High-dimensional longitudinal data is increasingly used in a wide range of scientific studies. However, there are few statistical methods for high-dimensional linear mixed models (LMMs), as most Bayesian variable selection or penalization methods are designed for independent observations. Additionally, the few available software packages for high-dimensional LMMs suffer from scalability issues. This work presents an efficient and accurate Bayesian framework for high-dimensional LMMs. We use empirical Bayes estimators of hyperparameters for increased flexibility and an Expectation-Conditional-Minimization (ECM) algorithm for computationally efficient maximum a posteriori probability (MAP) estimation of parameters. The novelty of the approach lies in its partitioning and parameter expansion as well as its fast and scalable computation. We illustrate Linear Mixed Modeling with PaRtitiOned empirical Bayes ECM (LMM-PROBE) in simulation studies evaluating fixed and random effects estimation along with computation time. A real-world example is provided using data from a study of lupus in children, where we identify genes and clinical factors associated with a new lupus biomarker and predict the biomarker over time.
相關內容
In this article we shall discuss the theory of geodesics in information geometry, and an application in astrophysics. We will study how gradient flows in information geometry describe geodesics, explore the related mechanics by introducing a constraint, and apply our theory to Gaussian model and black hole thermodynamics. Thus, we demonstrate how deformation of gradient flows leads to more general Randers-Finsler metrics, describe Hamiltonian mechanics that derive from a constraint, and prove duality via canonical transformation. We also verified our theories for a deformation of the Gaussian model, and described dynamical evolution of flat metrics for Kerr and Reissner-Nordstr\"om black holes.
Implementation of many statistical methods for large, multivariate data sets requires one to solve a linear system that, depending on the method, is of the dimension of the number of observations or each individual data vector. This is often the limiting factor in scaling the method with data size and complexity. In this paper we illustrate the use of Krylov subspace methods to address this issue in a statistical solution to a source separation problem in cosmology where the data size is prohibitively large for direct solution of the required system. Two distinct approaches, adapted from techniques in the literature, are described: one that uses the method of conjugate gradients directly to the Kronecker-structured problem and another that reformulates the system as a Sylvester matrix equation. We show that both approaches produce an accurate solution within an acceptable computation time and with practical memory requirements for the data size that is currently available.
In the realm of machine learning, the data may contain additional attributes, known as privileged information (PI). The main purpose of PI is to assist in the training of the model and then utilize the acquired knowledge to make predictions for unseen samples. Support vector regression (SVR) is an effective regression model, however, it has a low learning speed due to solving a convex quadratic problem (QP) subject to a pair of constraints. In contrast, twin support vector regression (TSVR) is more efficient than SVR as it solves two QPs each subject to one set of constraints. However, TSVR and its variants are trained only on regular features and do not use privileged features for training. To fill this gap, we introduce a fusion of TSVR with learning using privileged information (LUPI) and propose a novel approach called twin support vector regression with privileged information (TSVR+). The regularization terms in the proposed TSVR+ capture the essence of statistical learning theory and implement the structural risk minimization principle. We use the successive overrelaxation (SOR) technique to solve the optimization problem of the proposed TSVR+, which enhances the training efficiency. As far as our knowledge extends, the integration of the LUPI concept into twin variants of regression models is a novel advancement. The numerical experiments conducted on UCI, stock and time series data collectively demonstrate the superiority of the proposed model.
Longitudinal studies are often subject to missing data. The ICH E9(R1) addendum addresses the importance of defining a treatment effect estimand with the consideration of intercurrent events. Jump-to-reference (J2R) is one classically envisioned control-based scenario for the treatment effect evaluation using the hypothetical strategy, where the participants in the treatment group after intercurrent events are assumed to have the same disease progress as those with identical covariates in the control group. We establish new estimators to assess the average treatment effect based on a proposed potential outcomes framework under J2R. Various identification formulas are constructed under the assumptions addressed by J2R, motivating estimators that rely on different parts of the observed data distribution. Moreover, we obtain a novel estimator inspired by the efficient influence function, with multiple robustness in the sense that it achieves $n^{1/2}$-consistency if any pairs of multiple nuisance functions are correctly specified, or if the nuisance functions converge at a rate not slower than $n^{-1/4}$ when using flexible modeling approaches. The finite-sample performance of the proposed estimators is validated in simulation studies and an antidepressant clinical trial.
