Multisite schizophrenia classification by integrating structural magnetic resonance imaging data with polygenic risk score

Exploring Schizophrenia Classification Through Multimodal MRI and Deep Graph Neural Networks: Unveiling Brain Region-Specific Weight Discrepancies and Their Association With Cell-Type Specific Transcriptomic Features

BACKGROUND AND HYPOTHESIS

Schizophrenia (SZ) is a prevalent mental disorder that imposes significant health burdens. Diagnostic accuracy remains challenging due to clinical subjectivity. To address this issue, we explore magnetic resonance imaging (MRI) as a tool to enhance SZ diagnosis and provide objective references and biomarkers. Using deep learning with graph convolution, we represent MRI data as graphs, aligning with brain structure, and improving feature extraction, and classification. Integration of multiple modalities is expected to enhance classification.

STUDY DESIGN

Our study enrolled 683 SZ patients and 606 healthy controls from 7 hospitals, collecting structural MRI and functional MRI data. Both data types were represented as graphs, processed by 2 graph attention networks, and fused for classification. Grad-CAM with graph convolution ensured interpretability, and partial least squares analyzed gene expression in brain regions.

STUDY RESULTS

Our method excelled in the classification task, achieving 83.32% accuracy, 83.41% sensitivity, and 83.20% specificity in 10-fold cross-validation, surpassing traditional methods. And our multimodal approach outperformed unimodal methods. Grad-CAM identified potential brain biomarkers consistent with gene analysis and prior research.

CONCLUSIONS

Our study demonstrates the effectiveness of deep learning with graph attention networks, surpassing previous SZ diagnostic methods. Multimodal MRI's superiority over unimodal MRI confirms our initial hypothesis. Identifying potential brain biomarkers alongside gene biomarkers holds promise for advancing objective SZ diagnosis and research in SZ.

Schizophrenia and Neurodevelopment: Insights From Connectome Perspective

BACKGROUND

Schizophrenia is conceptualized as a brain connectome disorder that can emerge as early as late childhood and adolescence. However, the underlying neurodevelopmental basis remains unclear. Recent interest has grown in children and adolescent patients who experience symptom onset during critical brain development periods. Inspired by advanced methodological theories and large patient cohorts, Chinese researchers have made significant original contributions to understanding altered brain connectome development in early-onset schizophrenia (EOS).

STUDY DESIGN

We conducted a search of PubMed and Web of Science for studies on brain connectomes in schizophrenia and neurodevelopment. In this selective review, we first address the latest theories of brain structural and functional development. Subsequently, we synthesize Chinese findings regarding mechanisms of brain structural and functional abnormalities in EOS. Finally, we highlight several pivotal challenges and issues in this field.

STUDY RESULTS

Typical neurodevelopment follows a trajectory characterized by gray matter volume pruning, enhanced structural and functional connectivity, improved structural connectome efficiency, and differentiated modules in the functional connectome during late childhood and adolescence. Conversely, EOS deviates with excessive gray matter volume decline, cortical thinning, reduced information processing efficiency in the structural brain network, and dysregulated maturation of the functional brain network. Additionally, common functional connectome disruptions of default mode regions were found in early- and adult-onset patients.

CONCLUSIONS

Chinese research on brain connectomes of EOS provides crucial evidence for understanding pathological mechanisms. Further studies, utilizing standardized analyses based on large-sample multicenter datasets, have the potential to offer objective markers for early intervention and disease treatment.

Neuroimage Analysis Methods and Artificial Intelligence Techniques for Reliable Biomarkers and Accurate Diagnosis of Schizophrenia: Achievements Made by Chinese Scholars Around the Past Decade

BACKGROUND AND HYPOTHESIS

Schizophrenia (SZ) is characterized by significant cognitive and behavioral disruptions. Neuroimaging techniques, particularly magnetic resonance imaging (MRI), have been widely utilized to investigate biomarkers of SZ, distinguish SZ from healthy conditions or other mental disorders, and explore biotypes within SZ or across SZ and other mental disorders, which aim to promote the accurate diagnosis of SZ. In China, research on SZ using MRI has grown considerably in recent years.

