This paper focuses on the identification of graphical autoregressive models with dynamical latent variables. The dynamical structure of latent variables is described by a matrix polynomial transfer function. Taking account of the sparse interactions between the observed variables and the low-rank property of the latent-variable model, a new sparse plus low-rank optimization problem is formulated to identify the graphical auto-regressive part, which is then handled using the trace approximation and reweighted nuclear norm minimization. Afterwards, the dynamics of latent variables are recovered from low-rank spectral decomposition using the trace norm convex programming method. Simulation examples are used to illustrate the effectiveness of the proposed approach.
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This study focuses on the use of model and data fusion for improving the Spalart-Allmaras (SA) closure model for Reynolds-averaged Navier-Stokes solutions of separated flows. In particular, our goal is to develop of models that not-only assimilate sparse experimental data to improve performance in computational models, but also generalize to unseen cases by recovering classical SA behavior. We achieve our goals using data assimilation, namely the Ensemble Kalman Filtering approach (EnKF), to calibrate the coefficients of the SA model for separated flows. A holistic calibration strategy is implemented via a parameterization of the production, diffusion, and destruction terms. This calibration relies on the assimilation of experimental data collected velocity profiles, skin friction, and pressure coefficients for separated flows. Despite using of observational data from a single flow condition around a backward-facing step (BFS), the recalibrated SA model demonstrates generalization to other separated flows, including cases such as the 2D-bump and modified BFS. Significant improvement is observed in the quantities of interest, i.e., skin friction coefficient ($C_f$) and pressure coefficient ($C_p$) for each flow tested. Finally, it is also demonstrated that the newly proposed model recovers SA proficiency for external, unseparated flows, such as flow around a NACA-0012 airfoil without any danger of extrapolation, and that the individually calibrated terms in the SA model are targeted towards specific flow-physics wherein the calibrated production term improves the re-circulation zone while destruction improves the recovery zone.
High-order structures have been recognised as suitable models for systems going beyond the binary relationships for which graph models are appropriate. Despite their importance and surge in research on these structures, their random cases have been only recently become subjects of interest. One of these high-order structures is the oriented hypergraph, which relates couples of subsets of an arbitrary number of vertices. Here we develop the Erd\H{o}s-R\'enyi model for oriented hypergraphs, which corresponds to the random realisation of oriented hyperedges of the complete oriented hypergraph. A particular feature of random oriented hypergraphs is that the ratio between their expected number of oriented hyperedges and their expected degree or size is 3/2 for large number of vertices. We highlight the suitability of oriented hypergraphs for modelling large collections of chemical reactions and the importance of random oriented hypergraphs to analyse the unfolding of chemistry.
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous chromosomes of the human genome reveals allele-specific gene expression and allele-specific gene regulation by assessing allelic imbalance of read counts at individual sites. Here we formally describe an advanced statistical framework for detecting the allelic imbalance in allelic read counts at single-nucleotide variants detected in diverse omics studies (ChIP-Seq, ATAC-Seq, DNase-Seq, CAGE-Seq, and others). MIXALIME accounts for copy-number variants and aneuploidy, reference read mapping bias, and provides several scoring models to balance between sensitivity and specificity when scoring data with varying levels of experimental noise-caused overdispersion.
Diffusion models (DMs) demonstrate potent image generation capabilities in various generative modeling tasks. Nevertheless, their primary limitation lies in slow sampling speed, requiring hundreds or thousands of sequential function evaluations through large neural networks to generate high-quality images. Sampling from DMs can be seen as solving corresponding stochastic differential equations (SDEs) or ordinary differential equations (ODEs). In this work, we formulate the sampling process as an extended reverse-time SDE (ER SDE), unifying prior explorations into ODEs and SDEs. Leveraging the semi-linear structure of ER SDE solutions, we offer exact solutions and arbitrarily high-order approximate solutions for VP SDE and VE SDE, respectively. Based on the solution space of the ER SDE, we yield mathematical insights elucidating the superior performance of ODE solvers over SDE solvers in terms of fast sampling. Additionally, we unveil that VP SDE solvers stand on par with their VE SDE counterparts. Finally, we devise fast and training-free samplers, ER-SDE Solvers, elevating the efficiency of stochastic samplers to unprecedented levels. Experimental results demonstrate achieving 3.45 FID in 20 function evaluations and 2.24 FID in 50 function evaluations on the ImageNet 64$\times$64 dataset.
