Module detection for bacteria based on spectral clustering of protein-protein functional association networks

2011 ◽  
Author(s):  
Hongwei Wu ◽  
Yaming Lin ◽  
Fun Choi Chan ◽  
R. Alba-Flores
Keyword(s):  
Spectral Clustering ◽  
Functional Association ◽  
Module Detection

scholarly journals TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery

2021 ◽  
Vol 22 (S4) ◽  
Author(s):  
Yusong Liu ◽  
Xiufen Ye ◽  
Christina Y. Yu ◽  
Wei Shao ◽  
Jie Hou ◽  
...  
Keyword(s):  
Prior Knowledge ◽  
Spectral Clustering ◽  
Clustering Algorithm ◽  
Detection Algorithm ◽  
Complete Coverage ◽  
Survival Difference ◽  
Module Detection ◽  
Module Discovery ◽  
Module Size ◽  
Expression Module

Abstract Background Gene co-expression networks are widely studied in the biomedical field, with algorithms such as WGCNA and lmQCM having been developed to detect co-expressed modules. However, these algorithms have limitations such as insufficient granularity and unbalanced module size, which prevent full acquisition of knowledge from data mining. In addition, it is difficult to incorporate prior knowledge in current co-expression module detection algorithms. Results In this paper, we propose a novel module detection algorithm based on topology potential and spectral clustering algorithm to detect co-expressed modules in gene co-expression networks. By testing on TCGA data, our novel method can provide more complete coverage of genes, more balanced module size and finer granularity than current methods in detecting modules with significant overall survival difference. In addition, the proposed algorithm can identify modules by incorporating prior knowledge. Conclusion In summary, we developed a method to obtain as much as possible information from networks with increased input coverage and the ability to detect more size-balanced and granular modules. In addition, our method can integrate data from different sources. Our proposed method performs better than current methods with complete coverage of input genes and finer granularity. Moreover, this method is designed not only for gene co-expression networks but can also be applied to any general fully connected weighted network.

A Method for Multi-HVDC Grouping Based on Spectral Clustering

2020 ◽  
Author(s):  
Xiaohui Wang ◽  
Yu Bai ◽  
Yadong Gao ◽  
Dong Liu ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Spectral Clustering

scholarly journals A Novel Unsupervised Classification Method for Sandy Land Using Fully Polarimetric SAR Data

2021 ◽  
Vol 13 (3) ◽  
pp. 355
Author(s):  
Weixian Tan ◽  
Borong Sun ◽  
Chenyu Xiao ◽  
Pingping Huang ◽  
Wei Xu ◽  
...  
Keyword(s):  
Spectral Clustering ◽  
Large Scale ◽  
Clustering Algorithm ◽  
Feature Vector ◽  
Unsupervised Classification ◽  
Classification Method ◽  
Sandy Land ◽  
Classification Methods ◽  
The Many ◽  
Representative Points

Classification based on polarimetric synthetic aperture radar (PolSAR) images is an emerging technology, and recent years have seen the introduction of various classification methods that have been proven to be effective to identify typical features of many terrain types. Among the many regions of the study, the Hunshandake Sandy Land in Inner Mongolia, China stands out for its vast area of sandy land, variety of ground objects, and intricate structure, with more irregular characteristics than conventional land cover. Accounting for the particular surface features of the Hunshandake Sandy Land, an unsupervised classification method based on new decomposition and large-scale spectral clustering with superpixels (ND-LSC) is proposed in this study. Firstly, the polarization scattering parameters are extracted through a new decomposition, rather than other decomposition approaches, which gives rise to more accurate feature vector estimate. Secondly, a large-scale spectral clustering is applied as appropriate to meet the massive land and complex terrain. More specifically, this involves a beginning sub-step of superpixels generation via the Adaptive Simple Linear Iterative Clustering (ASLIC) algorithm when the feature vector combined with the spatial coordinate information are employed as input, and subsequently a sub-step of representative points selection as well as bipartite graph formation, followed by the spectral clustering algorithm to complete the classification task. Finally, testing and analysis are conducted on the RADARSAT-2 fully PolSAR dataset acquired over the Hunshandake Sandy Land in 2016. Both qualitative and quantitative experiments compared with several classification methods are conducted to show that proposed method can significantly improve performance on classification.

scholarly journals Spectral Clustering Reveals Different Profiles of Central Sensitization in Women with Carpal Tunnel Syndrome

Symmetry ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1042
Author(s):  
Oscar J. Pellicer-Valero ◽  
José D. Martín-Guerrero ◽  
César Fernández-de-las-Peñas ◽  
Ana I. De-la-Llave-Rincón ◽  
Jorge Rodríguez-Jiménez ◽  
...  
Keyword(s):  
Carpal Tunnel Syndrome ◽  
Clinical Features ◽  
Carpal Tunnel ◽  
Spectral Clustering ◽  
Grip Force ◽  
The Other ◽  
Pressure Pain ◽  
Thermal Pain ◽  
Pressure Pain Thresholds ◽  
Tunnel Syndrome

Identification of subgroups of patients with chronic pain provides meaningful insights into the characteristics of a specific population, helping to identify individuals at risk of chronification and to determine appropriate therapeutic strategies. This paper proposes the use of spectral clustering (SC) to distinguish subgroups (clusters) of individuals with carpal tunnel syndrome (CTS), making use of the obtained patient profiling to argue about potential management implications. SC is a powerful algorithm that builds a similarity graph among the data points (the patients), and tries to find the subsets of points that are strongly connected among themselves, but weakly connected to others. It was chosen due to its advantages with respect to other simpler clustering techniques, such as k-means, and the fact that it has been successfully applied to similar problems. Clinical (age, duration of symptoms, pain intensity, function, and symptom severity), psycho-physical (pressure pain thresholds—PPTs—over the three main nerve trunks of the upper extremity, cervical spine, carpal tunnel, and tibialis anterior), psychological (depressive levels), and motor (pinch tip grip force) variables were collected in 208 women with clinical/electromyographic diagnosis of CTS, whose symptoms usually started unilaterally but eventually evolved into bilateral symmetry. SC was used to identify clusters of patients without any previous assumptions, yielding three clusters. Patients in cluster 1 exhibited worse clinical features, higher widespread pressure pain hyperalgesia, higher depressive levels, and lower pinch tip grip force than the other two. Patients in cluster 2 showed higher generalized thermal pain hyperalgesia than the other two. Cluster 0 showed less hypersensitivity to pressure and thermal pain, less severe clinical features, and more normal motor output (tip grip force). The presence of subgroups of individuals with different altered nociceptive processing (one group being more sensitive to pressure pain and another group more sensitive to thermal pain) could lead to different therapeutic programs.

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