Invariant causal prediction (ICP, Peters et al. (2016)) provides a novel way to identify causal predictors of a response by utilizing heterogeneous data from different environments. One advantage of ICP is that it guarantees to make no false causal discoveries with high probability. Such a guarantee, however, can be too conservative in some applications, resulting in few or no discoveries. To address this, we propose simultaneous false discovery bounds for ICP, which provides users with extra flexibility in exploring causal predictors and can extract more informative results. These additional inferences come for free, in the sense that they do not require additional assumptions, and the same information obtained by the original ICP is retained. We demonstrate the practical usage of our method through simulations and a real dataset.
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We propose a simple empirical representation of expectations such that: For a number of samples above a certain threshold, drawn from any probability distribution with finite fourth-order statistic, the proposed estimator outperforms the empirical average when tested against the actual population, with respect to the quadratic loss. For datasets smaller than this threshold, the result still holds, but for a class of distributions determined by their first four statistics. Our approach leverages the duality between distributionally robust and risk-averse optimization.
By computing a feedback control via the linear quadratic regulator (LQR) approach and simulating a non-linear non-autonomous closed-loop system using this feedback, we combine two numerically challenging tasks. For the first task, the computation of the feedback control, we use the non-autonomous generalized differential Riccati equation (DRE), whose solution determines the time-varying feedback gain matrix. Regarding the second task, we want to be able to simulate non-linear closed-loop systems for which it is known that the regulator is only valid for sufficiently small perturbations. Thus, one easily runs into numerical issues in the integrators when the closed-loop control varies greatly. For these systems, e.g., the A-stable implicit Euler methods fails.\newline On the one hand, we implement non-autonomous versions of splitting schemes and BDF methods for the solution of our non-autonomous DREs. These are well-established DRE solvers in the autonomous case. On the other hand, to tackle the numerical issues in the simulation of the non-linear closed-loop system, we apply a fractional-step-theta scheme with time-adaptivity tuned specifically to this kind of challenge. That is, we additionally base the time-adaptivity on the activity of the control. We compare this approach to the more classical error-based time-adaptivity.\newline We describe techniques to make these two tasks computable in a reasonable amount of time and are able to simulate closed-loop systems with strongly varying controls, while avoiding numerical issues. Our time-adaptivity approach requires fewer time steps than the error-based alternative and is more reliable.
Colocalization analyses assess whether two traits are affected by the same or distinct causal genetic variants in a single gene region. A class of Bayesian colocalization tests are now routinely used in practice; for example, for genetic analyses in drug development pipelines. In this work, we consider an alternative frequentist approach to colocalization testing that examines the proportionality of genetic associations with each trait. The proportional colocalization approach uses markedly different assumptions to Bayesian colocalization tests, and therefore can provide valuable complementary evidence in cases where Bayesian colocalization results are inconclusive or sensitive to priors. We propose a novel conditional test of proportional colocalization, prop-coloc-cond, that aims to account for the uncertainty in variant selection, in order to recover accurate type I error control. The test can be implemented straightforwardly, requiring only summary data on genetic associations. Simulation evidence and an empirical investigation into GLP1R gene expression demonstrates how tests of proportional colocalization can offer important insights in conjunction with Bayesian colocalization tests.
We introduce a new stochastic algorithm for solving entropic optimal transport (EOT) between two absolutely continuous probability measures $\mu$ and $\nu$. Our work is motivated by the specific setting of Monge-Kantorovich quantiles where the source measure $\mu$ is either the uniform distribution on the unit hypercube or the spherical uniform distribution. Using the knowledge of the source measure, we propose to parametrize a Kantorovich dual potential by its Fourier coefficients. In this way, each iteration of our stochastic algorithm reduces to two Fourier transforms that enables us to make use of the Fast Fourier Transform (FFT) in order to implement a fast numerical method to solve EOT. We study the almost sure convergence of our stochastic algorithm that takes its values in an infinite-dimensional Banach space. Then, using numerical experiments, we illustrate the performances of our approach on the computation of regularized Monge-Kantorovich quantiles. In particular, we investigate the potential benefits of entropic regularization for the smooth estimation of multivariate quantiles using data sampled from the target measure $\nu$.
