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This paper revisits the performance of Rademacher random projections, establishing novel statistical guarantees that are numerically sharp and non-oblivious with respect to the input data. More specifically, the central result is the Schur-concavity property of Rademacher random projections with respect to the inputs. This offers a novel geometric perspective on the performance of random projections, while improving quantitatively on bounds from previous works. As a corollary of this broader result, we obtained the improved performance on data which is sparse or is distributed with small spread. This non-oblivious analysis is a novelty compared to techniques from previous work, and bridges the frequently observed gap between theory and practise. The main result uses an algebraic framework for proving Schur-concavity properties, which is a contribution of independent interest and an elegant alternative to derivative-based criteria.

We propose new tools for the geometric exploration of data objects taking values in a general separable metric space $(\Omega, d)$. Given a probability measure on $\Omega$, we introduce depth profiles, where the depth profile of an element $\omega\in\Omega$ refers to the distribution of the distances between $\omega$ and the other elements of $\Omega$. Depth profiles can be harnessed to define transport ranks, which capture the centrality of each element in $\Omega$ with respect to the entire data cloud based on optimal transport maps between depth profiles. We study the properties of transport ranks and show that they provide an effective device for detecting and visualizing patterns in samples of random objects and also entail notions of transport medians, modes, level sets and quantiles for data in general separable metric spaces. Specifically, we study estimates of depth profiles and transport ranks based on samples of random objects and establish the convergence of the empirical estimates to the population targets using empirical process theory. We demonstrate the usefulness of depth profiles and associated transport ranks and visualizations for distributional data through a sample of age-at-death distributions for various countries, for compositional data through energy usage for U.S. states and for network data through New York taxi trips.

Feynman integrals are solutions to linear partial differential equations with polynomial coefficients. Using a triangle integral with general exponents as a case in point, we compare $D$-module methods to dedicated methods developed for solving differential equations appearing in the context of Feynman integrals, and provide a dictionary of the relevant concepts. In particular, we implement an algorithm due to Saito, Sturmfels, and Takayama to derive canonical series solutions of regular holonomic $D$-ideals, and compare them to asymptotic series derived by the respective Fuchsian systems.

This paper proposes a methodology for discovering meaningful properties in data by exploring the latent space of unsupervised deep generative models. We combine manipulation of individual latent variables to extreme values outside the training range with methods inspired by causal inference into an approach we call causal disentanglement with extreme values (CDEV) and show that this approach yields insights for model interpretability. Using this technique, we can infer what properties of unknown data the model encodes as meaningful. We apply the methodology to test what is meaningful in the communication system of sperm whales, one of the most intriguing and understudied animal communication systems. We train a network that has been shown to learn meaningful representations of speech and test whether we can leverage such unsupervised learning to decipher the properties of another vocal communication system for which we have no ground truth. The proposed technique suggests that sperm whales encode information using the number of clicks in a sequence, the regularity of their timing, and audio properties such as the spectral mean and the acoustic regularity of the sequences. Some of these findings are consistent with existing hypotheses, while others are proposed for the first time. We also argue that our models uncover rules that govern the structure of communication units in the sperm whale communication system and apply them while generating innovative data not shown during training. This paper suggests that an interpretation of the outputs of deep neural networks with causal methodology can be a viable strategy for approaching data about which little is known and presents another case of how deep learning can limit the hypothesis space. Finally, the proposed approach combining latent space manipulation and causal inference can be extended to other architectures and arbitrary datasets.

In computational biology, $k$-mers and edit distance are fundamental concepts. However, little is known about the metric space of all $k$-mers equipped with the edit distance. In this work, we explore the structure of the $k$-mer space by studying its maximal independent sets (MISs). An MIS is a sparse sketch of all $k$-mers with nice theoretical properties, and therefore admits critical applications in clustering, indexing, hashing, and sketching large-scale sequencing data, particularly those with high error-rates. Finding an MIS is a challenging problem, as the size of a $k$-mer space grows geometrically with respect to $k$. We propose three algorithms for this problem. The first and the most intuitive one uses a greedy strategy. The second method implements two techniques to avoid redundant comparisons by taking advantage of the locality-property of the $k$-mer space and the estimated bounds on the edit distance. The last algorithm avoids expensive calculations of the edit distance by translating the edit distance into the shortest path in a specifically designed graph. These algorithms are implemented and the calculated MISs of $k$-mer spaces and their statistical properties are reported and analyzed for $k$ up to 15. Source code is freely available at //github.com/Shao-Group/kmerspace .

