Related papers: Robust Parameter Estimation for Biological Systems…

Mathematical modelling has become an established tool for studying the dynamics of biological systems. Current applications range from building models that reproduce quantitative data to identifying systems with predefined qualitative…

In this paper, we study the problem of parameter estimation in a sensor network, where the measurements and updates of some sensors might be arbitrarily manipulated by adversaries. Despite the presence of such misbehaviors, normally…

Markov community models have been applied to sessile organisms because such models facilitate estimation of transition probabilities by tracking species occupancy at many fixed observation points over multiple periods of time. Estimation of…

The last decade has seen a number of advances in computationally efficient algorithms for statistical methods subject to robustness constraints. An estimator may be robust in a number of different ways: to contamination of the dataset, to…

A major challenge for community ecology is using spatio-temporal data to infer parameters of dynamical models without conducting laborious experiments. We present a novel framework from statistical physics -- Maximum Caliber -- to…

We present methods for estimating loss-based measures of the performance of a prediction model in a target population that differs from the source population in which the model was developed, in settings where outcome and covariate data are…

Estimating a covariance matrix is central to high-dimensional data analysis. Empirical analyses of high-dimensional biomedical data, including genomics, proteomics, microbiome, and neuroimaging, among others, consistently reveal strong…

We consider the problem of counting (stable) equilibriums of an important family of algebraic differential equations modeling multistable biological regulatory systems. The problem can be solved, in principle, using real quantifier…

Interpreting the performance results of models that attempt to realize user behavior in platforms that employ recommenders is a big challenge that researchers and practitioners continue to face. Although current evaluation tools possess the…

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome…

In this work we combine two distinct machine learning methodologies, sequential Monte Carlo and Bayesian experimental design, and apply them to the problem of inferring the dynamical parameters of a quantum system. We design the algorithm…

This paper considers the problem of robustly estimating the parameters of a heavy-tailed multivariate distribution when the covariance matrix is known to have the structure of a low-rank matrix plus a diagonal matrix as considered in factor…

Microbial communities are ubiquitous in nature and come in a multitude of forms, ranging from communities dominated by a handful of species to communities containing a wide variety of metabolically distinct organisms. This huge range in…

We develop a variational Bayes approach for dynamic variable selection in high-dimensional regression models with time-varying parameters and predictors that exhibit a predefined group structure. Through comprehensive simulation studies, we…

The gut microbiome plays a crucial role in human health, yet the mechanisms underlying host-microbiome interactions remain unclear, limiting its translational potential. Recent microbiome multiomics studies, particularly paired…

Biophysical models describing complex, cellular phenomena typically include systems of nonlinear differential equations with many free parameters. While experimental measurements can fix some parameters, those describing internal cellular…

With the acceleration of urbanization and living standards, microorganisms play increasingly important roles in industrial production, bio-technique, and food safety testing. Microorganism biovolume measurements are one of the essential…

Ecosystems tend to fluctuate around stable equilibria in response to internal dynamics and environmental factors. Occasionally, they enter an unstable tipping region and collapse into an alternative stable state. Our understanding of how…

Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities,…

Identification of features is a critical task in microbiome studies that is complicated by the fact that microbial data are high dimensional and heterogeneous. Masked by the complexity of the data, the problem of separating signals from…