Recently there has been a great deal of interest in algorithms for constructing low-dimensional feature-space embeddings of high dimensional data sets in order to visualize inter- and intra-class relationships. In this paper we present a novel application of graph embedding in improving the accuracy of supervised classification schemes, especially in cases where object class labels cannot be reliably ascertained. By refining the initial training set of class labels we seek to improve the prior class distributions and thus classification accuracy. We also present a novel way of visualizing the class embeddings which makes it easy to appreciate inter-class relationships and to infer the presence of new classes which were not part of the original classification. We demonstrate the utility of the method in detecting prostatic adenocarcinoma from high-resolution MRI.
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http://dx.doi.org/10.1007/11566465_90 | DOI Listing |
Bioinformatics
January 2025
School of Computing and Artificial Intelligence, Southwest Jiaotong University, Sichuan 611756, China.
Motivation: The rapid development of single-cell RNA sequencing (scRNA-seq) has significantly advanced biomedical research. Clustering analysis, crucial for scRNA-seq data, faces challenges including data sparsity, high dimensionality, and variable gene expressions. Better low-dimensional embeddings for these complex data should maintain intrinsic information while making similar data close and dissimilar data distant.
View Article and Find Full Text PDFInterdiscip Sci
January 2025
School of Computer Science, Qufu Normal University, Rizhao, 276826, China.
Combination therapy, which synergistically enhances treatment efficacy and inhibits disease progression through the combined effects of multiple drugs, has emerged as a mainstream approach for treating complex diseases and alleviating symptoms. However, drug-drug interactions (DDIs) can sometimes lead to adverse reactions, potentially endangering lives. Therefore, developing efficient and accurate DDI prediction methods is crucial for elucidating drug mechanisms and preventing side effects.
View Article and Find Full Text PDFPLoS One
January 2025
School of Government, Adolfo Ibanez University, Santiago, Chile.
This study demonstrates the use of GPT-4 and variants, advanced language models readily accessible to many social scientists, in extracting political networks from text. This approach showcases the novel integration of GPT-4's capabilities in entity recognition, relation extraction, entity linking, and sentiment analysis into a single cohesive process. Based on a corpus of 1009 Chilean political news articles, the study validates the graph extraction method using 'legislative agreement', i.
View Article and Find Full Text PDFiScience
January 2025
Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi'an 710069, China.
Bacteriophages (phages) are increasingly viewed as a promising alternative for the treatment of antibiotic-resistant bacterial infections. However, the diversity of host ranges complicates the identification of target phages. Existing computational tools often fail to accurately identify phages across different bacterial species.
View Article and Find Full Text PDFJ Biomed Inform
January 2025
Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, 02115, MA, USA; VA Boston Healthcare System, 150 S Huntington Ave, Boston, 02130, MA, USA. Electronic address:
Objective: Electronic health record (EHR) systems contain a wealth of clinical data stored as both codified data and free-text narrative notes (NLP). The complexity of EHR presents challenges in feature representation, information extraction, and uncertainty quantification. To address these challenges, we proposed an efficient Aggregated naRrative Codified Health (ARCH) records analysis to generate a large-scale knowledge graph (KG) for a comprehensive set of EHR codified and narrative features.
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