We develop and analyze a parametric registration procedure for manifolds associated with the solutions to parametric partial differential equations in two-dimensional domains. Given the domain $\Omega \subset \mathbb{R}^2$ and the manifold $M=\{ u_{\mu} : \mu\in P\}$ associated with the parameter domain $P \subset \mathbb{R}^P$ and the parametric field $\mu\mapsto u_{\mu} \in L^2(\Omega)$, our approach takes as input a set of snapshots from $M$ and returns a parameter-dependent mapping $\Phi: \Omega \times P \to \Omega$, which tracks coherent features (e.g., shocks, shear layers) of the solution field and ultimately simplifies the task of model reduction. We consider mappings of the form $\Phi=\texttt{N}(\mathbf{a})$ where $\texttt{N}:\mathbb{R}^M \to {\rm Lip}(\Omega; \mathbb{R}^2)$ is a suitable linear or nonlinear operator; then, we state the registration problem as an unconstrained optimization statement for the coefficients $\mathbf{a}$. We identify minimal requirements for the operator $\texttt{N}$ to ensure the satisfaction of the bijectivity constraint; we propose a class of compositional maps that satisfy the desired requirements and enable non-trivial deformations over curved (non-straight) boundaries of $\Omega$; we develop a thorough analysis of the proposed ansatz for polytopal domains and we discuss the approximation properties for general curved domains. We perform numerical experiments for a parametric inviscid transonic compressible flow past a cascade of turbine blades to illustrate the many features of the method.
In this article we aim to obtain the Fisher Riemann geodesics for nonparametric families of probability densities as a weak limit of the parametric case with increasing number of parameters.
We propose a simple empirical representation of expectations such that: For a number of samples above a certain threshold, drawn from any probability distribution with finite fourth-order statistic, the proposed estimator outperforms the empirical average when tested against the actual population, with respect to the quadratic loss. For datasets smaller than this threshold, the result still holds, but for a class of distributions determined by their first four statistics. Our approach leverages the duality between distributionally robust and risk-averse optimization.
Hashing has been widely used in approximate nearest search for large-scale database retrieval for its computation and storage efficiency. Deep hashing, which devises convolutional neural network architecture to exploit and extract the semantic information or feature of images, has received increasing attention recently. In this survey, several deep supervised hashing methods for image retrieval are evaluated and I conclude three main different directions for deep supervised hashing methods. Several comments are made at the end. Moreover, to break through the bottleneck of the existing hashing methods, I propose a Shadow Recurrent Hashing(SRH) method as a try. Specifically, I devise a CNN architecture to extract the semantic features of images and design a loss function to encourage similar images projected close. To this end, I propose a concept: shadow of the CNN output. During optimization process, the CNN output and its shadow are guiding each other so as to achieve the optimal solution as much as possible. Several experiments on dataset CIFAR-10 show the satisfying performance of SRH.
Time Series Classification (TSC) is an important and challenging problem in data mining. With the increase of time series data availability, hundreds of TSC algorithms have been proposed. Among these methods, only a few have considered Deep Neural Networks (DNNs) to perform this task. This is surprising as deep learning has seen very successful applications in the last years. DNNs have indeed revolutionized the field of computer vision especially with the advent of novel deeper architectures such as Residual and Convolutional Neural Networks. Apart from images, sequential data such as text and audio can also be processed with DNNs to reach state-of-the-art performance for document classification and speech recognition. In this article, we study the current state-of-the-art performance of deep learning algorithms for TSC by presenting an empirical study of the most recent DNN architectures for TSC. We give an overview of the most successful deep learning applications in various time series domains under a unified taxonomy of DNNs for TSC. We also provide an open source deep learning framework to the TSC community where we implemented each of the compared approaches and evaluated them on a univariate TSC benchmark (the UCR/UEA archive) and 12 multivariate time series datasets. By training 8,730 deep learning models on 97 time series datasets, we propose the most exhaustive study of DNNs for TSC to date.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.
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