Related papers: The Function of Communities in Protein Interaction…

Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…

Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…

Crossover between neural networks is considered disruptive due to the strong functional dependency between connection weights. We propose a modularity-based linkage model at the weight level to preserve functionally dependent communities…

For data represented by networks, the community structure of the underlying graph is of great interest. A classical clustering problem is to uncover the overall ``best'' partition of nodes in communities. Here, a more elaborate description…

Using an intuitive concept of what constitutes a meaningful community, a novel metric is formulated for detecting non-overlapping communities in undirected, weighted heterogeneous networks. This metric, modularity density, is shown to be…

The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…

Many real-world networks can be modeled by networks of interacting agents. Analysis of these interactions can reveal fundamental properties from these networks. Estimating the amount of collaboration in a network corresponding to…

Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of…

Many networks are important because they are substrates for dynamical systems, and their pattern of functional connectivity can itself be dynamic -- they can functionally reorganize, even if their underlying anatomical structure remains…

Modularity structures are common in various social and biological networks. However, its dynamical origin remains an open question. In this work, we set up a dynamical model describing the evolution of a social network. Based on the…

Community structure is of paramount importance for the understanding of complex networks. Consequently, there is a tremendous effort in order to develop efficient community detection algorithms. Unfortunately, the issue of a fair assessment…

In this paper, we address the problem of identifying protein functionality using the information contained in its aminoacid sequence. We propose a method to define sequence similarity relationships that can be used as input for…

Detecting community structure is fundamental to clarify the link between structure and function in complex networks and is used for practical applications in many disciplines. A successful method relies on the optimization of a quantity…

An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…

The study of the sub-structure of complex networks is of major importance to relate topology and functionality. Many efforts have been devoted to the analysis of the modular structure of networks using the quality function known as…

A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…

The issue of partitioning a network into communities has attracted a great deal of attention recently. Most authors seem to equate this issue with the one of finding the maximum value of the modularity, as defined by Newman. Since the…

We propose a simple mixed membership model for social network clustering in this paper. A flexible function is adopted to measure affinities among a set of entities in a social network. The model not only allows each entity in the network…

Protein complexes conserved across species indicate processes that are core to cellular machinery (e.g. cell-cycle or DNA damage-repair complexes conserved across human and yeast). While numerous computational methods have been devised to…

Many biological networks have been labelled scale-free as their degree distribution can be approximately described by a powerlaw distribution. While the degree distribution does not summarize all aspects of a network it has often been…