Classification for psychiatric disorders including schizophrenia, bipolar disorder, and major depressive disorder using machine learning

Distinguishing schizophrenia and bipolar disorder through a Multiclass Classification model based on multimodal neuroimaging data

This study aimed to identify neural biomarkers for schizophrenia (SZ) and bipolar disorder (BP) by analyzing multimodal neuroimaging. Utilizing data from structural magnetic resonance imaging (sMRI), diffusion tensor imaging (DTI), and resting-state functional magnetic resonance imaging (rs-fMRI), multiclass classification models were created for SZ, BP, and healthy controls (HC). A total of 113 participants (BP: 31, SZ: 39, and HC: 43) were recruited under strict enrollment control, from which 272, 200, and 1875 features were extracted from sMRI, DTI, and rs-fMRI data, respectively. A support vector machine (SVM) with recursive feature elimination (RFE) was employed to build the models using a one-against-one approach and leave-one-out cross-validation, achieving a classification accuracy of 70.8%. The most discriminative features were primarily from rs-fMRI, along with significant findings in sMRI and DTI. Key biomarkers identified included the increased thickness of the left cuneus cortex and decreased regional functional connectivity strength (rFCS) in the left supramarginal gyrus as shared indicators for BP and SZ. Additionally, decreased fractional anisotropy in the left superior fronto-occipital fasciculus was suggested as specific to BP, while decreased rFCS in the left inferior parietal area might serve as a specific biomarker for SZ. These findings underscore the potential of multimodal neuroimaging in distinguishing between BP and SZ and contribute to the understanding of their neural underpinnings.

Testing the bipolar assumption of Singer-Loomis Type Deployment Inventory for Korean adults using classification and multidimensional scaling

In this study, we explored whether the Korean version of Singer Loomis Type Deployment Inventory II (K-SLTDI) captures the opposing tendencies of Jung's theory of psychological type. The types are Extroverted Sensing, Extroverted Intuition, Extroverted Feeling, Extroverted Thinking, Introverted Sensing, Introverted Intuition, Introverted Feeling, and Introverted Thinking. A nationwide online survey was conducted in South Korea. We performed multidimensional scaling and classification analyses based on 521 Korean adult profiles with eight psychological types to test the bipolarity assumption. The results showed that the Procrustes-rotated four-dimensional space successfully represented four types of opposing tendencies. Moreover, the bipolarity assumption in the four dimensions of Jungian typology was tested and compared between lower and higher psychological distress populations via cluster analysis. Lastly, we explored patterns of responses in lower and higher psychological distress populations using intersubject correlation. Both similarity analyses and classification results consistently support the theoretical considerations on the conceptualization of Jung's type in independent order that the types could be derived without bipolar assumption as Singer and Loomis expected in their Type Development Inventory. Limitations in our study include the sample being randomly selected internet users during the COVID-19 pandemic, despite excellence in the use of the internet in the general Korean population.

MultiClassMetabo: A Superior Classification Model Constructed Using Metabolic Markers in Multiclass Metabolomics

Multiclass metabolomics has become a popular technique for revealing the mechanisms underlying certain physiological processes, different tumor types, or different therapeutic responses. In multiclass metabolomics, it is highly important to uncover the underlying biological information on biosamples by identifying the metabolic markers with the most associations and classifying the different sample classes. The classification problem of multiclass metabolomics is more difficult than that of the binary problem. To date, various methods exist for constructing classification models and identifying metabolic markers consisting of well-established techniques and newly emerging machine learning algorithms. However, how to construct a superior classification model using these methods remains unclear for a given multiclass metabolomic data set. Herein, MultiClassMetabo has been developed for constructing a superior classification model using metabolic markers identified in multiclass metabolomics. MultiClassMetabo can enable online services, including (a) identifying metabolic markers by marker identification methods, (b) constructing classification models by classification methods, and (c) performing a comprehensive assessment from multiple perspectives to construct a superior classification model for multiclass metabolomics. In summary, MultiClassMetabo is distinguished for its capability to construct a superior classification model using the most appropriate method through a comprehensive assessment, which makes it an important complement to other available tools in multiclass metabolomics. MultiClassMetabo can be accessed at http://idrblab.cn/multiclassmetabo/.

