This study presents a trial analysis that uses brain activity information obtained from mice to detect rheumatoid arthritis (RA) in its presymptomatic stages. Specifically, we confirmed that F759 mice, serving as a mouse model of RA that is dependent on the inflammatory cytokine IL-6, and healthy wild-type mice can be classified on the basis of brain activity information. We clarified which brain regions are useful for the presymptomatic detection of RA. We introduced a matrix completion-based approach to handle missing brain activity information to perform the aforementioned analysis. In addition, we implemented a canonical correlation-based method capable of analyzing the relationship between various types of brain activity information. This method allowed us to accurately classify F759 and wild-type mice, thereby identifying essential features, including crucial brain regions, for the presymptomatic detection of RA. Our experiment obtained brain activity information from 15 F759 and 10 wild-type mice and analyzed the acquired data. By employing four types of classifiers, our experimental results show that the thalamus and periaqueductal gray are effective for the classification task. Furthermore, we confirmed that classification performance was maximized when seven brain regions were used, excluding the electromyogram and nucleus accumbens.

Motor performance (MP) is essential for functional independence and well-being, particularly in later life. However, the relationship between behavioural aspects such as sleep quality and depressive symptoms, which contribute to MP, and the underlying structural brain substrates of their interplay remains unclear. This study used three population-based cohorts of younger and older adults (n=1,950) from the Human Connectome Project-Young Adult (HCP-YA), HCP-Aging (HCP-A), and enhanced Nathan Kline Institute-Rockland sample (eNKI-RS). Several canonical correlation analyses were computed within a machine learning framework to assess the associations between each of the three domains (sleep quality, depressive symptoms, grey matter volume (GMV)) and MP. The HCP-YA analyses showed progressively stronger associations between MP and each domain: depressive symptoms (unexpectedly positive, r=0.13, SD=0.06), sleep quality (r=0.17, SD=0.05), and GMV (r=0.19, SD=0.06). Combining sleep and depressive symptoms significantly improved the canonical correlations (r=0.25, SD=0.05), while the addition of GMV exhibited no further increase (r=0.23, SD=0.06). In young adults, better sleep quality, mild depressive symptoms, and GMV of several brain regions were associated with better MP. This was conceptually replicated in young adults from the eNKI-RS cohort. In HCP-Aging, better sleep quality, fewer depressive symptoms, and increased GMV were associated with MP. Robust multivariate associations were observed between sleep quality, depressive symptoms and GMV with MP, as well as age-related variations in these factors. Future studies should further explore these associations and consider interventions targeting sleep and mental health to test the potential effects on MP across the lifespan.

BACKGROUND: The advent of multimodal omics data has provided an unprecedented opportunity to systematically investigate underlying biological mechanisms from distinct yet complementary angles. However, the joint analysis of multi-omics data remains challenging because it requires modeling interactions between multiple sets of high-throughput variables. Furthermore, these interaction patterns may vary across different clinical groups, reflecting disease-related biological processes.
RESULTS: We propose a novel approach called Differential Canonical Correlation Analysis (dCCA) to capture differential covariation patterns between two multivariate vectors across clinical groups. Unlike classical Canonical Correlation Analysis, which maximizes the correlation between two multivariate vectors, dCCA aims to maximally recover differentially expressed multivariate-to-multivariate covariation patterns between groups. We have developed computational algorithms and a toolkit to sparsely select paired subsets of variables from two sets of multivariate variables while maximizing the differential covariation. Extensive simulation analyses demonstrate the superior performance of dCCA in selecting variables of interest and recovering differential correlations. We applied dCCA to the Pan-Kidney cohort from the Cancer Genome Atlas Program database and identified differentially expressed covariations between noncoding RNAs and gene expressions.
METHODS: The R package that implements dCCA is available at https://github.com/hwiyoungstat/dCCA.

Steady-state visual evoked potentials (SSVEP) are generated in the parieto-occipital regions, accompanied by background noise and artifacts. A strong pre-processing method is required to reduce this background noise and artifacts. This study proposed a narrow band-pass filtered canonical correlation analysis (NBPFCCA) to recognize frequency components in SSVEP signals. The proposed method is tested on the publicly available 40 stimulus frequencies dataset recorded from 35 subjects and 4 class in-house dataset acquired from 10 subjects. The performance of the proposed NBPFCCA method is compared with the standard canonical correlation analysis (CCA) and the filter bank CCA (FBCCA). The mean frequency detection accuracy of the standard CCA is 86.21% for the benchmark dataset, and it is improved to 95.58% in the proposed method. Results indicate that the proposed method significantly outperforms the standard canonical correlation analysis with an increase of 9.37% and 17% in frequency recognition accuracy of the benchmark and in-house datasets, respectively.

