Related papers: Learning functional groups in complex microbiomes
Much effort has gone into understanding the modular nature of complex networks. Communities, also known as clusters or modules, are typically considered to be densely interconnected groups of nodes that are only sparsely connected to other…
Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these…
The fundamental relationship between the mesoscopic structure of neuronal circuits and organismic functions they subserve is one of the major challenges in contemporary neuroscience. Formation of structurally connected modules of neurons…
Communities are clusters of nodes with a higher than average density of internal connections. Their detection is of great relevance to better understand the structure and hierarchies present in a network. Modularity has become a standard…
Deep metric learning has yielded impressive results in tasks such as clustering and image retrieval by leveraging neural networks to obtain highly discriminative feature embeddings, which can be used to group samples into different classes.…
Our planet is roughly closed to matter, but open to energy input from the sun. However, to harness this energy, organisms must transform matter from one chemical (redox) state to another. For example, photosynthetic organisms can capture…
Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…
Soil microbial communities are known to be robust against perturbations such as nutrition inputs, which appears as an obstacle for the soil improvement. On the other hand, its adaptable aspect has been also reported. Here we propose simple…
Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows us…
A small number of (perhaps only 6) broken-symmetries, marked by the edges of a hierarchical series of physical {\em subsystem-types}, underlie the delicate correlation-based complexity of life on our planet's surface. Order-parameters…
A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…
Community detection is of great importance for understand-ing graph structure in social networks. The communities in real-world networks are often overlapped, i.e. some nodes may be a member of multiple clusters. How to uncover the…
Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…
Comprehending complex systems by simplifying and highlighting important dynamical patterns requires modeling and mapping higher-order network flows. However, complex systems come in many forms and demand a range of representations,…
Multicellular self-assembly into functional structures is a dynamic process that is critical in the development and diseases, including embryo development, organ formation, tumor invasion, and others. Being able to infer collective cell…
Microbiomes not only underpin Earth's biogeochemical cycles but also play crucial roles in both engineered and natural ecosystems, such as the soil, wastewater treatment, and the human gut. However, microbiome engineering faces significant…
A spacially extended model of the collective behavior of a large number of locally acting organisms is proposed in which organisms move probabilistically between local cells in space, but with weights dependent on local morphogenetic…
Feed-forward neural networks consist of a sequence of layers, in which each layer performs some processing on the information from the previous layer. A downside to this approach is that each layer (or module, as multiple modules can…
Microbes are often discussed in terms of dichotomies such as copiotrophic/oligotrophic and fast/slow-growing microbes, defined using the characterisation of microbial growth in isolated cultures. The dichotomies are usually qualitative…
Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational…