Related papers: Interactions between species introduce spurious as…
Our aim is to detect mechanistic interaction between the effects of two causal factors on a binary response, as an aid to identifying situations where the effects are mediated by a common mechanism. We propose a formalization of mechanistic…
Expanding a lower-dimensional problem to a higher-dimensional space and then projecting back is often beneficial. This article rigorously investigates this perspective in the context of finite mixture models, namely how to improve inference…
Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open…
Inductive inference is the process of extracting general rules from specific observations. This problem also arises in the analysis of biological networks, such as genetic regulatory networks, where the interactions are complex and the…
The majority of common diseases are influenced by multiple genetic and environmental factors such as Cancer. Even though uncovering the main causes of disease is deemed difficult due to the complexity of gene-gene and gene-environment…
Scientific hypotheses typically concern specific aspects of complex, imperfectly understood or entirely unknown mechanisms, such as the effect of gene expression levels on phenotypes or how microbial communities influence environmental…
Causality plays a central role in understanding interactions between variables in complex systems. These systems often exhibit state-dependent causal relationships, where both the strength and direction of causality vary with the value of…
Autism spectrum disorder (ASD) is one of the major developmental disorders affecting children. Recently, it has been hypothesized that ASD is associated with atypical brain connectivities. A substantial body of researches use Pearson's…
Antibiotic resistance is a major threat to global health. It emerges in multispecies microbial communities under antibiotic exposure. This makes antibiotic spectrum -- a drug's distribution of effects across species -- a potential key…
Observational studies can play a useful role in assessing the comparative effectiveness of competing treatments. In a clinical trial the randomization of participants to treatment and control groups generally results in well-balanced groups…
This review focuses on microbiomes associated with residues within the context of other microbial habitats in cereal-producing agroecosystems such as phyllosphere or rhizosphere. We connect residue microbiome with the survival of…
A mechanism of sympatric speciation is presented based on the interaction-induced developmental plasticity of phenotypes. First, phenotypes of individuals with identical genotypes split into a few groups, according to instability in the…
From pathogens and computer viruses to genes and memes, contagion models have found widespread utility across the natural and social sciences. Despite their success and breadth of adoption, the approach and structure of these models remain…
Mutualistic interactions, where individuals from different species can benefit from each other, are widespread across ecosystems. This study develops a general deterministic model of mutualism involving two populations, assuming that…
We wish to formally test for changes in the taxonomic diversity of a community, especially in the presence of high latent diversity. Drawing on the meta-analysis literature, we construct a model for diversity that accounts for covariate…
Determining associations among different species from citizen science databases is challenging due to observer behavior and intrinsic density variations that give rise to correlations that do not imply species associations. This paper…
Bipartite experiments are a recent object of study in causal inference, whereby treatment is applied to one set of units and outcomes of interest are measured on a different set of units. These experiments are particularly useful in…
Causal mediation analysis seeks to determine whether an independent variable affects a response variable directly or whether it does so indirectly, by way of a mediator. The existing statistical tests to determine the existence of an…
The behavior of ecological systems mainly relies on the interactions between the species it involves. We consider the problem of inferring the species interaction network from abundance data. To be relevant, any network inference…
The advent of molecular biology has led to the identification of definitive causative factors for a number of diseases, most of which are monogenic. Causes for most common diseases across the population, however, seem elusive and cannot be…