scholarly journals CSTNU Tool: A Java library for checking temporal networks

SoftwareX ◽  
2022 ◽  
Vol 17 ◽  
pp. 100905
Author(s):  
Roberto Posenato
1996 ◽  
Author(s):  
Eugene Santos ◽  
Young Jr. ◽  
Joel D.
Keyword(s):  

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qing Yao ◽  
Bingsheng Chen ◽  
Tim S. Evans ◽  
Kim Christensen

AbstractWe study the evolution of networks through ‘triplets’—three-node graphlets. We develop a method to compute a transition matrix to describe the evolution of triplets in temporal networks. To identify the importance of higher-order interactions in the evolution of networks, we compare both artificial and real-world data to a model based on pairwise interactions only. The significant differences between the computed matrix and the calculated matrix from the fitted parameters demonstrate that non-pairwise interactions exist for various real-world systems in space and time, such as our data sets. Furthermore, this also reveals that different patterns of higher-order interaction are involved in different real-world situations. To test our approach, we then use these transition matrices as the basis of a link prediction algorithm. We investigate our algorithm’s performance on four temporal networks, comparing our approach against ten other link prediction methods. Our results show that higher-order interactions in both space and time play a crucial role in the evolution of networks as we find our method, along with two other methods based on non-local interactions, give the best overall performance. The results also confirm the concept that the higher-order interaction patterns, i.e., triplet dynamics, can help us understand and predict the evolution of different real-world systems.


2021 ◽  
Vol 147 ◽  
pp. 110934
Author(s):  
Jialin Bi ◽  
Ji Jin ◽  
Cunquan Qu ◽  
Xiuxiu Zhan ◽  
Guanghui Wang ◽  
...  

SoftwareX ◽  
2021 ◽  
Vol 13 ◽  
pp. 100659
Author(s):  
Krzysztof Ciomek ◽  
Miłosz Kadziński

Author(s):  
Tomasz Zok

Abstract Motivation Biomolecular structures come in multiple representations and diverse data formats. Their incompatibility with the requirements of data analysis programs significantly hinders the analytics and the creation of new structure-oriented bioinformatic tools. Therefore, the need for robust libraries of data processing functions is still growing. Results BioCommons is an open-source, Java library for structural bioinformatics. It contains many functions working with the 2D and 3D structures of biomolecules, with a particular emphasis on RNA. Availability and implementation The library is available in Maven Central Repository and its source code is hosted on GitHub: https://github.com/tzok/BioCommons Supplementary information Supplementary data are available at Bioinformatics online.


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