AntNetAlign: Ant colony optimization for network alignment

The code (and data) in this article has been certified as Reproducible by Code Ocean: (https://codeocean.com/). More information on the Reproducibility Badge Initiative is available at https://www.elsevier.com/physical-sciences-andengineering/computer-science/journalsNetwork Alignment (NA) is a hard optimization problem with important applications such as, for example, the identification of orthologous relationships between different proteins and of phylogenetic relationships between species. Given two (or more) networks, the goal is to find an alignment between them, that is, a mapping between their respective nodes such that the topological and functional structure is well preserved. Although the problem has received great interest in recent years, there is still a need to unify the different trends that have emerged from diverse research areas. In this paper, we introduce AntNetAlign, an Ant Colony Optimization (ACO) approach for solving the problem. The proposed approach makes use of similarity information extracted from the input networks to guide the construction process. Combined with an improvement measure that depends on the current construction state, it is able to optimize any of the three main topological quality measures. We provide an extensive experimental evaluation using real-world instances that range from Protein–Protein Interaction (PPI) networks to Social Networks. Results show that our method outperforms other state-of-the-art approaches in two out of three of the tested scores within a reasonable amount of time, specially in the important score. Moreover, it is able to obtain near-optimal results when aligning networks with themselves. Furthermore, in larger instances, our algorithm was still able to compete with the best performing method in this regard.Christian Blum and Guillem Rodríguez Corominas, Spain were supported by grants PID2019-104156GB-I00 and TED2021- 129319B-I00 funded by MCIN/AEI/10.13039/501100011033. Maria J. Blesa acknowledges support from AEI, Spain under grant PID2020-112581GB-C21 (MOTION) and the Catalan Agency for Management of University and Research Grants (AGAUR), Spain under grant 2017-SGR-786 (ALBCOM).Peer ReviewedPostprint (published version

Fair Evaluation of Global Network Aligners

Biological network alignment identifies topologically and functionally conserved regions between networks of different species. It encompasses two algorithmic steps: node cost function (NCF), which measures similarities between nodes in different networks, and alignment strategy (AS), which uses these similarities to rapidly identify high-scoring alignments. Different methods use both different NCFs and different ASs. Thus, it is unclear whether the superiority of a method comes from its NCF, its AS, or both. We already showed on MI-GRAAL and IsoRankN that combining NCF of one method and AS of another method can lead to a new superior method. Here, we evaluate MI-GRAAL against newer GHOST to potentially further improve alignment quality. Also, we approach several important questions that have not been asked systematically thus far. First, we ask how much of the node similarity information in NCF should come from sequence data compared to topology data. Existing methods determine this more-less arbitrarily, which could affect the resulting alignment(s). Second, when topology is used in NCF, we ask how large the size of the neighborhoods of the compared nodes should be. Existing methods assume that larger neighborhood sizes are better. We find that MI-GRAAL's NCF is superior to GHOST's NCF, while the performance of the methods' ASs is data-dependent. Thus, the combination of MI-GRAAL's NCF and GHOST's AS could be a new superior method for certain data. Also, which amount of sequence information is used within NCF does not affect alignment quality, while the inclusion of topological information is crucial. Finally, larger neighborhood sizes are preferred, but often, it is the second largest size that is superior, and using this size would decrease computational complexity. Together, our results give several general recommendations for a fair evaluation of network alignment methods.Comment: 19 pages. 10 figures. Presented at the 2014 ISMB Conference, July 13-15, Boston, M

Complex Networks and Symmetry II: Reciprocity and Evolution of World Trade

We exploit the symmetry concepts developed in the companion review of this article to introduce a stochastic version of link reversal symmetry, which leads to an improved understanding of the reciprocity of directed networks. We apply our formalism to the international trade network and show that a strong embedding in economic space determines particular symmetries of the network, while the observed evolution of reciprocity is consistent with a symmetry breaking taking place in production space. Our results show that networks can be strongly affected by symmetry-breaking phenomena occurring in embedding spaces, and that stochastic network symmetries can successfully suggest, or rule out, possible underlying mechanisms.Comment: Final accepted versio

Complex networks in climate dynamics - Comparing linear and nonlinear network construction methods

Complex network theory provides a powerful framework to statistically investigate the topology of local and non-local statistical interrelationships, i.e. teleconnections, in the climate system. Climate networks constructed from the same global climatological data set using the linear Pearson correlation coefficient or the nonlinear mutual information as a measure of dynamical similarity between regions, are compared systematically on local, mesoscopic and global topological scales. A high degree of similarity is observed on the local and mesoscopic topological scales for surface air temperature fields taken from AOGCM and reanalysis data sets. We find larger differences on the global scale, particularly in the betweenness centrality field. The global scale view on climate networks obtained using mutual information offers promising new perspectives for detecting network structures based on nonlinear physical processes in the climate system.Comment: 24 pages, 10 figure