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We establish an asymptotic theory that justifies the third method of removing unwanted variation (RUV-III) theoretically.

Data assimilation addresses the problem of identifying plausible state trajectories of dynamical systems given noisy or incomplete observations. In geosciences, it presents challenges due to the high-dimensionality of geophysical dynamical systems, often exceeding millions of dimensions. This work assesses the scalability of score-based data assimilation (SDA), a novel data assimilation method, in the context of such systems. We propose modifications to the score network architecture aimed at significantly reducing memory consumption and execution time. We demonstrate promising results for a two-layer quasi-geostrophic model.

Current AI-based methods do not provide comprehensible physical interpretations of the utilized data, extracted features, and predictions/inference operations. As a result, deep learning models trained using high-resolution satellite imagery lack transparency and explainability and can be merely seen as a black box, which limits their wide-level adoption. Experts need help understanding the complex behavior of AI models and the underlying decision-making process. The explainable artificial intelligence (XAI) field is an emerging field providing means for robust, practical, and trustworthy deployment of AI models. Several XAI techniques have been proposed for image classification tasks, whereas the interpretation of image segmentation remains largely unexplored. This paper offers to bridge this gap by adapting the recent XAI classification algorithms and making them usable for muti-class image segmentation, where we mainly focus on buildings' segmentation from high-resolution satellite images. To benchmark and compare the performance of the proposed approaches, we introduce a new XAI evaluation methodology and metric based on "Entropy" to measure the model uncertainty. Conventional XAI evaluation methods rely mainly on feeding area-of-interest regions from the image back to the pre-trained (utility) model and then calculating the average change in the probability of the target class. Those evaluation metrics lack the needed robustness, and we show that using Entropy to monitor the model uncertainty in segmenting the pixels within the target class is more suitable. We hope this work will pave the way for additional XAI research for image segmentation and applications in the remote sensing discipline.

We propose a model-based reinforcement learning (RL) approach for noisy time-dependent gate optimization with improved sample complexity over model-free RL. Sample complexity is the number of controller interactions with the physical system. Leveraging an inductive bias, inspired by recent advances in neural ordinary differential equations (ODEs), we use an auto-differentiable ODE parametrised by a learnable Hamiltonian ansatz to represent the model approximating the environment whose time-dependent part, including the control, is fully known. Control alongside Hamiltonian learning of continuous time-independent parameters is addressed through interactions with the system. We demonstrate an order of magnitude advantage in the sample complexity of our method over standard model-free RL in preparing some standard unitary gates with closed and open system dynamics, in realistic numerical experiments incorporating single shot measurements, arbitrary Hilbert space truncations and uncertainty in Hamiltonian parameters. Also, the learned Hamiltonian can be leveraged by existing control methods like GRAPE for further gradient-based optimization with the controllers found by RL as initializations. Our algorithm that we apply on nitrogen vacancy (NV) centers and transmons in this paper is well suited for controlling partially characterised one and two qubit systems.

We consider the problem of sampling from a distribution governed by a potential function. This work proposes an explicit score based MCMC method that is deterministic, resulting in a deterministic evolution for particles rather than a stochastic differential equation evolution. The score term is given in closed form by a regularized Wasserstein proximal, using a kernel convolution that is approximated by sampling. We demonstrate fast convergence on various problems and show improved dimensional dependence of mixing time bounds for the case of Gaussian distributions compared to the unadjusted Langevin algorithm (ULA) and the Metropolis-adjusted Langevin algorithm (MALA). We additionally derive closed form expressions for the distributions at each iterate for quadratic potential functions, characterizing the variance reduction. Empirical results demonstrate that the particles behave in an organized manner, lying on level set contours of the potential. Moreover, the posterior mean estimator of the proposed method is shown to be closer to the maximum a-posteriori estimator compared to ULA and MALA in the context of Bayesian logistic regression. Additional examples demonstrate competitive performance for Bayesian neural network training.

We introduce a neural-preconditioned iterative solver for Poisson equations with mixed boundary conditions. The Poisson equation is ubiquitous in scientific computing: it governs a wide array of physical phenomena, arises as a subproblem in many numerical algorithms, and serves as a model problem for the broader class of elliptic PDEs. The most popular Poisson discretizations yield large sparse linear systems. At high resolution, and for performance-critical applications, iterative solvers can be advantageous for these -- but only when paired with powerful preconditioners. The core of our solver is a neural network trained to approximate the inverse of a discrete structured-grid Laplace operator for a domain of arbitrary shape and with mixed boundary conditions. The structure of this problem motivates a novel network architecture that we demonstrate is highly effective as a preconditioner even for boundary conditions outside the training set. We show that on challenging test cases arising from an incompressible fluid simulation, our method outperforms state-of-the-art solvers like algebraic multigrid as well as some recent neural preconditioners.

