Related papers: Learning functional groups in complex microbiomes
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…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
The design of biological networks using bacteria as the basic elements of the network is initially motivated by a phenomenon called quorum sensing. Through quorum sensing, each bacterium performs sensing the medium and communicating it to…
As the number of solved protein structures increases, the opportunities for meta-analysis of this dataset increase too. Protein structures are known to be formed of domains; structural and functional subunits that are often repeated across…
Integrating structural information and metadata, such as gender, social status, or interests, enriches networks and enables a better understanding of the large-scale structure of complex systems. However, existing approaches to metadata…
Collective animal movement fascinates children and scientists alike. One of the most commonly given explanations for collective animal movement is improved foraging. Animals are hypothesized to gain from searching for food in groups. Here,…
Microorganisms employ sophisticated mechanisms for intercellular communication and environmental sensing, with quorum sensing serving as a fundamental regulatory process. Dysregulation of quorum sensing has been implicated in various…
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…
Proteins perform essential biological functions, and accurate classification of their sequences is critical for understanding structure-function relationships, enzyme mechanisms, and molecular interactions. This study presents a deep…
Collective cell migration in response to a chemical cue occurs in many biological processes such as morphogenesis and cancer metastasis. Clusters of migratory cells in these systems are capable of responding to gradients of less than 1%…
Community detection in networks is the process of identifying unusually well-connected sub-networks and is a central component of many applied network analyses. The paradigm of modularity optimization stipulates a partition of the network's…
In order to efficiently explore the chemical space of all possible small molecules, a common approach is to compress the dimension of the system to facilitate downstream machine learning tasks. Towards this end, we present a data driven…
The investigation of community structures in networks is an important issue in many domains and disciplines. This problem is relevant for social tasks (objective analysis of relationships on the web), biological inquiries (functional…
An approach to improve neural network interpretability is via clusterability, i.e., splitting a model into disjoint clusters that can be studied independently. We define a measure for clusterability and show that pre-trained models form…
Unveiling the community structure of networks is a powerful methodology to comprehend interconnected systems across the social and natural sciences. To identify different types of functional modules in interaction data aggregated in a…
Living systems are made of active materials with microscopic components that work together to perform macroscopic biological tasks. The breakdown of these collective functionalities leads to diseases, which, conversely, could be treated by…
The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…
Functional connectivity analysis yields powerful insights into our understanding of the human brain. Group-wise functional community detection aims to partition the brain into clusters, or communities, in which functional activity is…
Genetic and pharmacological perturbation experiments, such as deleting a gene and monitoring gene expression responses, are powerful tools for studying cellular signal transduction pathways. However, it remains a challenge to automatically…
Microbes can affect processes from food production to human health. Such microbes are not isolated, but rather interact with each other and establish connections with their living environments. Understanding these interactions is essential…