Dense kernel matrices resulting from pairwise evaluations of a kernel function arise naturally in machine learning and statistics. Previous work in constructing sparse approximate inverse Cholesky factors of such matrices by minimizing Kullback-Leibler divergence recovers the Vecchia approximation for Gaussian processes. These methods rely only on the geometry of the evaluation points to construct the sparsity pattern. In this work, we instead construct the sparsity pattern by leveraging a greedy selection algorithm that maximizes mutual information with target points, conditional on all points previously selected. For selecting $k$ points out of $N$, the naive time complexity is $\mathcal{O}(N k^4)$, but by maintaining a partial Cholesky factor we reduce this to $\mathcal{O}(N k^2)$. Furthermore, for multiple ($m$) targets we achieve a time complexity of $\mathcal{O}(N k^2 + N m^2 + m^3)$, which is maintained in the setting of aggregated Cholesky factorization where a selected point need not condition every target. We apply the selection algorithm to image classification and recovery of sparse Cholesky factors. By minimizing Kullback-Leibler divergence, we apply the algorithm to Cholesky factorization, Gaussian process regression, and preconditioning with the conjugate gradient, improving over $k$-nearest neighbors selection.
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We study scalable machine learning models for full event reconstruction in high-energy electron-positron collisions based on a highly granular detector simulation. Particle-flow (PF) reconstruction can be formulated as a supervised learning task using tracks and calorimeter clusters or hits. We compare a graph neural network and kernel-based transformer and demonstrate that both avoid quadratic memory allocation and computational cost while achieving realistic PF reconstruction. We show that hyperparameter tuning on a supercomputer significantly improves the physics performance of the models. We also demonstrate that the resulting model is highly portable across hardware processors, supporting Nvidia, AMD, and Intel Habana cards. Finally, we demonstrate that the model can be trained on highly granular inputs consisting of tracks and calorimeter hits, resulting in a competitive physics performance with the baseline. Datasets and software to reproduce the studies are published following the findable, accessible, interoperable, and reusable (FAIR) principles.
The efficacy of numerical methods like integral estimates via Gaussian quadrature formulas depends on the localization of the zeros of the associated family of orthogonal polynomials. In this regard, following the renewed interest in quadrature formulas on the unit circle, and $R_{II}$-type polynomials, which include the complementary Romanovski-Routh polynomials, in this work we present a collection of properties of their zeros. Our results include extreme bounds, convexity, and density, alongside the connection of such polynomials to classical orthogonal polynomials via asymptotic formulas.
Next Point-of-Interest (POI) recommendation is a critical task in location-based services that aim to provide personalized suggestions for the user's next destination. Previous works on POI recommendation have laid focused on modeling the user's spatial preference. However, existing works that leverage spatial information are only based on the aggregation of users' previous visited positions, which discourages the model from recommending POIs in novel areas. This trait of position-based methods will harm the model's performance in many situations. Additionally, incorporating sequential information into the user's spatial preference remains a challenge. In this paper, we propose Diff-POI: a Diffusion-based model that samples the user's spatial preference for the next POI recommendation. Inspired by the wide application of diffusion algorithm in sampling from distributions, Diff-POI encodes the user's visiting sequence and spatial character with two tailor-designed graph encoding modules, followed by a diffusion-based sampling strategy to explore the user's spatial visiting trends. We leverage the diffusion process and its reversed form to sample from the posterior distribution and optimized the corresponding score function. We design a joint training and inference framework to optimize and evaluate the proposed Diff-POI. Extensive experiments on four real-world POI recommendation datasets demonstrate the superiority of our Diff-POI over state-of-the-art baseline methods. Further ablation and parameter studies on Diff-POI reveal the functionality and effectiveness of the proposed diffusion-based sampling strategy for addressing the limitations of existing methods.
Online machine learning (ML) is often used in self-adaptive systems to strengthen the adaptation mechanism and improve the system utility. Despite such benefits, applying online ML for self-adaptation can be challenging, and not many papers report its limitations. Recently, we experimented with applying online ML for self-adaptation of a smart farming scenario and we had faced several unexpected difficulties -- traps -- that, to our knowledge, are not discussed enough in the community. In this paper, we report our experience with these traps. Specifically, we discuss several traps that relate to the specification and online training of the ML-based estimators, their impact on self-adaptation, and the approach used to evaluate the estimators. Our overview of these traps provides a list of lessons learned, which can serve as guidance for other researchers and practitioners when applying online ML for self-adaptation.
The study of hidden structures in data presents challenges in modern statistics and machine learning. We introduce the $\mathbf{gips}$ package in R, which identifies permutation subgroup symmetries in Gaussian vectors. $\mathbf{gips}$ serves two main purposes: exploratory analysis in discovering hidden permutation symmetries and estimating the covariance matrix under permutation symmetry. It is competitive to canonical methods in dimensionality reduction while providing a new interpretation of the results. $\mathbf{gips}$ implements a novel Bayesian model selection procedure within Gaussian vectors invariant under the permutation subgroup introduced in Graczyk, Ishi, Ko{\l}odziejek, Massam, Annals of Statistics, 50 (3) (2022).
