相关论文: Optimal Estimation of Bacterial Growth Rates Based…

Motivated by recent research on quantifying bacterial growth dynamics based on genome assemblies, we consider a permuted monotone matrix model $Y=\Theta\Pi+Z$, where the rows represent different samples, the columns represent contigs in…

Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many…

In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory and metabolic degrees of freedom. In the standard sense,…

Given a matrix the seriation problem consists in permuting its rows in such way that all its columns have the same shape, for example, they are monotone increasing. We propose a statistical approach to this problem where the matrix of…

Experimentalists have observed phenotypic variability in isogenic bacteria populations. We explore the hypothesis that in fluctuating environments this variability is tuned to maximize a bacterium's expected log growth rate, potentially…

Many applications, including rank aggregation, crowd-labeling, and graphon estimation, can be modeled in terms of a bivariate isotonic matrix with unknown permutations acting on its rows and/or columns. We consider the problem of estimating…

Motivated by applications in single-cell biology and metagenomics, we investigate the problem of matrix reordering based on a noisy disordered monotone Toeplitz matrix model. We establish the fundamental statistical limit for this problem…

There has been a recent surge of interest in studying permutation-based models for ranking from pairwise comparison data. Despite being structurally richer and more robust than parametric ranking models, permutation-based models are less…

We consider a ranking problem where we have noisy observations from a matrix with isotonic columns whose rows have been permuted by some permutation $\pi$ *. This encompasses many models, including crowd-labeling and ranking in tournaments…

For a given finite set $\Sigma$ of matrices with nonnegative integer entries we study the growth of $$ \max_t(\Sigma) = \max\{\|A_{1}... A_{t}\|: A_i \in \Sigma\}.$$ We show how to determine in polynomial time whether the growth with $t$ is…

One important problem in microbiome analysis is to identify the bacterial taxa that are associated with a response, where the microbiome data are summarized as the composition of the bacterial taxa at different taxonomic levels. This paper…

Linear regression studies the problem of estimating a model parameter $\beta^* \in \mathbb{R}^p$, from $n$ observations $\{(y_i,\mathbf{x}_i)\}_{i=1}^n$ from linear model $y_i = \langle \mathbf{x}_i,\beta^* \rangle + \epsilon_i$. We…

In this paper, by introducing two temporal-derivative-dependent auxiliary variables, a linearized and decoupled fourth-order compact finite difference method is developed and analyzed for the nonlinear coupled bacterial systems. The…

We introduce a new method for estimating the support size of an unknown distribution which provably matches the performance bounds of the state-of-the-art techniques in the area and outperforms them in practice. In particular, we present…

In this paper we develop and test algorithmic techniques to estimate genotypes fitnesses by analysis of observed daily frequency data monitoring the long-term evolution of bacterial populations. In particular, we develop a non-linear least…

Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this…

The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…

Time-homogeneous Markov chains are often used as disease progression models in studies of cost-effectiveness and optimal decision-making. Maximum likelihood estimation of these models can be challenging when data are collected at a time…

High-throughput experimental techniques and bioinformatics tools make it possible to obtain reconstructions of the metabolism of microbial species. Combined with mathematical frameworks such as flux balance analysis, which assumes that…

We consider the problem of adaptive estimation of the regression function in a framework where we replace ergodicity assumptions (such as independence or mixing) by another structural assumption on the model. Namely, we propose adaptive…