Mapping brain-behaviour associations is paramount to understand and treat psychiatric disorders. Standard approaches involve investigating the association between one brain and one behavioural variable (univariate) or multiple variables against one brain/behaviour feature (\'single\' multivariate). Recently, large multimodal datasets have propelled a new wave of studies that leverage on \'doubly\' multivariate approaches capable of parsing the multifaceted nature of both brain and behaviour simultaneously. Within this movement, canonical correlation analysis (CCA) and partial least squares (PLS) emerge as the most popular techniques. Both seek to capture shared information between brain and behaviour in the form of latent variables. We provide an overview of these methods, review the literature in psychiatric disorders, and discuss the main challenges from a predictive modelling perspective. We identified 39 studies across four diagnostic groups: attention deficit and hyperactive disorder (ADHD, k = 4, N = 569), autism spectrum disorders (ASD, k = 6, N = 1731), major depressive disorder (MDD, k = 5, N = 938), psychosis spectrum disorders (PSD, k = 13, N = 1150) and one transdiagnostic group (TD, k = 11, N = 5731). Most studies (67%) used CCA and focused on the association between either brain morphology, resting-state functional connectivity or fractional anisotropy against symptoms and/or cognition. There were three main findings. First, most diagnoses shared a link between clinical/cognitive symptoms and two brain measures, namely frontal morphology/brain activity and white matter association fibres (tracts between cortical areas in the same hemisphere). Second, typically less investigated behavioural variables in multivariate models such as physical health (e.g., BMI, drug use) and clinical history (e.g., childhood trauma) were identified as important features. Finally, most studies were at risk of bias due to low sample size/feature ratio and/or in-sample testing only. We highlight the importance of carefully mitigating these sources of bias with an exemplar application of CCA.

Glioma is currently one of the most prevalent types of primary brain cancer. Given its high level of heterogeneity along with the complex biological molecular markers, many efforts have been made to accurately classify the type of glioma in each patient, which, in turn, is critical to improve early diagnosis and increase survival. Nonetheless, as a result of the fast-growing technological advances in high-throughput sequencing and evolving molecular understanding of glioma biology, its classification has been recently subject to significant alterations. In this study, we integrate multiple glioma omics modalities (including mRNA, DNA methylation, and miRNA) from The Cancer Genome Atlas (TCGA), while using the revised glioma reclassified labels, with a supervised method based on sparse canonical correlation analysis (DIABLO) to discriminate between glioma types. We were able to find a set of highly correlated features distinguishing glioblastoma from lower-grade gliomas (LGGs) that were mainly associated with the disruption of receptor tyrosine kinases signaling pathways and extracellular matrix organization and remodeling. Concurrently, the discrimination of the LGG types was characterized primarily by features involved in ubiquitination and DNA transcription processes. Furthermore, we could identify several novel glioma biomarkers likely helpful in both diagnosis and prognosis of the patients, including the genes PPP1R8, GPBP1L1, KIAA1614, C14orf23, CCDC77, BVES, EXD3, CD300A, and HEPN1. Collectively, this comprehensive approach not only allowed a highly accurate discrimination of the different TCGA glioma patients but also presented a step forward in advancing our comprehension of the underlying molecular mechanisms driving glioma heterogeneity. Ultimately, our study also revealed novel candidate biomarkers that might constitute potential therapeutic targets, marking a significant stride toward personalized and more effective treatment strategies for patients with glioma.

Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease that typically manifests late patient presentation and poor outcomes. Furthermore, PDAC recurrence is a common challenge. Distinct patterns of PDAC recurrence have been associated with differential activation of immune pathway-related genes and specific inflammatory responses in their tumour microenvironment. However, the molecular associations between and within cellular components that underpin PDAC recurrence require further development, especially from a multi-omics integration perspective. In this study, we identified stable molecular associations across multiple PDAC recurrences and utilised integrative analytics to identify stable and novel associations via simultaneous feature selection. Spatial transcriptome and proteome datasets were used to perform univariate analysis, Spearman partial correlation analysis, and univariate analyses by Machine Learning methods, including regularised canonical correlation analysis and sparse partial least squares. Furthermore, networks were constructed for reported and new stable associations. Our findings revealed gene and protein associations across multiple PDAC recurrence groups, which can provide a better understanding of the multi-layer disease mechanisms that contribute to PDAC recurrence. These findings may help to provide novel association targets for clinical studies for constructing precision medicine and personalised surveillance tools for patients with PDAC recurrence.

