Related papers: Topological network alignment uncovers biological …
Many complex systems can be represented as networks, and the problem of network comparison is becoming increasingly relevant. There are many techniques for network comparison, from simply comparing network summary statistics to…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for…
A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not…
We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The…
Network alignment, the process of finding correspondences between nodes in different graphs, has many scientific and industrial applications. Existing unsupervised network alignment methods find suboptimal alignments that break up node…
BLAST is a standard tool in bioinformatics for creating local sequence alignments using a "seed-and-extend" approach. Here we introduce an analogous seed-and-extend algorithm that produces local network alignments: BLANT (Basic Local…
Although neural networks are capable of reaching astonishing performances on a wide variety of contexts, properly training networks on complicated tasks requires expertise and can be expensive from a computational perspective. In industrial…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
Recent development of network structure analysis shows that it plays an important role in characterizing complex system of many branches of sciences. Different from previous network centrality measures, this paper proposes the notion of…
The topology of many real complex networks has been conjectured to be embedded in hidden metric spaces, where distances between nodes encode their likelihood of being connected. Besides of providing a natural geometrical interpretation of…
The topology of any complex system is key to understanding its structure and function. Fundamentally, algebraic topology guarantees that any system represented by a network can be understood through its closed paths. The length of each path…
Complex systems in the real world can be modeled as a network of connected components. The human brain, as a network of neurons among which the interactions cause perception, is a complex network. Synchronization is a dynamical phenomenon…
Inferring the network topology from the dynamics is a fundamental problem with wide applications in geology, biology and even counter-terrorism. Based on the propagation process, we present a simple method to uncover the network topology.…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
The ability to reroute and control flow is vital to the function of venation networks across a wide range of organisms. By modifying individual edges in these networks, either by adjusting edge conductances or creating and destroying edges,…
Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…
We consider networks of dynamical units that evolve in time according to different laws, and are coupled to each other in highly irregular ways. Studying how to steer the dynamics of such systems towards a desired evolution is of great…
Humans are increasingly stressing ecosystems via habitat destruction, climate change and global population movements leading to the widespread loss of biodiversity and the disruption of key ecological services. Ecosystems characterized…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…