Evaluating Machine Learning Methods of Analyzing Multiclass Metabolomics

Multiclass metabolomic studies have become popular for revealing the differences in multiple stages of complex diseases, various lifestyles, or the effects of specific treatments. In multiclass metabolomics, there are multiple data manipulation steps for analyzing raw data, which consist of data filtering, the imputation of missing values, data normalization, marker identification, sample separation, classification, and so on. In each step, several to dozens of machine learning methods can be chosen for the given data set, with potentially hundreds or thousands of method combinations in the whole data processing chain. Therefore, a clear understanding of these machine learning methods is helpful for selecting an appropriate method combination for obtaining stable and reliable analytical results of specific data. However, there has rarely been an overall introduction or evaluation of these methods based on multiclass metabolomic data. Herein, detailed descriptions of these machine learning methods in multiple data manipulation steps are reviewed. Moreover, an assessment of these methods was performed using a benchmark data set for multiclass metabolomics. First, 12 imputation methods for imputing missing values were evaluated based on the PSS (Procrustes statistical shape analysis) and NRMSE (normalized root-mean-square error) values. Second, 17 normalization methods for processing multiclass metabolomic data were evaluated by applying the PMAD (pooled median absolute deviation) value. Third, different methods of identifying markers of multiclass metabolomics were evaluated based on the CWrel (relative weighted consistency) value. Fourth, nine classification methods for constructing multiclass models were assessed using the AUC (area under the curve) value. Performance evaluations of machine learning methods are highly recommended to select the most appropriate method combination before performing the final analysis of the given data. Overall, detailed descriptions and evaluation of various machine learning methods are expected to improve analyses of multiclass metabolomic data.

miR-218-5p and miR-320a-5p as Biomarkers for Brain Disorders: Focus on the Major Depressive Disorder and Parkinson's Disease

Depression is one of the early and most persistent non-motor symptoms of Parkinson's disease (PD), which remains ignored, resulting in the underdiagnosis of PD. Unfortunately, scarce studies and the non-availability of diagnostic strategies cause countless complications, highlighting the need for appropriate diagnostic biomarkers. Recently, brain-enriched miRNAs regulating vital neurological functions have been proposed as potent biomarkers for therapeutic strategies. Therefore, the present study is aimed to identify the brain-enriched miR-218-5p and miR-320-5p in the serum of the Chinese depressed PD patients (n = 51) than healthy controls (n = 51) to identify their potency as biomarkers. For this purpose, depressive PD patients were recruited based on HAMA and HAMD scores and miR-218-5p and miR-320-5p and IL-6, and S100B levels were analyzed using real-time PCR (qRT-PCR) and ELISA assay, respectively. In silico analysis was performed to identify key biological pathways and hub genes involved in the psychopathology of depression in PD. Here, we found significantly downregulated miR-218-5p and miR-320-5p following higher levels of IL-6 and S100B in depressed PD patients than in control (p < 0.05). The correlation analysis revealed that both miRNAs were negatively correlated with HAMA and HAMD, and IL-6 scores, along with a positive correlation with PD duration and LEDD medication. ROC analysis showed AUC above 75% in both miRNAs in depressed PD patients, and in silico analysis revealed that both miRNA's targets regulate key neurological pathways such as axon guidance, dopaminergic synapse, and circadian rhythm. Additional analysis revealed PIK3R1, ATRX, BM1, PCDHA10, XRCC5, PPP1CB, MLLT3, CBL, PCDHA4, PLCG1, YWHAZ, CDH2, AGO3, PCDHA3, and PCDHA11 as hub-genes in PPI network. In summary, our findings show that miR-218-5p and miR-320-5p can be utilized as future biomarkers for depression in PD patients, which may aid in the early diagnosis and treatment of Parkinson's disease.

Critical Assessment of the Biomarker Discovery and Classification Methods for Multiclass Metabolomics

Multiclass metabolomics has been widely applied in clinical practice to understand pathophysiological processes involved in disease progression and diagnostic biomarkers of various disorders. In contrast to the binary problem, the multiclass classification problem is more difficult in terms of obtaining reliable and stable results due to the increase in the complexity of determining exact class decision boundaries. In particular, methods of biomarker discovery and classification have a significant effect on the multiclass model because different methods with significantly varied theories produce conflicting results even for the same dataset. However, a systematic assessment for selecting the most appropriate methods of biomarker discovery and classification for multiclass metabolomics is still lacking. Therefore, a comprehensive assessment is essential to measure the suitability of methods in multiclass classification models from multiple perspectives. In this study, five biomarker discovery methods and nine classification methods were assessed based on four benchmark datasets of multiclass metabolomics. The performance assessment of the biomarker discovery and classification methods was performed using three evaluation criteria: assessment a (cluster analysis of sample grouping), assessment b (biomarker consistency in multiple subgroups), and assessment c (accuracy in the classification model). As a result, 13 combining strategies with superior performance were selected under multiple criteria based on these benchmark datasets. In conclusion, superior strategies that performed consistently well are suggested for the discovery of biomarkers and the construction of a classification model for multiclass metabolomics.