With the increasing availability of large scale datasets, computational power and tools like automatic differentiation and expressive neural network architectures, sequential data are now often treated in a data-driven way, with a dynamical model trained from the observation data. While neural networks are often seen as uninterpretable black-box architectures, they can still benefit from physical priors on the data and from mathematical knowledge. In this paper, we use a neural network architecture which leverages the long-known Koopman operator theory to embed dynamical systems in latent spaces where their dynamics can be described linearly, enabling a number of appealing features. We introduce methods that enable to train such a model for long-term continuous reconstruction, even in difficult contexts where the data comes in irregularly-sampled time series. The potential for self-supervised learning is also demonstrated, as we show the promising use of trained dynamical models as priors for variational data assimilation techniques, with applications to e.g. time series interpolation and forecasting.
Developing an efficient computational scheme for high-dimensional Bayesian variable selection in generalised linear models and survival models has always been a challenging problem due to the absence of closed-form solutions for the marginal likelihood. The RJMCMC approach can be employed to samples model and coefficients jointly, but effective design of the transdimensional jumps of RJMCMC can be challenge, making it hard to implement. Alternatively, the marginal likelihood can be derived using data-augmentation scheme e.g. Polya-gamma data argumentation for logistic regression) or through other estimation methods. However, suitable data-augmentation schemes are not available for every generalised linear and survival models, and using estimations such as Laplace approximation or correlated pseudo-marginal to derive marginal likelihood within a locally informed proposal can be computationally expensive in the "large n, large p" settings. In this paper, three main contributions are presented. Firstly, we present an extended Point-wise implementation of Adaptive Random Neighbourhood Informed proposal (PARNI) to efficiently sample models directly from the marginal posterior distribution in both generalised linear models and survival models. Secondly, in the light of the approximate Laplace approximation, we also describe an efficient and accurate estimation method for the marginal likelihood which involves adaptive parameters. Additionally, we describe a new method to adapt the algorithmic tuning parameters of the PARNI proposal by replacing the Rao-Blackwellised estimates with the combination of a warm-start estimate and an ergodic average. We present numerous numerical results from simulated data and 8 high-dimensional gene fine mapping data-sets to showcase the efficiency of the novel PARNI proposal compared to the baseline add-delete-swap proposal.
The (modern) arbitrary derivative (ADER) approach is a popular technique for the numerical solution of differential problems based on iteratively solving an implicit discretization of their weak formulation. In this work, focusing on an ODE context, we investigate several strategies to improve this approach. Our initial emphasis is on the order of accuracy of the method in connection with the polynomial discretization of the weak formulation. We demonstrate that precise choices lead to higher-order convergences in comparison to the existing literature. Then, we put ADER methods into a Deferred Correction (DeC) formalism. This allows to determine the optimal number of iterations, which is equal to the formal order of accuracy of the method, and to introduce efficient $p$-adaptive modifications. These are defined by matching the order of accuracy achieved and the degree of the polynomial reconstruction at each iteration. We provide analytical and numerical results, including the stability analysis of the new modified methods, the investigation of the computational efficiency, an application to adaptivity and an application to hyperbolic PDEs with a Spectral Difference (SD) space discretization.
The knockoff filter of Barber and Candes (arXiv:1404.5609) is a flexible framework for multiple testing in supervised learning models, based on introducing synthetic predictor variables to control the false discovery rate (FDR). Using the conditional calibration framework of Fithian and Lei (arXiv:2007.10438), we introduce the calibrated knockoff procedure, a method that uniformly improves the power of any knockoff procedure. We implement our method for fixed-X knockoffs and show theoretically and empirically that the improvement is especially notable in two contexts where knockoff methods can be nearly powerless: when the rejection set is small, and when the structure of the design matrix prevents us from constructing good knockoff variables. In these contexts, calibrated knockoffs even outperform competing FDR-controlling methods like the (dependence-adjusted) Benjamini-Hochberg procedure in many scenarios.
Simulating physical problems involving multi-time scale coupling is challenging due to the need of solving these multi-time scale processes simultaneously. In response to this challenge, this paper proposed an explicit multi-time step algorithm coupled with a solid dynamic relaxation scheme. The explicit scheme simplifies the equation system in contrast to the implicit scheme, while the multi-time step algorithm allows the equations of different physical processes to be solved under different time step sizes. Furthermore, an implicit viscous damping relaxation technique is applied to significantly reduce computational iterations required to achieve equilibrium in the comparatively fast solid response process. To validate the accuracy and efficiency of the proposed algorithm, two distinct scenarios, i.e., a nonlinear hardening bar stretching and a fluid diffusion coupled with Nafion membrane flexure, are simulated. The results show good agreement with experimental data and results from other numerical methods, and the simulation time is reduced firstly by independently addressing different processes with the multi-time step algorithm and secondly decreasing solid dynamic relaxation time through the incorporation of damping techniques.
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