SPIRiT Regularization: Parallel MRI with a Combination of Sensitivity Encoding and Linear Predictability

Accelerated Magnetic Resonance Imaging (MRI) permits high quality images from fewer samples that can be collected with a faster scan. Two established methods for accelerating MRI include parallel imaging and compressed sensing. Two types of parallel imaging include linear predictability, which assumes that the Fourier samples are linearly related, and sensitivity encoding, which incorporates a priori knowledge of the sensitivity maps. In this work, we combine compressed sensing with both types of parallel imaging using a novel regularization term: SPIRiT regularization. When combined, the reconstructed images are improved. We demonstrate results on data of a brain, a knee, and an ankle.

Stochastic Subspace Descent Accelerated via Bi-fidelity Line Search

Efficient optimization remains a fundamental challenge across numerous scientific and engineering domains, especially when objective function and gradient evaluations are computationally expensive. While zeroth-order optimization methods offer effective approaches when gradients are inaccessible, their practical performance can be limited by the high cost associated with function queries. This work introduces the bi-fidelity stochastic subspace descent (BF-SSD) algorithm, a novel zeroth-order optimization method designed to reduce this computational burden. BF-SSD leverages a bi-fidelity framework, constructing a surrogate model from a combination of computationally inexpensive low-fidelity (LF) and accurate high-fidelity (HF) function evaluations. This surrogate model facilitates an efficient backtracking line search for step size selection, for which we provide theoretical convergence guarantees under standard assumptions. We perform a comprehensive empirical evaluation of BF-SSD across four distinct problems: a synthetic optimization benchmark, dual-form kernel ridge regression, black-box adversarial attacks on machine learning models, and transformer-based black-box language model fine-tuning. Numerical results demonstrate that BF-SSD consistently achieves superior optimization performance while requiring significantly fewer HF function evaluations compared to relevant baseline methods. This study highlights the efficacy of integrating bi-fidelity strategies within zeroth-order optimization, positioning BF-SSD as a promising and computationally efficient approach for tackling large-scale, high-dimensional problems encountered in various real-world applications.

Aligning to What? Limits to RLHF Based Alignment

Reinforcement Learning from Human Feedback (RLHF) is increasingly used to align large language models (LLMs) with human preferences. However, the effectiveness of RLHF in addressing underlying biases remains unclear. This study investigates the relationship between RLHF and both covert and overt biases in LLMs, particularly focusing on biases against African Americans. We applied various RLHF techniques (DPO, ORPO, and RLOO) to Llama 3 8B and evaluated the covert and overt biases of the resulting models using matched-guise probing and explicit bias testing. We performed additional tests with DPO on different base models and datasets; among several implications, we found that SFT before RLHF calcifies model biases. Additionally, we extend the tools for measuring biases to multi-modal models. Through our experiments we collect evidence that indicates that current alignment techniques are inadequate for nebulous tasks such as mitigating covert biases, highlighting the need for capable datasets, data curating techniques, or alignment tools.

WENDy for Nonlinear-in-Parameter ODEs

The Weak-form Estimation of Non-linear Dynamics (WENDy) algorithm is extended to accommodate systems of ordinary differential equations that are nonlinear-in-parameters (NiP). The extension rests on derived analytic expressions for a likelihood function, its gradient and its Hessian matrix. WENDy makes use of these to approximate a maximum likelihood estimator based on optimization routines suited for non-convex optimization problems. The resulting parameter estimation algorithm has better accuracy, a substantially larger domain of convergence, and is often orders of magnitude faster than the conventional output error least squares method (based on forward solvers). The WENDy.jl algorithm is efficiently implemented in Julia. We demonstrate the algorithm's ability to accommodate the weak form optimization for both additive normal and multiplicative log-normal noise, and present results on a suite of benchmark systems of ordinary differential equations. In order to demonstrate the practical benefits of our approach, we present extensive comparisons between our method and output error methods in terms of accuracy, precision, bias, and coverage.

Exploring Exploration in Bayesian Optimization

A well-balanced exploration-exploitation trade-off is crucial for successful acquisition functions in Bayesian optimization. However, there is a lack of quantitative measures for exploration, making it difficult to analyze and compare different acquisition functions. This work introduces two novel approaches - observation traveling salesman distance and observation entropy - to quantify the exploration characteristics of acquisition functions based on their selected observations. Using these measures, we examine the explorative nature of several well-known acquisition functions across a diverse set of black-box problems, uncover links between exploration and empirical performance, and reveal new relationships among existing acquisition functions. Beyond enabling a deeper understanding of acquisition functions, these measures also provide a foundation for guiding their design in a more principled and systematic manner.

