Related papers: Learning functional groups in complex microbiomes
Population analyses of functional connectivity have provided a rich understanding of how brain function differs across time, individual, and cognitive task. An important but challenging task in such population analyses is the identification…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
Collective animal behaviors are paradigmatic examples of fully decentralized operations involving complex collective computations such as collective turns in flocks of birds or collective harvesting by ants. These systems offer a unique…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
It is common in the study of networks to investigate meso-scale features to try to gain an understanding of network structure and function. For example, numerous algorithms have been developed to try to identify "communities," which are…
The analysis of multilayer networks is among the most active areas of network science, and there are now several methods to detect dense "communities" of nodes in multilayer networks. One way to define a community is as a set of nodes that…
The brain is a highly complex organ consisting of a myriad of subsystems that flexibly interact and adapt over time and context to enable perception, cognition, and behavior. Understanding the multi-scale nature of the brain, i.e., how…
The human brain is a complex network of interconnected brain regions organized into functional modules with distinct roles in cognition and behavior. An important question concerns the persistence and stability of these modules over the…
Genomics data such as RNA gene expression, methylation and micro RNA expression are valuable sources of information for various clinical predictive tasks. For example, predicting survival outcomes, cancer histology type and other patients'…
Cell differentiation in multicellular organisms is a complex process whose mechanism can be understood by a reductionist approach, in which the individual processes that control the generation of different cell types are identified.…
As two main focuses of the study of complex networks, the community structure and the dynamics on networks have both attracted much attention in various scientific fields. However, it is still an open question how the community structure is…
Multi-modal learning is typically performed with network architectures containing modality-specific layers and shared layers, utilizing co-registered images of different modalities. We propose a novel learning scheme for unpaired…
Community structure represents the local organization of complex networks and the single most important feature to extract functional relationships between nodes. In the last years, the problem of community detection has been reformulated…
We focus on the detection of communities in multi-scale networks, namely networks made of different levels of organization and in which modules exist at different scales. It is first shown that methods based on modularity are not…
Community detection for large networks poses challenges due to the high computational cost as well as heterogeneous community structures. In this paper, we consider widely existing real-world networks with ``grouped communities'' (or ``the…
Ocean microbes are critical to both ocean ecosystems and the global climate. Flow cytometry, which measures cell optical properties in fluid samples, is routinely used in oceanographic research. Despite decades of accumulated data,…
Microbiota profiles measure the structure of microbial communities in a defined environment (known as microbiomes). In the past decade, microbiome research has focused on health applications as a result of which the gut microbiome has been…
Metagenomics has revealed hundreds of bacterial species in almost all microbiota. In a few well-studied cases, bacterial communities have been observed to coordinate their metabolic fluxes. In principle, bacteria can divide tasks to reap…
Characterizing genes with semantic information is an important process regarding the description of gene products. In spite that complete genomes of many organisms have been already sequenced, the biological functions of all of their genes…
The competition for resources is a defining feature of microbial communities. In many contexts, from soils to host-associated communities, highly diverse microbes are organized into metabolic groups or guilds with similar resource…