Related papers: The Function of Communities in Protein Interaction…
In this paper, we propose MOUFLON, a fairness-aware, modularity-based community detection method that allows adjusting the importance of partition quality over fairness outcomes. MOUFLON uses a novel proportional balance fairness metric,…
Modular and hierarchical community structures are pervasive in real-world complex systems. A great deal of effort has gone into trying to detect and study these structures. Important theoretical advances in the detection of modular have…
Community detection algorithms have been widely used to study the organization of complex systems like the brain. A principal appeal of these techniques is their ability to identify a partition of brain regions (or nodes) into communities,…
Modularity is designed to measure the strength of division of a network into clusters (known also as communities). Networks with high modularity have dense connections between the vertices within clusters but sparse connections between…
Community detection and hierarchy extraction are usually thought of as separate inference tasks on networks. Considering only one of the two when studying real-world data can be an oversimplification. In this work, we present a generative…
Nestedness characterizes the linkage pattern of networked systems, indicating the likelihood that a node is linked to the nodes linked to the nodes with larger degrees than it. Networks of mutualistic relationship between distinct groups of…
Dense sub-graphs of sparse graphs (communities), which appear in most real-world complex networks, play an important role in many contexts. Most existing community detection algorithms produce a hierarchical structure of community and seek…
A number of recent studies have focused on the statistical properties of networked systems such as social networks and the World-Wide Web. Researchers have concentrated particularly on a few properties which seem to be common to many…
Here we review the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling…
Modularity for multilayer networks, also called multislice modularity, is parametric to a resolution factor and an inter-layer coupling factor. The former is useful to express layer-specific relevance and the latter quantifies the strength…
Many complex networks from the World-Wide-Web to biological networks are growing taking into account the heterogeneous features of the nodes. The feature of a node might be a discrete quantity such as a classification of a URL document as…
The advent of online social networks has led to the development of an abundant literature on the study of online social groups and their relationship to individuals' personalities as revealed by their textual productions. Social structures…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
The generalized version of modularity for multilayer networks, a.k.a. multislice modularity, is characterized by two model parameters, namely resolution factor and inter-layer coupling factor. The former corresponds to a notion of…
In the analysis of binary longitudinal data, it is of interest to model a dynamic relationship between a response and covariates as a function of time, while also investigating similar patterns of time-dependent interactions. We present a…
We study how to detect groups in a complex network each of which consists of component nodes sharing a similar connection pattern. Based on the mixture models and the exploratory analysis set up by Newman and Leicht (Newman and Leicht 2007…
The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other elements through the biosphere on a…
Experimental results often do not assess network structure; rather, the network structure is inferred by the dynamics of the nodes. From the dynamics of the nodes one then constructs a network of functional relations, termed the functional…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…