Differential abundance analysis is a key component of microbiome studies. While dozens of methods for it exist, currently, there is no consensus on the preferred methods. Correctness of results in differential abundance analysis is an ambiguous concept that cannot be evaluated without employing simulated data, but we argue that consistency of results across datasets should be considered as an essential quality of a well-performing method. We compared the performance of 14 differential abundance analysis methods employing datasets from 54 taxonomic profiling studies based on 16S rRNA gene or shotgun sequencing. For each method, we examined how the results replicated between random partitions of each dataset and between datasets from independent studies. While certain methods showed good consistency, some widely used methods were observed to produce a substantial number of conflicting findings. Overall, the highest consistency without unnecessary reduction in sensitivity was attained by analyzing relative abundances with a non-parametric method (Wilcoxon test or ordinal regression model) or linear regression (MaAsLin2). Comparable performance was also attained by analyzing presence/absence of taxa with logistic regression.
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The broad class of multivariate unified skew-normal (SUN) distributions has been recently shown to possess important conjugacy properties. When used as priors for the vector of parameters in general probit, tobit, and multinomial probit models, these distributions yield posteriors that still belong to the SUN family. Although such a core result has led to important advancements in Bayesian inference and computation, its applicability beyond likelihoods associated with fully-observed, discretized, or censored realizations from multivariate Gaussian models remains yet unexplored. This article covers such an important gap by proving that the wider family of multivariate unified skew-elliptical (SUE) distributions, which extends SUNs to more general perturbations of elliptical densities, guarantees conjugacy for broader classes of models, beyond those relying on fully-observed, discretized or censored Gaussians. Such a result leverages the closure under linear combinations, conditioning and marginalization of SUE to prove that this family is conjugate to the likelihood induced by general multivariate regression models for fully-observed, censored or dichotomized realizations from skew-elliptical distributions. This advancement enlarges the set of models that enable conjugate Bayesian inference to general formulations arising from elliptical and skew-elliptical families, including the multivariate Student's t and skew-t, among others.
Neural radiance fields (NeRFs) are a deep learning technique that can generate novel views of 3D scenes using sparse 2D images from different viewing directions and camera poses. As an extension of conventional NeRFs in underwater environment, where light can get absorbed and scattered by water, SeaThru-NeRF was proposed to separate the clean appearance and geometric structure of underwater scene from the effects of the scattering medium. Since the quality of the appearance and structure of underwater scenes is crucial for downstream tasks such as underwater infrastructure inspection, the reliability of the 3D reconstruction model should be considered and evaluated. Nonetheless, owing to the lack of ability to quantify uncertainty in 3D reconstruction of underwater scenes under natural ambient illumination, the practical deployment of NeRFs in unmanned autonomous underwater navigation is limited. To address this issue, we introduce a spatial perturbation field D_omega based on Bayes' rays in SeaThru-NeRF and perform Laplace approximation to obtain a Gaussian distribution N(0,Sigma) of the parameters omega, where the diagonal elements of Sigma correspond to the uncertainty at each spatial location. We also employ a simple thresholding method to remove artifacts from the rendered results of underwater scenes. Numerical experiments are provided to demonstrate the effectiveness of this approach.
A common method for estimating the Hessian operator from random samples on a low-dimensional manifold involves locally fitting a quadratic polynomial. Although widely used, it is unclear if this estimator introduces bias, especially in complex manifolds with boundaries and nonuniform sampling. Rigorous theoretical guarantees of its asymptotic behavior have been lacking. We show that, under mild conditions, this estimator asymptotically converges to the Hessian operator, with nonuniform sampling and curvature effects proving negligible, even near boundaries. Our analysis framework simplifies the intensive computations required for direct analysis.
We formulate and analyze a multiscale method for an elliptic problem with an oscillatory coefficient based on a skeletal (hybrid) formulation. More precisely, we employ hybrid discontinuous Galerkin approaches and combine them with the localized orthogonal decomposition methodology to obtain a coarse-scale skeletal method that effectively includes fine-scale information. This work is the first step in reliably merging hybrid skeletal formulations and localized orthogonal decomposition to unite the advantages of both strategies. Numerical experiments are presented to illustrate the theoretical findings.