STUDY DESIGN

The article reviews advanced neuroimaging and artificial intelligence (AI) methods using single-modal or multimodal MRI to reveal the mechanism of SZ and promote accurate diagnosis of SZ, with a particular emphasis on the achievements made by Chinese scholars around the past decade.

STUDY RESULTS

Our article focuses on the methods for capturing subtle brain functional and structural properties from the high-dimensional MRI data, the multimodal fusion and feature selection methods for obtaining important and sparse neuroimaging features, the supervised statistical analysis and classification for distinguishing disorders, and the unsupervised clustering and semi-supervised learning methods for identifying neuroimage-based biotypes. Crucially, our article highlights the characteristics of each method and underscores the interconnections among various approaches regarding biomarker extraction and neuroimage-based diagnosis, which is beneficial not only for comprehending SZ but also for exploring other mental disorders.

CONCLUSIONS

We offer a valuable review of advanced neuroimage analysis and AI methods primarily focused on SZ research by Chinese scholars, aiming to promote the diagnosis, treatment, and prevention of SZ, as well as other mental disorders, both within China and internationally.

Diagnosing schizophrenia using deep learning: Novel interpretation approaches and multi-site validation

Schizophrenia is a profound and enduring mental disorder that imposes significant negative impacts on individuals, their families, and society at large. The development of more accurate and objective diagnostic tools for schizophrenia can be expedited through the employment of deep learning (DL), that excels at deciphering complex hierarchical non-linear patterns. However, the limited interpretability of deep learning has eroded confidence in the model and restricted its clinical utility. At the same time, if the data source is only derived from a single center, the model's generalizability is difficult to test. To enhance the model's reliability and applicability, leave-one-center-out validation with a large and diverse sample from multiple centers is crucial. In this study, we utilized Nine different global centers to train and test the 3D Resnet model's generalizability, resulting in an 82% classification performance (area under the curve) on all datasets sourced from different countries, employing a leave-one-center-out-validation approach. Per our approximation of the feature significance of each region on the atlas, we identified marked differences in the thalamus, pallidum, and inferior frontal gyrus between individuals with schizophrenia and healthy controls, lending credence to prior research findings. At the same time, in order to translate the model's output into clinically applicable insights, the SHapley Additive exPlanations (SHAP) permutation explainer method with an anatomical atlas have been refined, thereby offering precise neuroanatomical and functional interpretations of different brain regions.

Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance

Many studies have been conducted with the goal of correctly predicting diagnostic status of a disorder using the combination of genomic data and machine learning. It is often hard to judge which components of a study led to better results and whether better reported results represent a true improvement or an uncorrected bias inflating performance. We extracted information about the methods used and other differentiating features in genomic machine learning models. We used these features in linear regressions predicting model performance. We tested for univariate and multivariate associations as well as interactions between features. Of the models reviewed, 46% used feature selection methods that can lead to data leakage. Across our models, the number of hyperparameter optimizations reported, data leakage due to feature selection, model type, and modeling an autoimmune disorder were significantly associated with an increase in reported model performance. We found a significant, negative interaction between data leakage and training size. Our results suggest that methods susceptible to data leakage are prevalent among genomic machine learning research, resulting in inflated reported performance. Best practice guidelines that promote the avoidance and recognition of data leakage may help the field avoid biased results.

Dissecting Psychiatric Heterogeneity and Comorbidity with Core Region-Based Machine Learning

Machine learning approaches are increasingly being applied to neuroimaging data from patients with psychiatric disorders to extract brain-based features for diagnosis and prognosis. The goal of this review is to discuss recent practices for evaluating machine learning applications to obsessive-compulsive and related disorders and to advance a novel strategy of building machine learning models based on a set of core brain regions for better performance, interpretability, and generalizability. Specifically, we argue that a core set of co-altered brain regions (namely 'core regions') comprising areas central to the underlying psychopathology enables the efficient construction of a predictive model to identify distinct symptom dimensions/clusters in individual patients. Hypothesis-driven and data-driven approaches are further introduced showing how core regions are identified from the entire brain. We demonstrate a broadly applicable roadmap for leveraging this core set-based strategy to accelerate the pursuit of neuroimaging-based markers for diagnosis and prognosis in a variety of psychiatric disorders.

