swMATH ID: 11002
Software Authors: Brendan J. Frey; Delbert Dueck; Ulrich Bodenhofer , Johannes Palme , Chrats Melkonian , Andreas Kothmeier
Description: Affinity propagation (AP) is a clustering algorithm that has been introduced by Brendan J. Frey and Delbert Dueck. The authors themselves describe affinity propagation as follows: ”An algorithm that identifies exemplars among data points and forms clusters of data points around these exemplars. It operates by simultaneously considering all data point as potential exemplars and exchanging messages between data points until a good set of exemplars and clusters emerges.” AP has been applied in various fields recently, among which bioinformatics is becoming increasingly important. Frey and Dueck have made their algorithm available as Matlab code. Matlab, however, is relatively uncommon in bioinformatics. Instead, the statistical computing platform R has become a widely accepted standard in this field. In order to leverage affinity propagation for bioinformatics applications, we have implemented affinity propagation as an R package. Note, however, that the given package is in no way restricted to bioinformatics applications. It is as generally applicable as Frey’s and Dueck’s original Matlab code. The package further implements leveraged affinity propagation, exemplar-based agglomerative clustering, and various tools for visual analysis of clustering results.
Homepage: http://www.mloss.org/software/view/264/
Dependencies: Matlab
Related Software: apcluster; UCI-ml; clusfind; AS 136; R; ElemStatLearn; mclust; k-means++; Kernlab; Silhouettes; PRMLT; SIFT; Pajek; Matlab; DAVID; clustervalidation; AutoClass; ReliefF; darch; cluster (R)
Cited in: 91 Publications

Standard Articles

1 Publication describing the Software, including 1 Publication in zbMATH Year
Clustering by passing messages between data points. Zbl 1226.94027
Frey, Brendan J.; Dueck, Delbert
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Cited by 258 Authors

3 Brusco, Michael J.
3 Farinelli, Alessandro
3 Khalid, Shehzad
3 Li, Tianrui
3 Wang, Hongjun
3 Xu, Dachuan
2 Anderlucci, Laura
2 Bayati, Mohsen Fathollah
2 Bicego, Manuele
2 Deng, Ping
2 Denitto, Matteo
2 Frey, Brendan J.
2 Lipovetsky, Stan
2 Nebel, David
2 Razzaq, Shahid
2 Steinley, Douglas L.
2 Ushakov, Anton Vladimirovich
2 Vasil’ev, Igor’ Leonidovich
2 Villmann, Thomas
2 Wu, Fei
2 Xia, Ding-yin
2 Zecchina, Riccardo
2 Zhang, Dongmei
2 Zhang, Wei
2 Zhang, Yinghui
1 Alemany, Sandra
1 Aloise, Daniel
1 An, Senjian
1 Angelov, Plamen Parvanov
1 Anirudh, Rushil
1 Antczak, Maciej
1 Baldi, Pierre
1 Bellemare, Marc-Emmanuel
1 Bhatnagar, Raj K.
1 Blanchard, Simon J.
1 Błażewicz, Jacek
1 Bohnsack, Andrea
1 Boiarov, A. A.
1 Borgs, Christian
1 Bottarelli, Lorenzo
1 Braunstein, Alfredo
1 Breiteneder, Christian J.
1 Brodinová, Šárka
1 Bulot, Rémy
1 Cao, Fuyuan
1 Castillo, Oscar
1 Castro, Juan R.
1 Chayes, Jennifer Tour
1 Chellappa, Rama
1 Chen, Bolun
1 Chen, Ling
1 Chen, Qianqian
1 Chen, Songcan
1 Chen, Yewang
1 Chen, Yingxia
1 Cheng, Dongdong
1 Cheng, Yu
1 Cheong, LoongFah
1 Chunaev, Petr
1 Chung, Fu-Lai
1 Coelho, André L. V.
1 Comas-Cufí, Marc
1 Cradit, J. Dennis
1 D. C. Struppa, D. C.
1 Dai, Guowei
1 Dehghanian, Amin
1 Deng, Zhihong
1 Di Pierro, Alessandra
1 Ding, Jundi
1 Dobaie, Abdullah M.
1 Du, Donglei
1 Dueck, Delbert
1 Epifanio, Irene
1 Fang, Qianhao
1 Ferguson, Andrew L.
1 Figueiredo, Mário A. T.
1 Filzmoser, Peter
1 Fortunato, Francesca
1 Gadde, Raghudeep
1 Gao, Jun
1 Givoni, Inmar E.
1 Glotin, Hervé
1 Gong, Maoguo
1 Granichin, Oleg N.
1 Gu, Xiaowei
1 Guo, Yuefei
1 Hammer, Barbara
1 Han, Lu
1 Hang, Wenlong
1 Hasenfuß, Alexander
1 He, Hanzhi
1 He, Li
1 He, Ye
1 Hennig, Christian
1 Hino, Hideitsu
1 Hinton, Geoffrey Everest
1 Hirayama, Junichiro
1 Horng, Shi-Jinn
1 Hu, Chenyue W.
1 Hu, Guangfei
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Cited in 48 Serials

9 Pattern Recognition
8 Information Sciences
6 International Journal of Computer Vision
5 Journal of Classification
5 Neural Computation
4 Machine Learning
3 European Journal of Operational Research
2 Mathematical Biosciences
2 Applied Mathematical Modelling
2 Mathematical Problems in Engineering
2 Data Mining and Knowledge Discovery
2 Journal of Zhejiang University. Science A
2 Statistical Analysis and Data Mining
2 Journal of Theoretical Biology
1 ACM Computing Surveys
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1 Journal of Mathematical Physics
1 Physics Reports
1 Psychometrika
1 Applied Mathematics and Computation
1 British Journal of Mathematical & Statistical Psychology
1 Journal of Computational and Applied Mathematics
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1 Asia-Pacific Journal of Operational Research
1 SIAM Journal on Discrete Mathematics
1 Journal of Global Optimization
1 Designs, Codes and Cryptography
1 Automation and Remote Control
1 Computational Statistics and Data Analysis
1 Journal of Mathematical Imaging and Vision
1 Applied and Computational Harmonic Analysis
1 Complexity
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1 Journal of Combinatorial Optimization
1 International Journal of Applied Mathematics and Computer Science
1 Statistical Modelling
1 Natural Computing
1 Computational Biology and Chemistry
1 Advances in Data Analysis and Classification. ADAC
1 Computational & Mathematical Methods in Medicine
1 Science
1 Electronic Journal of Statistics
1 Algorithms
1 Diskretnyĭ Analiz i Issledovanie Operatsiĭ
1 Computer Science Review
1 International Journal of Systems Science. Principles and Applications of Systems and Integration
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