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A comprehensive benchmarking for evaluating TCR embeddings in modeling TCR-epitope interactions.
Brief Bioinform
November 2024
Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, 999077, China.
The complexity of T cell receptor (TCR) sequences, particularly within the complementarity-determining region 3 (CDR3), requires efficient embedding methods for applying machine learning to immunology. While various TCR CDR3 embedding strategies have been proposed, the absence of their systematic evaluations created perplexity in the community. Here, we extracted CDR3 embedding models from 19 existing methods and benchmarked these models with four curated datasets by accessing their impact on the performance of TCR downstream tasks, including TCR-epitope binding affinity prediction, epitope-specific TCR identification, TCR clustering, and visualization analysis.
View Article and Find Full Text PDFUsing Large Language Models to Detect and Understand Drug Discontinuation Events in Web-Based Forums: Development and Validation Study.
J Med Internet Res
January 2025
Department of Industrial and Systems Engineering, The University of Florida, GAINESVILLE, FL, United States.
Background: The implementation of large language models (LLMs), such as BART (Bidirectional and Auto-Regressive Transformers) and GPT-4, has revolutionized the extraction of insights from unstructured text. These advancements have expanded into health care, allowing analysis of social media for public health insights. However, the detection of drug discontinuation events (DDEs) remains underexplored.
View Article and Find Full Text PDFIntroduction: Metabolic and bariatric surgery (MBS) is increasingly used for obesity and metabolic disease, with safety profiles showing it is among the safest major operations. The last 20 + years have noted significantly improved safety that has been accompanied by decreasing length of stay and select populations electing for outpatient surgery, leading to continued decreases in cost. Regardless, readmissions and complications still occur, requiring inpatient postoperative care (IP-POC).
View Article and Find Full Text PDFExplanatory review on DDR inhibitors: their biological activity, synthetic route, and structure-activity relationship.
Mol Divers
January 2025
Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India.
Discoidin domain receptors (DDR) are categorized under tyrosine kinase receptors (RTKs) and play a crucial role in various etiological conditions such as cancer, fibrosis, atherosclerosis, osteoarthritis, and inflammatory diseases. The structural domain rearrangement of DDR1 and DDR2 involved six domains of interest namely N-terminal DS, DS-like, intracellular juxtamembrane, transmembrane juxtamembrane, extracellular juxtamembrane intracellular kinase domain, and the tail portion contains small C-tail linkage. DDR has not been explored to a wide extent to be declared as a prime target for any particular pathological condition.
View Article and Find Full Text PDFA new HCM heart sound classification method based on weighted bispectrum features.
Phys Eng Sci Med
January 2025
School of Electrical Engineering and Electronic Information, Xihua University, Chengdu, China.
Hypertrophic cardiomyopathy (HCM), including obstructive HCM and non-obstructive HCM, can lead to sudden cardiac arrest in adolescents and athletes. Early diagnosis and treatment through auscultation of different types of HCM can prevent the occurrence of malignant events. However, it is challenging to distinguish the pathological information of HCM related to differential left ventricular outflow tract pressure gradients.
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