In algorithms for solving optimization problems constrained to a smooth manifold, retractions are a well established tool to ensure that the iterates stay on the manifold. More recently, it has been demonstrated that retractions are a useful concept for other computational tasks on manifold as well, including interpolation tasks. In this work, we consider the application of retractions to the numerical integration of differential equations on fixed-rank matrix manifolds. This is closely related to dynamical low-rank approximation (DLRA) techniques. In fact, any retraction leads to a numerical integrator and, vice versa, certain DLRA techniques bear a direct relation with retractions. As an example for the latter, we introduce a new retraction, called KLS retraction, that is derived from the so-called unconventional integrator for DLRA. We also illustrate how retractions can be used to recover known DLRA techniques and to design new ones. In particular, this work introduces two novel numerical integration schemes that apply to differential equations on general manifolds: the accelerated forward Euler (AFE) method and the Ralston-Hermite (RH) method. Both methods build on retractions by using them as a tool for approximating curves on manifolds. The two methods are proven to have local truncation error of order three. Numerical experiments on classical DLRA examples highlight the advantages and shortcomings of these new methods.
We propose a novel estimation approach for a general class of semi-parametric time series models where the conditional expectation is modeled through a parametric function. The proposed class of estimators is based on a Gaussian quasi-likelihood function and it relies on the specification of a parametric pseudo-variance that can contain parametric restrictions with respect to the conditional expectation. The specification of the pseudo-variance and the parametric restrictions follow naturally in observation-driven models with bounds in the support of the observable process, such as count processes and double-bounded time series. We derive the asymptotic properties of the estimators and a validity test for the parameter restrictions. We show that the results remain valid irrespective of the correct specification of the pseudo-variance. The key advantage of the restricted estimators is that they can achieve higher efficiency compared to alternative quasi-likelihood methods that are available in the literature. Furthermore, the testing approach can be used to build specification tests for parametric time series models. We illustrate the practical use of the methodology in a simulation study and two empirical applications featuring integer-valued autoregressive processes, where assumptions on the dispersion of the thinning operator are formally tested, and autoregressions for double-bounded data with application to a realized correlation time series.
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.
We introduce the concept of a rank saturating system and outline its correspondence to a rank-metric code with a given covering radius. We consider the problem of finding the value of $s_{q^m/q}(k,\rho)$, which is the minimum $\mathbb{F}_q$-dimension of a $q$-system in $\mathbb{F}_{q^m}^k$ which is rank $\rho$-saturating. This is equivalent to the covering problem in the rank metric. We obtain upper and lower bounds on $s_{q^m/q}(k,\rho)$ and evaluate it for certain values of $k$ and $\rho$. We give constructions of rank $\rho$-saturating systems suggested from geometry.
We present a novel approach for finding multiple noisily embedded template graphs in a very large background graph. Our method builds upon the graph-matching-matched-filter technique proposed in Sussman et al., with the discovery of multiple diverse matchings being achieved by iteratively penalizing a suitable node-pair similarity matrix in the matched filter algorithm. In addition, we propose algorithmic speed-ups that greatly enhance the scalability of our matched-filter approach. We present theoretical justification of our methodology in the setting of correlated Erdos-Renyi graphs, showing its ability to sequentially discover multiple templates under mild model conditions. We additionally demonstrate our method's utility via extensive experiments both using simulated models and real-world dataset, include human brain connectomes and a large transactional knowledge base.
Humans effortlessly infer the 3D shape of objects. What computations underlie this ability? Although various computational models have been proposed, none of them capture the human ability to match object shape across viewpoints. Here, we ask whether and how this gap might be closed. We begin with a relatively novel class of computational models, 3D neural fields, which encapsulate the basic principles of classic analysis-by-synthesis in a deep neural network (DNN). First, we find that a 3D Light Field Network (3D-LFN) supports 3D matching judgments well aligned to humans for within-category comparisons, adversarially-defined comparisons that accentuate the 3D failure cases of standard DNN models, and adversarially-defined comparisons for algorithmically generated shapes with no category structure. We then investigate the source of the 3D-LFN's ability to achieve human-aligned performance through a series of computational experiments. Exposure to multiple viewpoints of objects during training and a multi-view learning objective are the primary factors behind model-human alignment; even conventional DNN architectures come much closer to human behavior when trained with multi-view objectives. Finally, we find that while the models trained with multi-view learning objectives are able to partially generalize to new object categories, they fall short of human alignment. This work provides a foundation for understanding human shape inferences within neurally mappable computational architectures.
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