The paper presents a stochastic analysis of the growth rate of viscous fingers in miscible displacement in a heterogeneous porous medium. The statistical parameters characterizing the permeability distribution of a reservoir vary over a wide range. The formation of fingers is provided by the mixing of different-viscosity fluids -- water and polymer solution. The distribution functions of the growth rate of viscous fingers are numerically determined and visualized. Careful data processing reveals the non-monotonic nature of the dependence of the front end of the mixing zone on the correlation length of the permeability (describing the medium graininess) of the reservoir formation. It is demonstrated that an increase in graininess up to a certain value causes an expansion of the distribution shape and a shift of the distribution maximum to the region of higher velocities. In addition, an increase in the standard deviation of permeability leads to a slight change in the shape and characteristics of the density distribution of the growth rates of viscous fingers. The theoretical predictions within the framework of the transverse flow equilibrium approximation and the Koval model are contrasted with the numerically computed velocity distributions.

The recent explosion of genetic and high dimensional biobank and 'omic' data has provided researchers with the opportunity to investigate the shared genetic origin (pleiotropy) of hundreds to thousands of related phenotypes. However, existing methods for multi-phenotype genome-wide association studies (GWAS) do not model pleiotropy, are only applicable to a small number of phenotypes, or provide no way to perform inference. To add further complication, raw genetic and phenotype data are rarely observed, meaning analyses must be performed on GWAS summary statistics whose statistical properties in high dimensions are poorly understood. We therefore developed a novel model, theoretical framework, and set of methods to perform Bayesian inference in GWAS of high dimensional phenotypes using summary statistics that explicitly model pleiotropy, beget fast computation, and facilitate the use of biologically informed priors. We demonstrate the utility of our procedure by applying it to metabolite GWAS, where we develop new nonparametric priors for genetic effects on metabolite levels that use known metabolic pathway information and foster interpretable inference at the pathway level.

This paper considers the problem of inference in cluster randomized experiments when cluster sizes are non-ignorable. Here, by a cluster randomized experiment, we mean one in which treatment is assigned at the level of the cluster; by non-ignorable cluster sizes we mean that "large'' clusters and "small'' clusters may be heterogeneous, and, in particular, the effects of the treatment may vary across clusters of differing sizes. In order to permit this sort of flexibility, we consider a sampling framework in which cluster sizes themselves are random. In this way, our analysis departs from earlier analyses of cluster randomized experiments in which cluster sizes are treated as non-random. We distinguish between two different parameters of interest: the equally-weighted cluster-level average treatment effect, and the size-weighted cluster-level average treatment effect. For each parameter, we provide methods for inference in an asymptotic framework where the number of clusters tends to infinity and treatment is assigned using a covariate-adaptive stratified randomization procedure. We additionally permit the experimenter to sample only a subset of the units within each cluster rather than the entire cluster and demonstrate the implications of such sampling for some commonly used estimators. A small simulation study and empirical demonstration show the practical relevance of our theoretical results.

Learning precise surrogate models of complex computer simulations and physical machines often require long-lasting or expensive experiments. Furthermore, the modeled physical dependencies exhibit nonlinear and nonstationary behavior. Machine learning methods that are used to produce the surrogate model should therefore address these problems by providing a scheme to keep the number of queries small, e.g. by using active learning and be able to capture the nonlinear and nonstationary properties of the system. One way of modeling the nonstationarity is to induce input-partitioning, a principle that has proven to be advantageous in active learning for Gaussian processes. However, these methods either assume a known partitioning, need to introduce complex sampling schemes or rely on very simple geometries. In this work, we present a simple, yet powerful kernel family that incorporates a partitioning that: i) is learnable via gradient-based methods, ii) uses a geometry that is more flexible than previous ones, while still being applicable in the low data regime. Thus, it provides a good prior for active learning procedures. We empirically demonstrate excellent performance on various active learning tasks.

While it is nearly effortless for humans to quickly assess the perceptual similarity between two images, the underlying processes are thought to be quite complex. Despite this, the most widely used perceptual metrics today, such as PSNR and SSIM, are simple, shallow functions, and fail to account for many nuances of human perception. Recently, the deep learning community has found that features of the VGG network trained on the ImageNet classification task has been remarkably useful as a training loss for image synthesis. But how perceptual are these so-called "perceptual losses"? What elements are critical for their success? To answer these questions, we introduce a new Full Reference Image Quality Assessment (FR-IQA) dataset of perceptual human judgments, orders of magnitude larger than previous datasets. We systematically evaluate deep features across different architectures and tasks and compare them with classic metrics. We find that deep features outperform all previous metrics by huge margins. More surprisingly, this result is not restricted to ImageNet-trained VGG features, but holds across different deep architectures and levels of supervision (supervised, self-supervised, or even unsupervised). Our results suggest that perceptual similarity is an emergent property shared across deep visual representations.