treatments might work best for an individual patient. To improve the current state-of-the-art and to be able to help a growing number of patients with mental health disorders more efficiently, the discovery of biomarkers predictive of treatment outcome and prognosis is needed. In addition, the application of machine learning methods provides an improvement over the standard group-level analysis approach since it allows for individualized predictions. Machine learning models can also be tested for their generalization capabilities to new patients which would quantify their potential for clinical applicability. In this thesis, these approaches were combined and investigated across a set of different neuropsychiatric disorders. The investigated applications included the prediction of disease course in patients with anxiety disorders, early detection of behavioural frontotemporal dementia in at-risk individuals using structural magnetic resonance imaging (MRI), prediction of deep-brain stimulation treatment-outcome in patients with therapy-resistant obsessive compulsive disorder using structural MRI and prediction of treatment-response for adult and youth patients with posttraumatic stress disorder using resting-state functional MRI scans. Across all studies this thesis showed that machine learning methods combined with neuroimaging data can be utilized to identify biomarkers predictive of future clinical outcomes in neuropsychiatric disorders. Promising as it seems, this can only be the first step for the inclusion of these new approaches into clinical practice as further studies utilizing larger sample sizes are necessary to validate the discovered biomarkers

Addressing heterogeneity (and homogeneity) in treatment mechanisms in depression and the potential to develop diagnostic and predictive biomarkers

It has been 10 years since machine learning was first applied to neuroimaging data in psychiatric disorders to identify diagnostic and prognostic markers at the level of the individual. Proof of concept findings in major depression have since been extended in international samples and are beginning to include hundreds of samples from multisite data. Neuroimaging provides the unique capability to detect an acute depressive state in major depression, while we would not expect perfect classification with current diagnostic criteria which are based solely on clinical features. We review developments and the potential impact of heterogeneity, as well as homogeneity, on classification for diagnosis and prediction of clinical outcome. It is likely that there are distinct biotypes which comprise the disorder and which predict clinical outcome. Neuroimaging-based biotypes could aid in identifying the illness in individuals who are unable to recognise their illness and perhaps to identify the treatment resistant form early in the course of the illness. We propose that heterogeneous symptom profiles can arise from a limited number of neural biotypes and that apparently heterogeneous clinical outcomes include a common baseline predictor and common mechanism of treatment. Baseline predictors of clinical outcome reflect factors which indicate the general likelihood of response as well as those which are selective for a particular form of treatment. Irrespective of the mechanism, the capacity for response will moderate the outcome, which includes inherent models of interpersonal relationships that could be associated with genetic risk load and represented by patterns of functional and structural neural correlates as a predictive biomarker. We propose that methods which directly address heterogeneity are essential and that a synergistic combination could bring together data-driven inductive and symptom-based deductive approaches. Through this iterative process, major depression can develop from being syndrome characterized by a collection of symptoms to a disease with an identifiable pathophysiology

Development And Evaluation Of A Multimodal Marker Of Major Depressive Disorder

This study aimed to identify biomarkers of major depressive disorder (MDD), by relating neuroimage-derived measures to binary (MDD/control), ordinal (severe MDD/mild MDD/control), or continuous (depression severity) outcomes. To address MDD heterogeneity, factors (severity of psychic depression, motivation, anxiety, psychosis, and sleep disturbance) were also used as outcomes. A multisite, multimodal imaging (diffusion MRI [dMRI] and structural MRI [sMRI]) cohort (52 controls and 147 MDD patients) and several modeling techniques—penalized logistic regression, random forest, and support vector machine (SVM)—were used. An additional cohort (25 controls and 83 MDD patients) was used for validation. The optimally performing classifier (SVM) had a 26.0% misclassification rate (binary), 52.2 ± 1.69% accuracy (ordinal) and r = .36 correlation coefficient (p < .001, continuous). Using SVM, R2 values for prediction of any MDD factors were <10%. Binary classification in the external data set resulted in 87.95% sensitivity and 32.00% specificity. Though observed classification rates are too low for clinical utility, four image-based features contributed to accuracy across all models and analyses—two dMRI-based measures (average fractional anisotropy in the right cuneus and left insula) and two sMRI-based measures (asymmetry in the volume of the pars triangularis and the cerebellum) and may serve as a priori regions for future analyses. The poor accuracy of classification and predictive results found here reflects current equivocal findings and sheds light on challenges of using these modalities for MDD biomarker identification. Further, this study suggests a paradigm (e.g., multiple classifier evaluation with external validation) for future studies to avoid nongeneralizable results

Superior longitudinal fasciculus microstructure and its functional triple-network mechanisms in depressive rumination

Depressive rumination, which involves a repetitive focus on one's distress, is associated with function connectivity disturbances of Default-Mode, Salience, and Executive-Control networks, comprising the so-called "triple-network" of attention. Missing, however, is a multimodal account of rumination that neuroanatomically explains the perseveration of these dysfunctional networks as a stable human trait. Using diffusion and functional Magnetic Resonance Imaging, we explored multimodal relationships between rumination severity, white-matter microstructure, and resting-state functional connectivity in N=39 depressed adults, and then directly replicated our findings in a demographically-matched, independent sample (N=39). Among the fully-replicated results, three core findings emerged. First, rumination severity is associated with both disintegrated and desegregated functional connectivity of the triple-network. Second, global microstructural inefficiency of the right Superior Longitudinal Fasciculus (SLF) provides a neuroanatomical connectivity basis for rumination and accounts for anywhere between 25-37% of the variance in rumination (Discovery: p corr<0.01; Replication: p corr<0.01; MSE=0.05). Finally, microstructure of the right SLF and auxiliary white-matter is strongly associated with functional connectivity biomarkers of rumination, both within and between components of the triple-network (Discovery: R²=0.36, p corr<0.05; Replication: R²=0.25, p corr<0.05; MSE=0.04-0.06). By cross-validating discovery with replication, our findings advance a reproducible microstructural-functional brain connectivity model of depressive rumination that unifies neurodevelopmental and neurocognitive perspectives.Psycholog