We use the information present in a bipartite network to detect cores of communities of each set of the bipartite system. Cores of communities are found by investigating statistically validated projected networks obtained using information present in the bipartite network. Cores of communities are highly informative and robust with respect to the presence of errors or missing entries in the bipartite network. We assess the statistical robustness of cores by investigating an artificial benchmark network, the coauthorship network, and the actor-movie network. The accuracy and precision of the partition obtained with respect to the reference partition are measured in terms of the adjusted Rand index and the adjusted Wallace index, respectively. The detection of cores is highly precise, although the accuracy of the methodology can be limited in some cases.
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http://dx.doi.org/10.1103/PhysRevE.96.022321 | DOI Listing |
Anal Chem
January 2025
State Key Laboratory of Cellular Stress Biology, Institute of Artificial Intelligence, School of Life Sciences, Faculty of Medicine and Life Sciences, National Institute for Data Science in Health and Medicine, XMU-HBN skin biomedical research center, Xiamen University, Xiamen, Fujian 361102, China.
In metabolomic analysis based on liquid chromatography coupled with mass spectrometry, detecting and quantifying intricate objects is a massive job. Current peak picking methods still cause high rates of incorrectly picked peaks to influence the reliability and reproducibility of results. To address these challenges, we developed QuanFormer, a deep learning method based on object detection designed to accurately quantify peak signals.
View Article and Find Full Text PDFBiostatistics
December 2024
Department of Biostatistics, Yale University School of Public Health, 60 College Street, New Haven, CT06511, United States.
Evaluating air quality interventions is confronted with the challenge of interference since interventions at a particular pollution source likely impact air quality and health at distant locations, and air quality and health at any given location are likely impacted by interventions at many sources. The structure of interference in this context is dictated by complex atmospheric processes governing how pollution emitted from a particular source is transformed and transported across space and can be cast with a bipartite structure reflecting the two distinct types of units: (i) interventional units on which treatments are applied or withheld to change pollution emissions; and (ii) outcome units on which outcomes of primary interest are measured. We propose new estimands for bipartite causal inference with interference that construe two components of treatment: a "key-associated" (or "individual") treatment and an "upwind" (or "neighborhood") treatment.
View Article and Find Full Text PDFNat Commun
January 2025
Beijing Advanced Innovation Center for Integrated Circuits, School of Integrated Circuits, Peking University, Beijing, China.
Compute-in-memory based on resistive random-access memory has emerged as a promising technology for accelerating neural networks on edge devices. It can reduce frequent data transfers and improve energy efficiency. However, the nonvolatile nature of resistive memory raises concerns that stored weights can be easily extracted during computation.
View Article and Find Full Text PDFNeural Netw
January 2025
School of Cyber Science and Engineering, Xi'an Jiaotong University, China. Electronic address:
Detecting anomalies in attributed networks has become a subject of interest in both academia and industry due to its wide spectrum of applications. Although most existing methods achieve desirable performance by the merit of various graph neural networks, the way they bundle node-affiliated multidimensional attributes into a whole for embedding calculation hinders their ability to model and analyze anomalies at the fine-grained feature level. To characterize anomalies from each feature dimension, we propose Eagle, a deep framework based on bipartitE grAph learninG for anomaLy dEtection.
View Article and Find Full Text PDFBrief Bioinform
November 2024
Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
Cryo-electron tomography (cryo-ET) is confronted with the intricate task of unveiling novel structures. General class discovery (GCD) seeks to identify new classes by learning a model that can pseudo-label unannotated (novel) instances solely using supervision from labeled (base) classes. While 2D GCD for image data has made strides, its 3D counterpart remains unexplored.
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