Creating a dataset for training supervised machine learning algorithms can be a demanding task. This is especially true for medical image segmentation since one or more specialists are usually required for image annotation, and creating ground truth labels for just a single image can take up to several hours. In addition, it is paramount that the annotated samples represent well the different conditions that might affect the imaged tissues as well as possible changes in the image acquisition process. This can only be achieved by considering samples that are typical in the dataset as well as atypical, or even outlier, samples. We introduce a new sampling methodology for selecting relevant images from a large dataset in a way that evenly considers both prototypical as well as atypical samples. The methodology involves the generation of a uniform grid from a feature space representing the samples, which is then used for randomly drawing relevant images. The selected images provide a uniform covering of the original dataset, and thus define a heterogeneous set of images that can be annotated and used for training supervised segmentation algorithms. We provide a case example by creating a dataset containing a representative set of blood vessel microscopy images selected from a larger dataset containing thousands of images. The dataset, which we call VessMAP, is being made available online to aid the development of new blood vessel segmentation algorithms.
In biomedical research, computational methods have become indispensable and their use is increasing, making the efficient allocation of computing resources paramount. Practitioners routinely allocate resources far in excess of what is required for batch processing jobs, leading to not just inflated wait times and costs, but also unnecessary carbon emissions. This is not without reason however, as accurately determining resource needs is complex, affected by the nature of tools, data size, and analysis parameters, especially on popular servers that handle numerous jobs. The Galaxy platform, a web-based hub for biomedical analysis used globally by scientists, exemplifies this challenge. Serving nearly half a million registered users and managing around 2 million monthly jobs, Galaxy's growth outpaces the resources at its disposal. This is necessitating smarter resource utilization. To address this, we have developed a tool named Total Perspective Vortex (TPV) - a software package that right-sizes resource allocations for each job. TPV is able to dynamically set resource requirements for individual jobs and perform meta-scheduling across heterogeneous resources. It also includes a first-ever community-curated database of default resource requirements for nearly 1,000 popular bioinformatics tools. Deployments in Galaxy Australia and Europe demonstrate its effectiveness with meta-scheduling user jobs and an improved experience for systems administrators managing Galaxy servers.
In many applications, it is desired to obtain extreme eigenvalues and eigenvectors of large Hermitian matrices by efficient and compact algorithms. In particular, orthogonalization-free methods are preferred for large-scale problems for finding eigenspaces of extreme eigenvalues without explicitly computing orthogonal vectors in each iteration. For the top $p$ eigenvalues, the simplest orthogonalization-free method is to find the best rank-$p$ approximation to a positive semi-definite Hermitian matrix by algorithms solving the unconstrained Burer-Monteiro formulation. We show that the nonlinear conjugate gradient method for the unconstrained Burer-Monteiro formulation is equivalent to a Riemannian conjugate gradient method on a quotient manifold with the Bures-Wasserstein metric, thus its global convergence to a stationary point can be proven. Numerical tests suggest that it is efficient for computing the largest $k$ eigenvalues for large-scale matrices if the largest $k$ eigenvalues are nearly distributed uniformly.
In recent years, circuit simulators and Boolean satisfiability (SAT) solvers have been tightly integrated to provide efficient logic synthesis and verification. Circuit simulation can generate highly expressive simulation patterns that can either enumerate or filter out most candidates for synthesis. Subsequently, SAT solvers are employed to check those that remain, thereby making the logic synthesis process more efficient. This paper introduces a novel circuit simulator of k-input lookup table (k-LUT) networks, based on semi-tensor product (STP). STP-based simulators use computation of logic matrices, the primitives of logic networks, as opposed to relying on bitwise logic operations for simulation of k-LUT networks. Experimental results show that our STP-based simulator reduces the runtime by an average of 7.2x. Furthermore, we integrate this proposed simulator into a SAT-sweeping engine known as SAT sweeper. Through a combination of structural hashing, simulation, and SAT queries, SAT sweeper simplifies logic networks by systematically merging graph vertices from input to output. To enhance the efficiency, we used STP-based exhaustive simulation, which significantly reduces the number of false equivalence class candidates, thereby improving the computational efficiency by reducing the number of SAT calls required. When compared to the SOTA SAT sweeper, our method demonstrates an average 35% runtime reduction.
The new era of technology has brought us to the point where it is convenient for people to share their opinions over an abundance of platforms. These platforms have a provision for the users to express themselves in multiple forms of representations, including text, images, videos, and audio. This, however, makes it difficult for users to obtain all the key information about a topic, making the task of automatic multi-modal summarization (MMS) essential. In this paper, we present a comprehensive survey of the existing research in the area of MMS.
Recently, ensemble has been applied to deep metric learning to yield state-of-the-art results. Deep metric learning aims to learn deep neural networks for feature embeddings, distances of which satisfy given constraint. In deep metric learning, ensemble takes average of distances learned by multiple learners. As one important aspect of ensemble, the learners should be diverse in their feature embeddings. To this end, we propose an attention-based ensemble, which uses multiple attention masks, so that each learner can attend to different parts of the object. We also propose a divergence loss, which encourages diversity among the learners. The proposed method is applied to the standard benchmarks of deep metric learning and experimental results show that it outperforms the state-of-the-art methods by a significant margin on image retrieval tasks.
小貼士
登錄享
相關主題
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191