相关论文: Interactions between species introduce spurious as…
Experimental and observational studies often lead to spurious association between the outcome and independent variables describing the intervention, because of confounding to third-party factors. Even in randomized clinical trials,…
In settings where interference between units is possible, we define the prevalence of indirect effects to be the number of units who are affected by the treatment of others. This quantity does not fully identify an indirect effect, but may…
We consider a setting in which we have a treatment and a large number of covariates for a set of observations, and wish to model their relationship with an outcome of interest. We propose a simple method for modeling interactions between…
Identifying which taxa in our microbiota are associated with traits of interest is important for advancing science and health. However, the identification is challenging because the measured vector of taxa counts (by amplicon sequencing) is…
Inflammatory bowel diseases (IBD) are complex diseases in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when they are exposed to yet unclear environmental factors. The complexity of this class…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
Microbiology is the science of microbes, particularly bacteria. Many bacteria are motile: they are capable of self-propulsion. Among these, a significant class execute so-called run-and-tumble motion: they follow a fairly straight path for…
During the last decades macroecology has identified broad-scale patterns of abundances and diversity of microbial communities and put forward some potential explanations for them. However, these advances are not paralleled by a full…
Machine learning has been successfully used in critical domains, such as medicine. However, extracting meaningful insights from biomedical data is often constrained by the lack of their available disease labels. In this research, we…
Microbial ecology serves as a foundation for a wide range of scientific and biomedical studies. Rapidly-evolving high-throughput sequencing technology enables the comprehensive search for microbial biomarkers using longitudinal experiments.…
Growth rates and biomass yields are key descriptors used in microbiology studies to understand how microbial species respond to changes in the environment. Of these, biomass yield estimates are typically obtained using cell counts and…
Determining the relative importance of environmental factors, biotic interactions and stochasticity in assembling and maintaining species-rich communities remains a major challenge in ecology. In plant communities, interactions between…
Bacterial Vaginosis (BV) affects nearly 23-29% of women worldwide and increases risk of miscarriage, preterm birth, and sexually transmitted infections. It involves a shift in the vaginal microbiome from Lactobacillus dominance to a diverse…
Numerous studies have shown that microbial metabolites, which represent the products of bacteria in the human gut, play a key role in shaping cancer risk and response to treatment. However, metabolite data typically contain a large…
Deep learning models are known to often learn features that spuriously correlate with the class label during training but are irrelevant to the prediction task. Existing methods typically address this issue by annotating potential spurious…
Migration of cells can be characterized by two, prototypical types of motion: individual and collective migration. We propose a statistical-inference approach designed to detect the presence of cell-cell interactions that give rise to…
Compositional data arise in many areas of research in the natural and biomedical sciences. One prominent example is in the study of the human gut microbiome, where one can measure the relative abundance of many distinct microorganisms in a…
Clinical decisions to treat and diagnose patients are affected by implicit biases formed by racism, ableism, sexism, and other stereotypes. These biases reflect broader systemic discrimination in healthcare and risk marginalizing already…
The microbial community composition in the human gut has a profound effect on human health. This observation has lead to extensive use of microbiome therapies, including over-the-counter ``probiotic" treatments intended to alter the…
Learning causal relationships between pairs of complex traits from observational studies is of great interest across various scientific domains. However, most existing methods assume the absence of unmeasured confounding and restrict causal…