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.

scholarly journals An Improved Spectral Clustering Community Detection Algorithm Based on Probability Matrix

2020 ◽  
Vol 2020 ◽  
pp. 1-6
Author(s):  
Shuxia Ren ◽  
Shubo Zhang ◽  
Tao Wu
Keyword(s):  
Community Detection ◽  
Spectral Clustering ◽  
Clustering Algorithm ◽  
Transition Probability ◽  
Clustering Algorithms ◽  
Detection Algorithm ◽  
Community Information ◽  
The Mean ◽  
Community Detection Algorithm ◽  
Spectral Clustering Algorithm

The similarity graphs of most spectral clustering algorithms carry lots of wrong community information. In this paper, we propose a probability matrix and a novel improved spectral clustering algorithm based on the probability matrix for community detection. First, the Markov chain is used to calculate the transition probability between nodes, and the probability matrix is constructed by the transition probability. Then, the similarity graph is constructed with the mean probability matrix. Finally, community detection is achieved by optimizing the NCut objective function. The proposed algorithm is compared with SC, WT, FG, FluidC, and SCRW on artificial networks and real networks. Experimental results show that the proposed algorithm can detect communities more accurately and has better clustering performance.

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 An Enhanced Spectral Clustering Algorithm with S-Distance

Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 596
Author(s):  
Krishna Kumar Sharma ◽  
Ayan Seal ◽  
Enrique Herrera-Viedma ◽  
Ondrej Krejcar
Keyword(s):  
Spectral Clustering ◽  
Clustering Algorithm ◽  
Spatial Clustering ◽  
Clustering Algorithms ◽  
Rank Test ◽  
Customer Churn ◽  
Signed Rank ◽  
Signed Rank Test ◽  
Spectral Clustering Algorithm ◽  
Industrial Databases

Calculating and monitoring customer churn metrics is important for companies to retain customers and earn more profit in business. In this study, a churn prediction framework is developed by modified spectral clustering (SC). However, the similarity measure plays an imperative role in clustering for predicting churn with better accuracy by analyzing industrial data. The linear Euclidean distance in the traditional SC is replaced by the non-linear S-distance (Sd). The Sd is deduced from the concept of S-divergence (SD). Several characteristics of Sd are discussed in this work. Assays are conducted to endorse the proposed clustering algorithm on four synthetics, eight UCI, two industrial databases and one telecommunications database related to customer churn. Three existing clustering algorithms—k-means, density-based spatial clustering of applications with noise and conventional SC—are also implemented on the above-mentioned 15 databases. The empirical outcomes show that the proposed clustering algorithm beats three existing clustering algorithms in terms of its Jaccard index, f-score, recall, precision and accuracy. Finally, we also test the significance of the clustering results by the Wilcoxon’s signed-rank test, Wilcoxon’s rank-sum test, and sign tests. The relative study shows that the outcomes of the proposed algorithm are interesting, especially in the case of clusters of arbitrary shape.

scholarly journals Community Detection Based on Graph Representation Learning in Evolutionary Networks

2021 ◽  
Vol 11 (10) ◽  
pp. 4497
Author(s):  
Dongming Chen ◽  
Mingshuo Nie ◽  
Jie Wang ◽  
Yun Kong ◽  
Dongqi Wang ◽  
...  
Keyword(s):  
Community Detection ◽  
Network Structure ◽  
Clustering Algorithm ◽  
Laplacian Matrix ◽  
Representation Learning ◽  
Detection Algorithm ◽  
Graph Representation ◽  
Time Slice ◽  
Current Time ◽  
Evolutionary Networks

Aiming at analyzing the temporal structures in evolutionary networks, we propose a community detection algorithm based on graph representation learning. The proposed algorithm employs a Laplacian matrix to obtain the node relationship information of the directly connected edges of the network structure at the previous time slice, the deep sparse autoencoder learns to represent the network structure under the current time slice, and the K-means clustering algorithm is used to partition the low-dimensional feature matrix of the network structure under the current time slice into communities. Experiments on three real datasets show that the proposed algorithm outperformed the baselines regarding effectiveness and feasibility.

The Spectrum Segmentation Algorithm of Multimode Vibration Signal Based on Spectral Clustering

2011 ◽  
Vol 121-126 ◽  
pp. 2372-2376
Author(s):  
Dan Dan Wang ◽  
Yu Zhou ◽  
Qing Wei Ye ◽  
Xiao Dong Wang
Keyword(s):  
Wave Packet ◽  
Frequency Domain ◽  
Spectral Clustering ◽  
Clustering Algorithm ◽  
Wave Packets ◽  
Vibration Signal ◽  
Segmentation Algorithm ◽  
Frequency Curve ◽  
Macroscopic Observation ◽  
Spectral Clustering Algorithm

The mode peaks in frequency domain of vibration signal are strongly interfered by strong noise, causing the inaccuracy mode parameters. According to this situation, this paper comes up with the thought of mode-peak segmentation based on the spectral clustering algorithm. First, according to the concept of wave packet, the amplitude-frequency of vibration signal is divided into wave packets. Taking each wave packet as a sample of clustering algorithm, the spectral clustering algorithm is used to classify these wave packets. The amplitude-frequency curve of a mode peak becomes a big wave packet in macroscopic. The experiment to simulation signals indicates that this spectral clustering algorithm could accord with the macroscopic observation of mode segmentation effectively, and has outstanding performance especially in strong noise.

Research on Spectral Clustering

2014 ◽  
Vol 687-691 ◽  
pp. 1350-1353
Author(s):  
Li Li Fu ◽  
Yong Li Liu ◽  
Li Jing Hao
Keyword(s):  
Spectral Clustering ◽  
Clustering Algorithm ◽  
Theoretical Foundation ◽  
Clustering Algorithms ◽  
Spectral Graph Theory ◽  
Graph Partition ◽  
Mining Areas ◽  
Spectral Graph ◽  
Definition Of ◽  
Spectral Clustering Algorithm

Spectral clustering algorithm is a kind of clustering algorithm based on spectral graph theory. As spectral clustering has deep theoretical foundation as well as the advantage in dealing with non-convex distribution, it has received much attention in machine learning and data mining areas. The algorithm is easy to implement, and outperforms traditional clustering algorithms such as K-means algorithm. This paper aims to give some intuitions on spectral clustering. We describe different graph partition criteria, the definition of spectral clustering, and clustering steps, etc. Finally, in order to solve the disadvantage of spectral clustering, some improvements are introduced briefly.

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