We study knowable informational dependence between empirical questions, modeled as continuous functional dependence between variables in a topological setting. We also investigate epistemic independence in topological terms and show that it is compatible with functional (but non-continuous) dependence. We then proceed to study a stronger notion of knowability based on uniformly continuous dependence. On the technical logical side, we determine the complete logics of languages that combine general functional dependence, continuous dependence, and uniformly continuous dependence.
The approach to analysing compositional data has been dominated by the use of logratio transformations, to ensure exact subcompositional coherence and, in some situations, exact isometry as well. A problem with this approach is that data zeros, found in most applications, have to be replaced to allow the logarithmic transformation. An alternative new approach, called the `chiPower' transformation, which allows data zeros, is to combine the standardization inherent in the chi-square distance in correspondence analysis, with the essential elements of the Box-Cox power transformation. The chiPower transformation is justified because it} defines between-sample distances that tend to logratio distances for strictly positive data as the power parameter tends to zero, and are then equivalent to transforming to logratios. For data with zeros, a value of the power can be identified that brings the chiPower transformation as close as possible to a logratio transformation, without having to substitute the zeros. Especially in the area of high-dimensional data, this alternative approach can present such a high level of coherence and isometry as to be a valid approach to the analysis of compositional data. Furthermore, in a supervised learning context, if the compositional variables serve as predictors of a response in a modelling framework, for example generalized linear models, then the power can be used as a tuning parameter in optimizing the accuracy of prediction through cross-validation. The chiPower-transformed variables have a straightforward interpretation, since they are each identified with single compositional parts, not ratios.
Effective application of mathematical models to interpret biological data and make accurate predictions often requires that model parameters are identifiable. Approaches to assess the so-called structural identifiability of models are well-established for ordinary differential equation models, yet there are no commonly adopted approaches that can be applied to assess the structural identifiability of the partial differential equation (PDE) models that are requisite to capture spatial features inherent to many phenomena. The differential algebra approach to structural identifiability has recently been demonstrated to be applicable to several specific PDE models. In this brief article, we present general methodology for performing structural identifiability analysis on partially observed reaction-advection-diffusion (RAD) PDE models that are linear in the unobserved quantities. We show that the differential algebra approach can always, in theory, be applied to such models. Moreover, despite the perceived complexity introduced by the addition of advection and diffusion terms, identifiability of spatial analogues of non-spatial models cannot decrease in structural identifiability. We conclude by discussing future possibilities and the computational cost of performing structural identifiability analysis on more general PDE models.
Principal component analysis (PCA) is a longstanding and well-studied approach for dimension reduction. It rests upon the assumption that the underlying signal in the data has low rank, and thus can be well-summarized using a small number of dimensions. The output of PCA is typically represented using a scree plot, which displays the proportion of variance explained (PVE) by each principal component. While the PVE is extensively reported in routine data analyses, to the best of our knowledge the notion of inference on the PVE remains unexplored. In this paper, we consider inference on the PVE. We first introduce a new population quantity for the PVE with respect to an unknown matrix mean. Critically, our interest lies in the PVE of the sample principal components (as opposed to unobserved population principal components); thus, the population PVE that we introduce is defined conditional on the sample singular vectors. We show that it is possible to conduct inference, in the sense of confidence intervals, p-values, and point estimates, on this population quantity. Furthermore, we can conduct valid inference on the PVE of a subset of the principal components, even when the subset is selected using a data-driven approach such as the elbow rule. We demonstrate the proposed approach in simulation and in an application to a gene expression dataset.
There has been significant interest in understanding how practical constraints on contemporary quantum devices impact the complexity of quantum learning. For the classic question of tomography, recent work tightly characterized the copy complexity for any protocol that can only measure one copy of the unknown state at a time, showing it is polynomially worse than if one can make fully-entangled measurements. While we now have a fairly complete picture of the rates for such tasks in the near-term and fault-tolerant regimes, it remains poorly understood what the landscape in between looks like. In this work, we study tomography in the natural setting where one can make measurements of $t$ copies at a time. For sufficiently small $\epsilon$, we show that for any $t \le d^2$, $\widetilde{\Theta}(\frac{d^3}{\sqrt{t}\epsilon^2})$ copies are necessary and sufficient to learn an unknown $d$-dimensional state $\rho$ to trace distance $\epsilon$. This gives a smooth and optimal interpolation between the known rates for single-copy and fully-entangled measurements. To our knowledge, this is the first smooth entanglement-copy tradeoff known for any quantum learning task, and for tomography, no intermediate point on this curve was known, even at $t = 2$. An important obstacle is that unlike the optimal single-copy protocol, the optimal fully-entangled protocol is inherently biased and thus precludes naive batching approaches. Instead, we devise a novel two-stage procedure that uses Keyl's algorithm to refine a crude estimate for $\rho$ based on single-copy measurements. A key insight is to use Schur-Weyl sampling not to estimate the spectrum of $\rho$, but to estimate the deviation of $\rho$ from the maximally mixed state. When $\rho$ is far from the maximally mixed state, we devise a novel quantum splitting procedure that reduces to the case where $\rho$ is close to maximally mixed.