A Unified Framework for Entropy Search and Expected Improvement in Bayesian Optimization

Bayesian optimization is a widely used method for optimizing expensive black-box functions, with Expected Improvement being one of the most commonly used acquisition functions. In contrast, information-theoretic acquisition functions aim to reduce uncertainty about the function's optimum and are often considered fundamentally distinct from EI. In this work, we challenge this prevailing perspective by introducing a unified theoretical framework, Variational Entropy Search, which reveals that EI and information-theoretic acquisition functions are more closely related than previously recognized. We demonstrate that EI can be interpreted as a variational inference approximation of the popular information-theoretic acquisition function, named Max-value Entropy Search. Building on this insight, we propose VES-Gamma, a novel acquisition function that balances the strengths of EI and MES. Extensive empirical evaluations across both low- and high-dimensional synthetic and real-world benchmarks demonstrate that VES-Gamma is competitive with state-of-the-art acquisition functions and in many cases outperforms EI and MES.

Evaluation of data driven low-rank matrix factorization for accelerated solutions of the Vlasov equation

Low-rank methods have shown success in accelerating simulations of a collisionless plasma described by the Vlasov equation, but still rely on computationally costly linear algebra every time step. We propose a data-driven factorization method using artificial neural networks, specifically with convolutional layer architecture, that trains on existing simulation data. At inference time, the model outputs a low-rank decomposition of the distribution field of the charged particles, and we demonstrate that this step is faster than the standard linear algebra technique. Numerical experiments show that the method effectively interpolates time-series data, generalizing to unseen test data in a manner beyond just memorizing training data; patterns in factorization also inherently followed the same numerical trend as those within algebraic methods (e.g., truncated singular-value decomposition). However, when training on the first 70% of a time-series data and testing on the remaining 30%, the method fails to meaningfully extrapolate. Despite this limiting result, the technique may have benefits for simulations in a statistical steady-state or otherwise showing temporal stability.

Optimization of Array Encoding for Ultrasound Imaging

Objective: The transmit encoding model for synthetic aperture imaging is a robust and flexible framework for understanding the effect of acoustic transmission on ultrasound image reconstruction. Our objective is to use machine learning (ML) to construct scanning sequences, parameterized by time delays and apodization weights, that produce high quality B-mode images. Approach: We use an ML model in PyTorch and simulated RF data from Field II to probe the space of possible encoding sequences for those that minimize a loss function that describes image quality. This approach is made computationally feasible by a novel formulation of the derivative for delay-and-sum beamforming. We demonstrate these results experimentally on wire targets and a tissue-mimicking phantom. Main Results: When trained according to a given set of imaging parameters (imaging domain, hardware restrictions), our ML imaging model produces optimized encoding sequences that improve a number of standard quality metrics including resolution, field of view, and contrast, over conventional sequences. Significance: This work demonstrates that the set of encoding schemes that are commonly used represent only a narrow subset of those available. Additionally, it demonstrates the value for ML tasks in synthetic transmit aperture imaging to consider the beamformer within the model, instead of as purely post-processing.

Variational Entropy Search for Adjusting Expected Improvement

Bayesian optimization is a widely used technique for optimizing black-box functions, with Expected Improvement (EI) being the most commonly utilized acquisition function in this domain. While EI is often viewed as distinct from other information-theoretic acquisition functions, such as entropy search (ES) and max-value entropy search (MES), our work reveals that EI can be considered a special case of MES when approached through variational inference (VI). In this context, we have developed the Variational Entropy Search (VES) methodology and the VES-Gamma algorithm, which adapts EI by incorporating principles from information-theoretic concepts. The efficacy of VES-Gamma is demonstrated across a variety of test functions and read datasets, highlighting its theoretical and practical utilities in Bayesian optimization scenarios.

In Situ Framework for Coupling Simulation and Machine Learning with Application to CFD

Recent years have seen many successful applications of machine learning (ML) to facilitate fluid dynamic computations. As simulations grow, generating new training datasets for traditional offline learning creates I/O and storage bottlenecks. Additionally, performing inference at runtime requires non-trivial coupling of ML framework libraries with simulation codes. This work offers a solution to both limitations by simplifying this coupling and enabling in situ training and inference workflows on heterogeneous clusters. Leveraging SmartSim, the presented framework deploys a database to store data and ML models in memory, thus circumventing the file system. On the Polaris supercomputer, we demonstrate perfect scaling efficiency to the full machine size of the data transfer and inference costs thanks to a novel co-located deployment of the database. Moreover, we train an autoencoder in situ from a turbulent flow simulation, showing that the framework overhead is negligible relative to a solver time step and training epoch.