Related papers: A hierarchical Bayesian model for predicting ecolo…
In this paper we introduce a novel Bayesian approach for linking multiple social networks in order to discover the same real world person having different accounts across networks. In particular, we develop a latent model that allow us to…
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…
Recent technological advances and long-term data studies provide interaction data that can be modelled through dynamic networks, i.e a sequence of different snapshots of an evolving ecological network. Most often time is the parameter along…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Growing anthropogenic pressures have increased the need for robust predictive models. Meeting this demand requires approaches that can handle bigger data to yield forecasts that capture the variability and underlying uncertainty of…
Gene-gene and gene-environment interactions are widely believed to play significant roles in explaining the variability of complex traits. While substantial research exists in this area, a comprehensive statistical framework that addresses…
We present a probabilistic framework for overlapping community discovery and link prediction for relational data, given as a graph. The proposed framework has: (1) a deep architecture which enables us to infer multiple layers of latent…
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to…
We consider the concept of mutual information in ecological networks, and use this idea to analyse the Tangled Nature model of co-evolution. We show that this measure of correlation has two distinct behaviours depending on how we define the…
In ecology we may find scenarios where the same phenomenon (species occurrence, species abundance, etc.) is observed using two different types of samplers. For instance, species data can be collected from scientific sampling with a…
Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
As the availability and importance of temporal interaction data--such as email communication--increases, it becomes increasingly important to understand the underlying structure that underpins these interactions. Often these interactions…
Cooperative behaviors are deeply embedded in structured biological and social systems. Networks are often employed to portray pairwise interactions among individuals, where network nodes represent individuals and links indicate who…
Determining which proteins interact together is crucial to a systems-level understanding of the cell. Recently, algorithms based on Direct Coupling Analysis (DCA) pairwise maximum-entropy models have allowed to identify interaction partners…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
In data analysis, latent variables play a central role because they help provide powerful insights into a wide variety of phenomena, ranging from biological to human sciences. The latent tree model, a particular type of probabilistic…
Networks can describe the structure of a wide variety of complex systems by specifying which pairs of entities in the system are connected. While such pairwise representations are flexible, they are not necessarily appropriate when the…
Microorganisms play a critical role in host health. The advancement of high-throughput sequencing technology provides opportunities for a deeper understanding of microbial interactions. However, due to the limitations of 16S ribosomal RNA…
Patterns of nestedness and specialization asymmetry, where specialist species interact mainly with generalists while generalists interact with both generalists and specialists, are often observed in mutualistic and antagonistic bi-partite…