scholarly journals Graph theory and stability analysis of protein complex interaction networks

2016 ◽  
Vol 10 (2) ◽  
pp. 64-75 ◽  
Author(s):  
Chien-Hung Huang ◽  
Teng-Hung Chen ◽  
Ka-Lok Ng
2021 ◽  
Vol 11 (9) ◽  
pp. 4005
Author(s):  
Asep Maulana ◽  
Martin Atzmueller

Anomaly detection in complex networks is an important and challenging task in many application domains. Examples include analysis and sensemaking in human interactions, e.g., in (social) interaction networks, as well as the analysis of the behavior of complex technical and cyber-physical systems such as suspicious transactions/behavior in financial or routing networks; here, behavior and/or interactions typically also occur on different levels and layers. In this paper, we focus on detecting anomalies in such complex networks. In particular, we focus on multi-layer complex networks, where we consider the problem of finding sets of anomalous nodes for group anomaly detection. Our presented method is based on centrality-based many-objective optimization on multi-layer networks. Starting from the Pareto Front obtained via many-objective optimization, we rank anomaly candidates using the centrality information on all layers. This ranking is formalized via a scoring function, which estimates relative deviations of the node centralities, considering the density of the network and its respective layers. In a human-centered approach, anomalous sets of nodes can then be identified. A key feature of this approach is its interpretability and explainability, since we can directly assess anomalous nodes in the context of the network topology. We evaluate the proposed method using different datasets, including both synthetic as well as real-world network data. Our results demonstrate the efficacy of the presented approach.


2021 ◽  
Author(s):  
Sylvie Rebuffat

This review unveils current knowledge on the complex interaction networks involving ribosomally synthesized peptides, either modified or not, being at play in microbial interactions and symbioses.


2018 ◽  
Author(s):  
Guy Bunin

Many ecological community dynamics display some degree of directionality, known as succession patterns. But complex interaction networks frequently tend to non-directional dynamics such as chaos, unless additional structures or mechanisms impose some form of, often fragile or shot-lived, directionality. We exhibit here a novel property of emergent long-lasting directionality in competitive communities, which relies on very minimal assumptions. We model communities where each species has a few strong competitive interactions, and many weak ones. We find that, at high enough diversity, the dynamics become directional, meaning that the community state can be characterized by a function that increases in time, which we call "maturity". In the presence of noise, the community composition changes toward increasingly stable and productive states. This scenario occupies a middle ground between deterministic succession and purely random species associations: there are many overlapping stable states, with stochastic transitions, that are nevertheless biased in a particular direction. When a spatial dimension is added in the form of a meta-community, higher-maturity community states are able to expand in space, replacing others by (exact or approximate) copies of themselves. This leads to community-level selection, with the same maturity function acting as fitness. Classic concepts from evolutionary dynamics provide a powerful analogy to understand this strictly ecological, community-level phenomenon of emergent directionality.


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