Related papers: CFinder: Locating cliques and overlapping modules …
Community discovery in complex networks is an interesting problem with a number of applications, especially in the knowledge extraction task in social and information networks. However, many large networks often lack a particular community…
Modularity is one of the most prominent properties of real-world complex networks. Here, we address the issue of module identification in two important classes of networks: bipartite networks and directed unipartite networks. Nodes in…
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…
Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…
Clustering is a widely-used data mining tool, which aims to discover partitions of similar items in data. We introduce a new clustering paradigm, \emph{accordant clustering}, which enables the discovery of (predefined) group level insights.…
Our work is motivated by and illustrated with application of association networks in computational biology, specifically in the context of gene/protein regulatory networks. Association networks represent systems of interacting elements,…
Community detection and link prediction are both of great significance in network analysis, which provide very valuable insights into topological structures of the network from different perspectives. In this paper, we propose a novel…
Cell instance segmentation in cytology images has significant importance for biology analysis and cancer screening, while remains challenging due to 1) the extensive overlapping translucent cell clusters that cause the ambiguous boundaries,…
Large datasets with interactions between objects are common to numerous scientific fields (i.e. social science, internet, biology...). The interactions naturally define a graph and a common way to explore or summarize such dataset is graph…
Many real-world networks, including nervous systems, exhibit meso-scale structure. This means that their elements can be grouped into meaningful sub-networks. In general, these sub-networks are unknown ahead of time and must be "discovered"…
Roughly speaking, clustering evolving networks aims at detecting structurally dense subgroups in networks that evolve over time. This implies that the subgroups we seek for also evolve, which results in many additional tasks compared to…
To better understand the overlapping modular organization of large networks with respect to flow, here we introduce the map equation for overlapping modules. In this information-theoretic framework, we use the correspondence between…
Essential protein plays a crucial role in the process of cell life. The identification of essential proteins can not only promote the development of drug target technology, but also contribute to the mechanism of biological evolution. There…
In this paper, we present an accurate and scalable approach to the face clustering task. We aim at grouping a set of faces by their potential identities. We formulate this task as a link prediction problem: a link exists between two faces…
Exact maximum clique finders have progressed to the point where we can investigate cliques in million-node social and information networks, as well as find strongly connected components in temporal networks. We use one such finder to study…
This paper is an extensive survey of literature on complex network communities and clustering. Complex networks describe a widespread variety of systems in nature and society especially systems composed by a large number of highly…
Multi-scale biomedical knowledge networks are expanding with emerging experimental technologies that generates multi-scale biomedical big data. Link prediction is increasingly used especially in bipartite biomedical networks to identify…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context.…
In some social and biological networks, the majority of nodes belong to multiple communities. It has recently been shown that a number of the algorithms that are designed to detect overlapping communities do not perform well in such highly…