This comprehensive review aims to clarify the growing impact of Transformer‐based models in the fields of neuroscience, neurology, and psychiatry. Originally developed as a solution for analyzing sequential data, the Transformer architecture has evolved to effectively capture complex spatiotemporal relationships and long‐range dependencies that are common in biomedical data. Its adaptability and effectiveness in deciphering intricate patterns within medical studies have established it as a key tool in advancing our understanding of neural functions and disorders, representing a significant departure from traditional computational methods. The review begins by introducing the structure and principles of Transformer architectures. It then explores their applicability, ranging from disease diagnosis and prognosis to the evaluation of cognitive processes and neural decoding. The specific design modifications tailored for these applications and their subsequent impact on performance are also discussed. We conclude by providing a comprehensive assessment of recent advancements, prevailing challenges, and future directions, highlighting the shift in neuroscientific research and clinical practice towards an artificial intelligence‐centric paradigm, particularly given the prominence of Transformer architecture in the most successful large pre‐trained models. This review serves as an informative reference for researchers, clinicians, and professionals who are interested in understanding and harnessing the transformative potential of Transformer‐based models in neuroscience, neurology, and psychiatry.

Brain imaging genetics studies the genetic basis of brain structures and functionalities via integrating genotypic data such as single nucleotide polymorphisms (SNPs) and imaging quantitative traits (QTs). In this area, both multi-task learning (MTL) and sparse canonical correlation analysis (SCCA) methods are widely used since they are superior to those independent and pairwise univariate analysis. MTL methods generally incorporate a few of QTs and could not select features from multiple QTs; while SCCA methods typically employ one modality of QTs to study its association with SNPs. Both MTL and SCCA are computational expensive as the number of SNPs increases. In this paper, we propose a novel multi-task SCCA (MTSCCA) method to identify bi-multivariate associations between SNPs and multi-modal imaging QTs. MTSCCA could make use of the complementary information carried by different imaging modalities. MTSCCA enforces sparsity at the group level via the ${\mathrm G}_{2,1}$ -norm, and jointly selects features across multiple tasks for SNPs and QTs via the $\ell _{2,1}$ -norm. A fast optimization algorithm is proposed using the grouping information of SNPs. Compared with conventional SCCA methods, MTSCCA obtains better correlation coefficients and canonical weights patterns. In addition, MTSCCA runs very fast and easy-to-implement, indicating its potential power in genome-wide brain-wide imaging genetics.

Background: Adverse drug events (ADEs) often occur as a result of drug-drug interactions (DDIs). The use of data mining for detecting effects of drug combinations on ADE has attracted growing attention and interest, however, most studies focused on analyzing pairwise DDIs. Recent efforts have been made to explore the directional relationships among high-dimensional drug combinations and have shown effectiveness on prediction of ADE risk. However, the existing approaches become inefficient from both computational and illustrative perspectives when considering more than three drugs. Methods: We proposed an efficient approach to estimate the directional effects of high-order DDIs through frequent itemset mining, and further developed a novel visualization method to organize and present the high-order directional DDI effects involving more than three drugs in an interactive, concise and comprehensive manner. We demonstrated its performance by mining the directional DDIs associated with myopathy using a publicly available FAERS dataset. Results: Directional effects of DDIs involving up to seven drugs were reported. Our analysis confirmed previously reported myopathy associated DDIs including interactions between fusidic acid with simvastatin and atorvastatin. Furthermore, we uncovered a number of novel DDIs leading to increased risk for myopathy, such as the co-administration of zoledronate with different types of drugs including antibiotics (ciprofloxacin, levofloxacin) and analgesics (acetaminophen, fentanyl, gabapentin, oxycodone). Finally, we visualized directional DDI findings via the proposed tool, which allows one to interactively select any drug combination as the baseline and zoom in/out to obtain both detailed and overall picture of interested drugs. Conclusions: We developed a more efficient data mining strategy to identify high-order directional DDIs, and designed a scalable tool to visualize high-order DDI findings. The proposed method and tool have the potential to contribute to the drug interaction research and ultimately impact patient health care. Availability and implementation: http://lishenlab.com/d3i/explorer.html