Interpolation of data on non-Euclidean spaces is an active research area fostered by its numerous applications. This work considers the Hermite interpolation problem: finding a sufficiently smooth manifold curve that interpolates a collection of data points on a Riemannian manifold while matching a prescribed derivative at each point. We propose a novel procedure relying on the general concept of retractions to solve this problem on a large class of manifolds, including those for which computing the Riemannian exponential or logarithmic maps is not straightforward, such as the manifold of fixed-rank matrices. We analyze the well-posedness of the method by introducing and showing the existence of retraction-convex sets, a generalization of geodesically convex sets. We extend to the manifold setting a classical result on the asymptotic interpolation error of Hermite interpolation. We finally illustrate these results and the effectiveness of the method with numerical experiments on the manifold of fixed-rank matrices and the Stiefel manifold of matrices with orthonormal columns.
This essay provides a comprehensive analysis of the optimization and performance evaluation of various routing algorithms within the context of computer networks. Routing algorithms are critical for determining the most efficient path for data transmission between nodes in a network. The efficiency, reliability, and scalability of a network heavily rely on the choice and optimization of its routing algorithm. This paper begins with an overview of fundamental routing strategies, including shortest path, flooding, distance vector, and link state algorithms, and extends to more sophisticated techniques.
Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately in relation to the underlying research problem. This could be attributed to a lack of accessibility of metric-related knowledge: While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Focusing on biomedical image analysis but with the potential of transfer to other fields, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. To facilitate comprehension, illustrations and specific examples accompany each pitfall. As a structured body of information accessible to researchers of all levels of expertise, this work enhances global comprehension of a key topic in image analysis validation.
We present Surjective Sequential Neural Likelihood (SSNL) estimation, a novel method for simulation-based inference in models where the evaluation of the likelihood function is not tractable and only a simulator that can generate synthetic data is available. SSNL fits a dimensionality-reducing surjective normalizing flow model and uses it as a surrogate likelihood function which allows for conventional Bayesian inference using either Markov chain Monte Carlo methods or variational inference. By embedding the data in a low-dimensional space, SSNL solves several issues previous likelihood-based methods had when applied to high-dimensional data sets that, for instance, contain non-informative data dimensions or lie along a lower-dimensional manifold. We evaluate SSNL on a wide variety of experiments and show that it generally outperforms contemporary methods used in simulation-based inference, for instance, on a challenging real-world example from astrophysics which models the magnetic field strength of the sun using a solar dynamo model.
We propose a novel algorithm for the support estimation of partially known Gaussian graphical models that incorporates prior information about the underlying graph. In contrast to classical approaches that provide a point estimate based on a maximum likelihood or a maximum a posteriori criterion using (simple) priors on the precision matrix, we consider a prior on the graph and rely on annealed Langevin diffusion to generate samples from the posterior distribution. Since the Langevin sampler requires access to the score function of the underlying graph prior, we use graph neural networks to effectively estimate the score from a graph dataset (either available beforehand or generated from a known distribution). Numerical experiments demonstrate the benefits of our approach.
Mendelian randomization uses genetic variants as instrumental variables to make causal inferences about the effects of modifiable risk factors on diseases from observational data. One of the major challenges in Mendelian randomization is that many genetic variants are only modestly or even weakly associated with the risk factor of interest, a setting known as many weak instruments. Many existing methods, such as the popular inverse-variance weighted (IVW) method, could be biased when the instrument strength is weak. To address this issue, the debiased IVW (dIVW) estimator, which is shown to be robust to many weak instruments, was recently proposed. However, this estimator still has non-ignorable bias when the effective sample size is small. In this paper, we propose a modified debiased IVW (mdIVW) estimator by multiplying a modification factor to the original dIVW estimator. After this simple correction, we show that the bias of the mdIVW estimator converges to zero at a faster rate than that of the dIVW estimator under some regularity conditions. Moreover, the mdIVW estimator has smaller variance than the dIVW estimator.We further extend the proposed method to account for the presence of instrumental variable selection and balanced horizontal pleiotropy. We demonstrate the improvement of the mdIVW estimator over the dIVW estimator through extensive simulation studies and real data analysis.