相关论文: A Phylogeny-based Test of Mediation Effect in Micr…
Prevalent in biomedical applications (e.g., human phenotype research), multimodal datasets can provide valuable insights into the underlying physiological mechanisms. However, current machine learning (ML) models designed to analyze these…
Mutations in a microbial population can increase the frequency of a genotype not only by increasing its exponential growth rate, but also by decreasing its lag time or adjusting the yield (resource efficiency). The contribution of multiple…
To unbiasedly estimate a causal effect on an outcome unconfoundedness is often assumed. If there is sufficient knowledge on the underlying causal structure then existing confounder selection criteria can be used to select subsets of the…
Multidimensional scaling (MDS) is a dimensionality reduction technique for microbial ecology data analysis that represents the multivariate structure while preserving pairwise distances between samples. While its improvement has enhanced…
We study treatment effect modifiers for causal analysis in a social network, where neighbors' characteristics or network structure may affect the outcome of a unit, and the goal is to identify sub-populations with varying treatment effects…
Deciding on an appropriate intervention requires a causal model of a treatment, the outcome, and potential mediators. Causal mediation analysis lets us distinguish between direct and indirect effects of the intervention, but has mostly been…
Phylogenetics is a fundamental component of evolutionary analysis frameworks in biology and linguistics. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has highlighted the necessity for phylogenetic software to…
In some conditions, bacteria self-organise into biofilms, supracellular structures made of a self-produced embedding matrix, mainly composed on polysaccharides, DNA, proteins and lipids. It is known that bacteria change their colony/matrix…
Interactions between organisms are mediated by an intricate network of physico-chemical substances and other organisms. Understanding the dynamics of mediators and how they shape the population spatial distribution is key to predict…
Neuroimaging measures of the brain's white matter connections can enable the prediction of non-imaging phenotypes, such as demographic and cognitive measures. Existing works have investigated traditional microstructure and connectivity…
We analyze publicly available data on Affymetrix microarrays spike-in experiments on the human HGU133 chipset in which sequences are added in solution at known concentrations. The spike-in set contains sequences of bacterial, human and…
An important task in microbiome studies is to test the existence of and give characterization to differences in the microbiome composition across groups of samples. Important challenges of this problem include the large within-group…
Mediation analysis extending beyond single mediators has gained significant attention in recent years. However, related methods often assume the absence of unmeasured mediator-outcome confounding. To address this, we develop a mediation…
The relationship between microscopic observations and macroscopic behavior is a fundamental open question in biophysical systems. Here, we develop a unified approach that---in contrast with existing methods---predicts cell type from…
Synthetic microbiomes offer new possibilities for modulating microbiota, to address the barriers in multidtug resistance (MDR) research. We present a Bayesian optimization approach to enable efficient searching over the space of synthetic…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the…
Many studies have shown that Physarum polycephalum slime mold is able to find the shortest path in a maze. In this paper we study this behavior in a network, using a hyperbolic model of chemotaxis. Suitable transmission and boundary…
As a widely observable social effect, influence diffusion refers to a process where innovations, trends, awareness, etc. spread across the network via the social impact among individuals. Motivated by such social effect, the concept of…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…