Meta-analysis aims to combine effect measures from several studies. For continuous outcomes, the most popular effect measures use simple or standardized differences in sample means. However, a number of applications focus on the absolute values of these effect measures (i.e., unsigned magnitude effects). We provide statistical methods for meta-analysis of magnitude effects based on standardized mean differences. We propose a suitable statistical model for random-effects meta-analysis of absolute standardized mean differences (ASMD), investigate a number of statistical methods for point and interval estimation, and provide practical recommendations for choosing among them.

Integrating first-order logic constraints (FOLCs) with neural networks is a crucial but challenging problem since it involves modeling intricate correlations to satisfy the constraints. This paper proposes a novel neural layer, LogicMP, whose layers perform mean-field variational inference over an MLN. It can be plugged into any off-the-shelf neural network to encode FOLCs while retaining modularity and efficiency. By exploiting the structure and symmetries in MLNs, we theoretically demonstrate that our well-designed, efficient mean-field iterations effectively mitigate the difficulty of MLN inference, reducing the inference from sequential calculation to a series of parallel tensor operations. Empirical results in three kinds of tasks over graphs, images, and text show that LogicMP outperforms advanced competitors in both performance and efficiency.

Generalization to out-of-distribution (OOD) data is a critical challenge in machine learning. Ensemble-based methods, like weight space ensembles that interpolate model parameters, have been shown to achieve superior OOD performance. However, the underlying mechanism for their effectiveness remains unclear. In this study, we closely examine WiSE-FT, a popular weight space ensemble method that interpolates between a pre-trained and a fine-tuned model. We observe an unexpected phenomenon, in which WiSE-FT successfully corrects many cases where each individual model makes incorrect predictions, which contributes significantly to its OOD effectiveness. To gain further insights, we conduct theoretical analysis in a multi-class setting with a large number of spurious features. Our analysis predicts the above phenomenon and it further shows that ensemble-based models reduce prediction errors in the OOD settings by utilizing a more diverse set of spurious features. Contrary to the conventional wisdom that focuses on learning invariant features for better OOD performance, our findings suggest that incorporating a large number of diverse spurious features weakens their individual contributions, leading to improved overall OOD generalization performance. Empirically we demonstrate the effectiveness of utilizing diverse spurious features on a MultiColorMNIST dataset, and our experimental results are consistent with the theoretical analysis. Building upon the new theoretical insights into the efficacy of ensemble methods, we further identify an issue of WiSE-FT caused by the overconfidence of fine-tuned models in OOD situations. This overconfidence magnifies the fine-tuned model's incorrect prediction, leading to deteriorated OOD ensemble performance. To remedy this problem, we propose a novel method called BAlaNced averaGing (BANG), which significantly enhances the OOD performance of WiSE-FT.

Motivation: Read mapping is a computationally expensive process and a major bottleneck in genomics analyses. The performance of read mapping is mainly limited by the performance of three key computational steps: Index Querying, Seed Chaining, and Sequence Alignment. The first step is dominated by how fast and frequent it accesses the main memory (i.e., memory-bound), while the latter two steps are dominated by how fast the CPU can compute their computationally-costly dynamic programming algorithms (i.e., compute-bound). Accelerating these three steps by exploiting new algorithms and new hardware devices is essential to accelerate most genome analysis pipelines that widely use read mapping. Given the large body of work on accelerating Sequence Alignment, this work focuses on significantly improving the remaining steps. Results: We introduce GateSeeder, the first CPU-FPGA-based near-memory acceleration of both short and long read mapping. GateSeeder exploits near-memory computation capability provided by modern FPGAs that couple a reconfigurable compute fabric with high-bandwidth memory (HBM) to overcome the memory-bound and compute-bound bottlenecks. GateSeeder also introduces a new lightweight algorithm for finding the potential matching segment pairs. Using real ONT, HiFi, and Illumina sequences, we experimentally demonstrate that GateSeeder outperforms Minimap2, without performing sequence alignment, by up to 40.3x, 4.8x, and 2.3x, respectively. When performing read mapping with sequence alignment, GateSeeder outperforms Minimap2 by 1.15-4.33x (using KSW2) and by 1.97-13.63x (using WFA-GPU). Availability: //github.com/CMU-SAFARI/GateSeeder