Clustering nodes with attributes via graph alignment

Author(s):  
Dimitrios Rafailidis
Keyword(s):  
2021 ◽  
Author(s):  
Linyi Ding ◽  
Weijie Yuan ◽  
Kui Meng ◽  
Gongshen Liu

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Mikko Rautiainen ◽  
Tobias Marschall

Abstract Genome graphs can represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pangenome graph. Yet, so far, this step is often prohibitively slow. We present GraphAligner, a tool for aligning long reads to genome graphs. Compared to the state-of-the-art tools, GraphAligner is 13x faster and uses 3x less memory. When employing GraphAligner for error correction, we find it to be more than twice as accurate and over 12x faster than extant tools.Availability: Package manager: https://anaconda.org/bioconda/graphalignerand source code: https://github.com/maickrau/GraphAligner


2011 ◽  
Vol 8 (5) ◽  
pp. 1330-1343 ◽  
Author(s):  
M. Mernberger ◽  
G. Klebe ◽  
E. Hullermeier
Keyword(s):  

2020 ◽  
Vol 146 ◽  
pp. 113205 ◽  
Author(s):  
Mahdi Bakhshi ◽  
Mohammadali Nematbakhsh ◽  
Mehran Mohsenzadeh ◽  
Amir Masoud Rahmani

2020 ◽  
Vol 34 (05) ◽  
pp. 9354-9361
Author(s):  
Kun Xu ◽  
Linfeng Song ◽  
Yansong Feng ◽  
Yan Song ◽  
Dong Yu

Existing entity alignment methods mainly vary on the choices of encoding the knowledge graph, but they typically use the same decoding method, which independently chooses the local optimal match for each source entity. This decoding method may not only cause the “many-to-one” problem but also neglect the coordinated nature of this task, that is, each alignment decision may highly correlate to the other decisions. In this paper, we introduce two coordinated reasoning methods, i.e., the Easy-to-Hard decoding strategy and joint entity alignment algorithm. Specifically, the Easy-to-Hard strategy first retrieves the model-confident alignments from the predicted results and then incorporates them as additional knowledge to resolve the remaining model-uncertain alignments. To achieve this, we further propose an enhanced alignment model that is built on the current state-of-the-art baseline. In addition, to address the many-to-one problem, we propose to jointly predict entity alignments so that the one-to-one constraint can be naturally incorporated into the alignment prediction. Experimental results show that our model achieves the state-of-the-art performance and our reasoning methods can also significantly improve existing baselines.


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