BACKGROUND: Classifying breast cancer subtypes is crucial for clinical diagnosis and treatment. However, the early symptoms of breast cancer may not be apparent. Rapid advances in high-throughput sequencing technology have led to generating large number of multi-omics biological data. Leveraging and integrating the available multi-omics data can effectively enhance the accuracy of identifying breast cancer subtypes. However, few efforts focus on identifying the associations of different omics data to predict the breast cancer subtypes.
RESULTS: In this paper, we propose a differential sparse canonical correlation analysis network (DSCCN) for classifying the breast cancer subtypes. DSCCN performs differential analysis on multi-omics expression data to identify differentially expressed (DE) genes and adopts sparse canonical correlation analysis (SCCA) to mine highly correlated features between multi-omics DE-genes. Meanwhile, DSCCN uses multi-task deep learning neural network separately to train the correlated DE-genes to predict breast cancer subtypes, which spontaneously tackle the data heterogeneity problem in integrating multi-omics data.
CONCLUSIONS: The experimental results show that by mining the associations among multi-omics data, DSCCN is more capable of accurately classifying breast cancer subtypes than the existing methods.

BACKGROUND: Adolescent depression shows high clinical heterogeneity. Brain functional networks serve as a powerful tool for investigating neural mechanisms underlying depression profiles. A key challenge is to characterize how variation in brain functional organization links to behavioral features and psychosocial environmental influences.
METHODS: We recruited 80 adolescents with major depressive disorder (MDD) and 42 healthy controls (HCs). First, we estimated the differences in functional connectivity of resting-state networks (RSN) between the two groups. Then, we used sparse canonical correlation analysis to characterize patterns of associations between RSN connectivity and symptoms, cognition, and psychosocial environmental factors in MDD adolescents. Clustering analysis was applied to stratify patients into homogenous subtypes according to these brain-behavior-environment associations.
RESULTS: MDD adolescents showed significantly hyperconnectivity between the ventral attention and cingulo-opercular networks compared with HCs. We identified one reliable pattern of covariation between RSN connectivity and clinical/environmental features in MDD adolescents. In this pattern, psychosocial factors, especially the interpersonal and family relationships, were major contributors to variation in connectivity of salience, cingulo-opercular, ventral attention, subcortical and somatosensory-motor networks. Based on this association, we categorized patients into two subgroups which showed different environment and symptoms characteristics, and distinct connectivity alterations. These differences were covered up when the patients were taken as a whole group.
CONCLUSIONS: This study identified the environmental exposures associated with specific functional networks in MDD youths. Our findings emphasize the importance of the psychosocial context in assessing brain function alterations in adolescent depression and have the potential to promote targeted treatment and precise prevention.

Commands in brain-computer interface (BCI) applications often rely on the decoding of event-related potentials (ERP). For instance, the P300 potential is frequently used as a marker of attention to an oddball event. Error-related potentials and the N2pc signal are further examples of ERPs used for BCI control. One challenge in decoding brain activity from the electroencephalogram (EEG) is the selection of the most suitable channels and appropriate features for a particular classification approach. Here we introduce a toolbox that enables ERP-based decoding using the full set of channels, while automatically extracting informative components from relevant channels. The strength of our approach is that it handles sequences of stimuli that encode multiple items using binary classification, such as target vs. nontarget events typically used in ERP-based spellers. We demonstrate examples of application scenarios and evaluate the performance of four openly available datasets: a P300-based matrix speller, a P300-based rapid serial visual presentation (RSVP) speller, a binary BCI based on the N2pc, and a dataset capturing error potentials. We show that our approach achieves performances comparable to those in the original papers, with the advantage that only conventional preprocessing is required by the user, while channel weighting and decoding algorithms are internally performed. Thus, we provide a tool to reliably decode ERPs for BCI use with minimal programming requirements.