A text-to-tabular approach to generate synthetic patient data using LLMs

Access to large-scale high-quality healthcare databases is key to accelerate medical research and make insightful discoveries about diseases. However, access to such data is often limited by patient privacy concerns, data sharing restrictions and high costs. To overcome these limitations, synthetic patient data has emerged as an alternative. However, synthetic data generation (SDG) methods typically rely on machine learning (ML) models trained on original data, leading back to the data scarcity problem. We propose an approach to generate synthetic tabular patient data that does not require access to the original data, but only a description of the desired database. We leverage prior medical knowledge and in-context learning capabilities of large language models (LLMs) to generate realistic patient data, even in a low-resource setting. We quantitatively evaluate our approach against state-of-the-art SDG models, using fidelity, privacy, and utility metrics. Our results show that while LLMs may not match the performance of state-of-the-art models trained on the original data, they effectively generate realistic patient data with well-preserved clinical correlations. An ablation study highlights key elements of our prompt contributing to high-quality synthetic patient data generation. This approach, which is easy to use and does not require original data or advanced ML skills, is particularly valuable for quickly generating custom-designed patient data, supporting project implementation and providing educational resources.

Human-in-the-Loop Optimization for Deep Stimulus Encoding in Visual Prostheses

Neuroprostheses show potential in restoring lost sensory function and enhancing human capabilities, but the sensations produced by current devices often seem unnatural or distorted. Exact placement of implants and differences in individual perception lead to significant variations in stimulus response, making personalized stimulus optimization a key challenge. Bayesian optimization could be used to optimize patient-specific stimulation parameters with limited noisy observations, but is not feasible for high-dimensional stimuli. Alternatively, deep learning models can optimize stimulus encoding strategies, but typically assume perfect knowledge of patient-specific variations. Here we propose a novel, practically feasible approach that overcomes both of these fundamental limitations. First, a deep encoder network is trained to produce optimal stimuli for any individual patient by inverting a forward model mapping electrical stimuli to visual percepts. Second, a preferential Bayesian optimization strategy utilizes this encoder to optimize patient-specific parameters for a new patient, using a minimal number of pairwise comparisons between candidate stimuli. We demonstrate the viability of this approach on a novel, state-of-the-art visual prosthesis model. We show that our approach quickly learns a personalized stimulus encoder, leads to dramatic improvements in the quality of restored vision, and is robust to noisy patient feedback and misspecifications in the underlying forward model. Overall, our results suggest that combining the strengths of deep learning and Bayesian optimization could significantly improve the perceptual experience of patients fitted with visual prostheses and may prove a viable solution for a range of neuroprosthetic technologies.

Contextual Bayesian optimization with binary outputs

Bayesian optimization (BO) is an efficient method to optimize expensive black-box functions. It has been generalized to scenarios where objective function evaluations return stochastic binary feedback, such as success/failure in a given test, or preference between different parameter settings. In many real-world situations, the objective function can be evaluated in controlled 'contexts' or 'environments' that directly influence the observations. For example, one could directly alter the 'difficulty' of the test that is used to evaluate a system's performance. With binary feedback, the context determines the information obtained from each observation. For example, if the test is too easy/hard, the system will always succeed/fail, yielding uninformative binary outputs. Here we combine ideas from Bayesian active learning and optimization to efficiently choose the best context and optimization parameter on each iteration. We demonstrate the performance of our algorithm and illustrate how it can be used to tackle a concrete application in visual psychophysics: efficiently improving patients' vision via corrective lenses, using psychophysics measurements.

Efficient Exploration in Binary and Preferential Bayesian Optimization

Bayesian optimization (BO) is an effective approach to optimize expensive black-box functions, that seeks to trade-off between exploitation (selecting parameters where the maximum is likely) and exploration (selecting parameters where we are uncertain about the objective function). In many real-world situations, direct measurements of the objective function are not possible, and only binary measurements such as success/failure or pairwise comparisons are available. To perform efficient exploration in this setting, we show that it is important for BO algorithms to distinguish between different types of uncertainty: epistemic uncertainty, about the unknown objective function, and aleatoric uncertainty, which comes from noisy observations and cannot be reduced. In effect, only the former is important for efficient exploration. Based on this, we propose several new acquisition functions that outperform state-of-the-art heuristics in binary and preferential BO, while being fast to compute and easy to implement. We then generalize these acquisition rules to batch learning, where multiple queries are performed simultaneously.