Related papers: Inference of ecological interaction networks

Inference and prediction are fundamental to the study of complex systems, where network data are often incomplete, inaccurate or obtained indirectly. In this paper, we review recent advances in network sampling and comparison, as well as in…

One challenge of physics is to explain how collective properties arise from microscopic interactions. Indeed, interactions form the building blocks of almost all physical theories and are described by polynomial terms in the action. The…

Network inference approaches are now widely used in biological applications to probe regulatory relationships between molecular components such as genes or proteins. Many methods have been proposed for this setting, but the connections and…

Understanding the architectural subtleties of ecological networks, believed to confer them enhanced stability and robustness, is a subject of outmost relevance. Mutualistic interactions have been profusely studied and their corresponding…

Networks effectively capture interactions among components of complex systems, and have thus become a mainstay in many scientific disciplines. Growing evidence, especially from biology, suggest that networks undergo changes over time, and…

Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…

Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…

We develop a matrix-based approach to predict and verify indirect interactions in gene and protein regulatory networks. It is based on the approximate transitivity of indirect regulations (e.g. A regulates B and B regulates C often implies…

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…

Ecological networks describe the interactions between different species, informing us of how they rely on one another for food, pollination and survival. If a species in an ecosystem is under threat of extinction, it can affect other…

Networks are widely used in the biological, physical, and social sciences as a concise mathematical representation of the topology of systems of interacting components. Understanding the structure of these networks is one of the outstanding…

Network economics is the study of a rich class of equilibrium problems that occur in the real world, from traffic management to supply chains and two-sided online marketplaces. In this paper we explore causal inference in network economics,…

We present a physically-inspired model and an efficient algorithm to infer hierarchical rankings of nodes in directed networks. It assigns real-valued ranks to nodes rather than simply ordinal ranks, and it formalizes the assumption that…

Descriptive and inferential social network analysis has become common in public administration studies of network governance and management. A large literature has developed in two broad categories: antecedents of network structure, and…

The automated inference of physically interpretable (bio)chemical reaction network models from measured experimental data is a challenging problem whose solution has significant commercial and academic ramifications. It is demonstrated,…

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…

Graphs and networks provide a canonical representation of relational data, with massive network data sets becoming increasingly prevalent across a variety of scientific fields. Although tools from mathematics and computer science have been…

One can often make inferences about a growing network from its current state alone. For example, it is generally possible to determine how a network changed over time or pick among plausible mechanisms explaining its growth. In practice,…

I introduce an axiomatic representation, called ecoset, to consider interactions between species in ecological systems. For interspecific competition, the exclusion conjecture (Gause) is put in a symbolic way and used as a basic operational…

Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…