Non-negative matrix factorization (NMF) has been widely used in machine learning and data mining fields. As an extension of NMF, non-negative matrix tri-factorization (NMTF) provides more degrees of freedom than NMF. However, standard NMTF algorithm utilizes Frobenius norm to calculate residual error, which can be dramatically affected by noise and outliers. Moreover, the hidden geometric information in feature manifold and sample manifold is rarely learned. Hence, a novel robust capped norm dual hyper-graph regularized non-negative matrix tri-factorization (RCHNMTF) is proposed. First, a robust capped norm is adopted to handle extreme outliers. Second, dual hyper-graph regularization is considered to exploit intrinsic geometric information in feature manifold and sample manifold. Third, orthogonality constraints are added to learn unique data presentation and improve clustering performance. The experiments on seven datasets testify the robustness and superiority of RCHNMTF.
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http://dx.doi.org/10.3934/mbe.2023556 | DOI Listing |
Nature
January 2025
Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA.
Hepatocellular carcinoma (HCC) originates from differentiated hepatocytes undergoing compensatory proliferation in livers damaged by viruses or metabolic-dysfunction-associated steatohepatitis (MASH). While increasing HCC risk, MASH triggers p53-dependent hepatocyte senescence, which we found to parallel hypernutrition-induced DNA breaks. How this tumour-suppressive response is bypassed to license oncogenic mutagenesis and enable HCC evolution was previously unclear.
View Article and Find Full Text PDFAdv Sci (Weinh)
December 2024
State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory of Pathobiology Ministry of Education, China-Japan Union Hospital of Jilin University, Changchun, 130033, China.
In the post-large era, various COVID-19 sequelae are getting more and more attention to health problems. Although the mortality rate of the COVID-19 infection is now declining, it is often accompanied by new clinical sequelae with different symptoms such as fatigue after infection, loss of smell. The degree of age, gender, virus infection seems to be weakly correlated with clinical symptoms.
View Article and Find Full Text PDFTransl Oncol
December 2024
Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou 450052, China; Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou 450052, China. Electronic address:
5-Methylcytosine (m5C) is a ubiquitous RNA modification that is closely related to various cellular functions. However, no studies have comprehensively demonstrated the role of m5C in hepatocellular carcinoma (HCC) progression. In this study, six pairs of HCC and adjacent tissue samples were subjected to methylated RNA immunoprecipitation sequencing to identify precise m5C loci.
View Article and Find Full Text PDFBioinformatics
December 2024
School of Computer Science and Engineering, The Hebrew University of Jerusalem.
Motivation: Non-negative Matrix Factorization (NMF) is a powerful tool often applied to genomic data, to identify non-negative latent components that constitute linearly mixed samples. It is useful when the observed signal combines contributions from multiple sources, such as cell types in bulk measurements of heterogeneous tissue. NMF accounts for two types of variation between samples-disparities in the proportions of sources and observation noise.
View Article and Find Full Text PDFSci Rep
December 2024
College of A&F Engineering and Planning, Tongren University, Tongren, 554300, China.
The Wanshan mercury mining area (WMMA) in Guizhou Province, China, has been identified as a region at high ecological risk owing to heavy metal contamination. This study employed non-lethal sampling methods, using the phalanges of Pelophylax nigromaculatus in the WMMA as analytical material. Ten heavy metal (metalloid) elements were selected for analysis, including Hg, Cr, Mn, Ni, Cu, Zn, Cd, Pb, As, and Se.
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