Psychotic Symptom, Mood, and Cognition-associated Multimodal MRI Reveal Shared Links to the Salience Network Within the Psychosis Spectrum Disorders

Schizophrenia (SZ), schizoaffective disorder (SAD), and psychotic bipolar disorder share substantial overlap in clinical phenotypes, associated brain abnormalities and risk genes, making reliable diagnosis among the three illness challenging, especially in the absence of distinguishing biomarkers. This investigation aims to identify multimodal brain networks related to psychotic symptom, mood, and cognition through reference-guided fusion to discriminate among SZ, SAD, and BP. Psychotic symptom, mood, and cognition were used as references to supervise functional and structural magnetic resonance imaging (MRI) fusion to identify multimodal brain networks for SZ, SAD, and BP individually. These features were then used to assess the ability in discriminating among SZ, SAD, and BP. We observed shared links to functional and structural covariation in prefrontal, medial temporal, anterior cingulate, and insular cortices among SZ, SAD, and BP, although they were linked with different clinical domains. The salience (SAN), default mode (DMN), and fronto-limbic (FLN) networks were the three identified multimodal MRI features within the psychosis spectrum disorders from psychotic symptom, mood, and cognition associations. In addition, using these networks, we can classify patients and controls and distinguish among SZ, SAD, and BP, including their first-degree relatives. The identified multimodal SAN may be informative regarding neural mechanisms of comorbidity for psychosis spectrum disorders, along with DMN and FLN may serve as potential biomarkers in discriminating among SZ, SAD, and BP, which may help investigators better understand the underlying mechanisms of psychotic comorbidity from three different disorders via a multimodal neuroimaging perspective.

Predicting Treatment Response in Schizophrenia With Magnetic Resonance Imaging and Polygenic Risk Score

Background: Prior studies have separately demonstrated that magnetic resonance imaging (MRI) and schizophrenia polygenic risk score (PRS) are predictive of antipsychotic medication treatment outcomes in schizophrenia. However, it remains unclear whether MRI combined with PRS can provide superior prognostic performance. Besides, the relative importance of these measures in predictions is not investigated.

Methods: We collected 57 patients with schizophrenia, all of which had baseline MRI and genotype data. All these patients received approximately 6 weeks of antipsychotic medication treatment. Psychotic symptom severity was assessed using the Positive and Negative Syndrome Scale (PANSS) at baseline and follow-up. We divided these patients into responders (N = 20) or non-responders (N = 37) based on whether their percentages of PANSS total reduction were above or below 50%. Nine categories of MRI measures and PRSs with 145 different p-value thresholding ranges were calculated. We trained machine learning classifiers with these baseline predictors to identify whether a patient was a responder or non-responder.

Results: The extreme gradient boosting (XGBoost) technique was applied to build binary classifiers. Using a leave-one-out cross-validation scheme, we achieved an accuracy of 86% with all MRI and PRS features. Other metrics were also estimated, including sensitivity (85%), specificity (86%), F1-score (81%), and area under the receiver operating characteristic curve (0.86). We found excluding a single feature category of gray matter volume (GMV), amplitude of low-frequency fluctuation (ALFF), and surface curvature could lead to a maximum accuracy drop of 10.5%. These three categories contributed more than half of the top 10 important features. Besides, removing PRS features caused a modest accuracy drop (8.8%), which was not the least decrease (1.8%) among all feature categories.

Conclusions: Our classifier using both MRI and PRS features was stable and not biased to predicting either responder or non-responder. Combining with MRI measures, PRS could provide certain extra predictive power of antipsychotic medication treatment outcomes in schizophrenia. PRS exhibited medium importance in predictions, lower than GMV, ALFF, and surface curvature, but higher than measures of cortical thickness, cortical volume, and surface sulcal depth. Our findings inform the contributions of PRS in predictions of treatment outcomes in schizophrenia.