Adaptive Gaussian Process Search for Simulation-Based Sample Size Estimation in Clinical Prediction Models: Validation of the pmsims R Package

Background: Determining an adequate sample size is essential for developing reliable and generalisable clinical prediction models, yet practical guidance on selecting appropriate methods remains limited. Existing analytical and simulation-based approaches often rely on restrictive assumptions and focus on mean-based criteria. We present and validate pmsims, an R package that uses Gaussian process surrogate modelling to provide a flexible and computationally efficient simulation-based framework for sample size determination across diverse prediction settings. Methods: We conducted a comprehensive simulation study with two aims. First, we compared three search engines implemented in pmsims: a Gaussian process-based adaptive method, a deterministic bisection method, and a hybrid approach, across binary, continuous, and survival outcomes. Second, we benchmarked the best-performing pmsims engine against existing analytical (pmsampsize) and simulation-based (samplesizedev) methods, evaluating recommended sample sizes, computational time, and achieved performance on large independent validation datasets. Results: The Gaussian process-based method consistently produced the most stable sample size estimates, particularly in low-signal, high-dimensional settings. In benchmarking, pmsims achieved performance close to prespecified targets across all outcome types, matching simulation-based approaches and outperforming analytical methods in more challenging scenarios. Conclusions: pmsims provides an efficient and flexible framework for principled sample size planning in clinical prediction modelling, requiring fewer model evaluations than non-adaptive simulation approaches.

Determinants of Training Corpus Size for Clinical Text Classification

Introduction: Clinical text classification using natural language processing (NLP) models requires adequate training data to achieve optimal performance. For that, 200-500 documents are typically annotated. The number is constrained by time and costs and lacks justification of the sample size requirements and their relationship to text vocabulary properties. Methods: Using the publicly available MIMIC-III dataset containing hospital discharge notes with ICD-9 diagnoses as labels, we employed pre-trained BERT embeddings followed by Random Forest classifiers to identify 10 randomly selected diagnoses, varying training corpus sizes from 100 to 10,000 documents, and analyzed vocabulary properties by identifying strong and noisy predictive words through Lasso logistic regression on bag-of-words embeddings. Results: Learning curves varied significantly across the 10 classification tasks despite identical preprocessing and algorithms, with 600 documents sufficient to achieve 95% of the performance attainable with 10,000 documents for all tasks. Vocabulary analysis revealed that more strong predictors and fewer noisy predictors were associated with steeper learning curves, where every 100 additional noisy words decreased accuracy by approximately 0.02 while 100 additional strong predictors increased maximum accuracy by approximately 0.04.

Sample Size in Natural Language Processing within Healthcare Research

Sample size calculation is an essential step in most data-based disciplines. Large enough samples ensure representativeness of the population and determine the precision of estimates. This is true for most quantitative studies, including those that employ machine learning methods, such as natural language processing, where free-text is used to generate predictions and classify instances of text. Within the healthcare domain, the lack of sufficient corpora of previously collected data can be a limiting factor when determining sample sizes for new studies. This paper tries to address the issue by making recommendations on sample sizes for text classification tasks in the healthcare domain. Models trained on the MIMIC-III database of critical care records from Beth Israel Deaconess Medical Center were used to classify documents as having or not having Unspecified Essential Hypertension, the most common diagnosis code in the database. Simulations were performed using various classifiers on different sample sizes and class proportions. This was repeated for a comparatively less common diagnosis code within the database of diabetes mellitus without mention of complication. Smaller sample sizes resulted in better results when using a K-nearest neighbours classifier, whereas larger sample sizes provided better results with support vector machines and BERT models. Overall, a sample size larger than 1000 was sufficient to provide decent performance metrics. The simulations conducted within this study provide guidelines that can be used as recommendations for selecting appropriate sample sizes and class proportions, and for predicting expected performance, when building classifiers for textual healthcare data. The methodology used here can be modified for sample size estimates calculations with other datasets.