We propose a topological mapping and localization system able to operate on real human colonoscopies, despite significant shape and illumination changes. The map is a graph where each node codes a colon location by a set of real images, while edges represent traversability between nodes. For close-in-time images, where scene changes are minor, place recognition can be successfully managed with the recent transformers-based local feature matching algorithms. However, under long-term changes -- such as different colonoscopies of the same patient -- feature-based matching fails. To address this, we train on real colonoscopies a deep global descriptor achieving high recall with significant changes in the scene. The addition of a Bayesian filter boosts the accuracy of long-term place recognition, enabling relocalization in a previously built map. Our experiments show that ColonMapper is able to autonomously build a map and localize against it in two important use cases: localization within the same colonoscopy or within different colonoscopies of the same patient. Code: //github.com/jmorlana/ColonMapper.
Artificial Intelligence (AI) is revolutionizing biodiversity research by enabling advanced data analysis, species identification, and habitats monitoring, thereby enhancing conservation efforts. Ensuring reproducibility in AI-driven biodiversity research is crucial for fostering transparency, verifying results, and promoting the credibility of ecological findings.This study investigates the reproducibility of deep learning (DL) methods within the biodiversity domain. We design a methodology for evaluating the reproducibility of biodiversity-related publications that employ DL techniques across three stages. We define ten variables essential for method reproducibility, divided into four categories: resource requirements, methodological information, uncontrolled randomness, and statistical considerations. These categories subsequently serve as the basis for defining different levels of reproducibility. We manually extract the availability of these variables from a curated dataset comprising 61 publications identified using the keywords provided by biodiversity experts. Our study shows that the dataset is shared in 47% of the publications; however, a significant number of the publications lack comprehensive information on deep learning methods, including details regarding randomness.
Several new geometric quantile-based measures for multivariate dispersion, skewness, kurtosis, and spherical asymmetry are defined. These measures differ from existing measures, which use volumes and are easy to calculate. Some theoretical justification is given, followed by experiments illustrating that they are reasonable measures of these distributional characteristics and computing confidence regions with the desired coverage.
One of the most promising applications of machine learning (ML) in computational physics is to accelerate the solution of partial differential equations (PDEs). The key objective of ML-based PDE solvers is to output a sufficiently accurate solution faster than standard numerical methods, which are used as a baseline comparison. We first perform a systematic review of the ML-for-PDE solving literature. Of articles that use ML to solve a fluid-related PDE and claim to outperform a standard numerical method, we determine that 79% (60/76) compare to a weak baseline. Second, we find evidence that reporting biases, especially outcome reporting bias and publication bias, are widespread. We conclude that ML-for-PDE solving research is overoptimistic: weak baselines lead to overly positive results, while reporting biases lead to underreporting of negative results. To a large extent, these issues appear to be caused by factors similar to those of past reproducibility crises: researcher degrees of freedom and a bias towards positive results. We call for bottom-up cultural changes to minimize biased reporting as well as top-down structural reforms intended to reduce perverse incentives for doing so.
Mediation analyses allow researchers to quantify the effect of an exposure variable on an outcome variable through a mediator variable. If a binary mediator variable is misclassified, the resulting analysis can be severely biased. Misclassification is especially difficult to deal with when it is differential and when there are no gold standard labels available. Previous work has addressed this problem using a sensitivity analysis framework or by assuming that misclassification rates are known. We leverage a variable related to the misclassification mechanism to recover unbiased parameter estimates without using gold standard labels. The proposed methods require the reasonable assumption that the sum of the sensitivity and specificity is greater than 1. Three correction methods are presented: (1) an ordinary least squares correction for Normal outcome models, (2) a multi-step predictive value weighting method, and (3) a seamless expectation-maximization algorithm. We apply our misclassification correction strategies to investigate the mediating role of gestational hypertension on the association between maternal age and pre-term birth.
This paper delves into the equivalence problem of Smith forms for multivariate polynomial matrices. Generally speaking, multivariate ($n \geq 2$) polynomial matrices and their Smith forms may not be equivalent. However, under certain specific condition, we derive the necessary and sufficient condition for their equivalence. Let $F\in K[x_1,\ldots,x_n]^{l\times m}$ be of rank $r$, $d_r(F)\in K[x_1]$ be the greatest common divisor of all the $r\times r$ minors of $F$, where $K$ is a field, $x_1,\ldots,x_n$ are variables and $1 \leq r \leq \min\{l,m\}$. Our key findings reveal the result: $F$ is equivalent to its Smith form if and only if all the $i\times i$ reduced minors of $F$ generate $K[x_1,\ldots,x_n]$ for $i=1,\ldots,r$.
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