Benchmarking uncertainty quantification for protein engineering

Kevin P Greenman, Ava P Amini and Kevin K Yang

PLOS Computational Biology, 2025, vol. 21, issue 1, 1-19

Abstract: Machine learning sequence-function models for proteins could enable significant advances in protein engineering, especially when paired with state-of-the-art methods to select new sequences for property optimization and/or model improvement. Such methods (Bayesian optimization and active learning) require calibrated estimations of model uncertainty. While studies have benchmarked a variety of deep learning uncertainty quantification (UQ) methods on standard and molecular machine-learning datasets, it is not clear if these results extend to protein datasets. In this work, we implemented a panel of deep learning UQ methods on regression tasks from the Fitness Landscape Inference for Proteins (FLIP) benchmark. We compared results across different degrees of distributional shift using metrics that assess each UQ method’s accuracy, calibration, coverage, width, and rank correlation. Additionally, we compared these metrics using one-hot encoding and pretrained language model representations, and we tested the UQ methods in retrospective active learning and Bayesian optimization settings. Our results indicate that there is no single best UQ method across all datasets, splits, and metrics, and that uncertainty-based sampling is often unable to outperform greedy sampling in Bayesian optimization. These benchmarks enable us to provide recommendations for more effective design of biological sequences using machine learning.Author summary: Protein engineering has previously benefited from the use of machine learning models to guide the choice of new experiments. In many cases, the goal of conducting new experiments is optimizing for a property or improving the machine learning model. Many standard methods for these two tasks require good estimates of the uncertainty in the model’s predictions. Several methods for quantifying this uncertainty exist and have been benchmarked on datasets from other domains (e.g. small molecules), but it is not clear whether these results also apply for proteins. To address this, we evaluated a range of uncertainty quantification approaches on tasks derived from a protein-focused benchmark dataset. We tested performance on different degrees of distributional shift between the training and testing sets and on different representations of the sequences, and we assessed performance in terms of several standard metrics. Finally, we used the uncertainties for property optimization and model improvement. Our findings indicate that no single uncertainty estimation method excels across all scenarios. Moreover, uncertainty-based strategies for property optimization often did not outperform simpler methods that did not consider uncertainty. This research offers insights for the more efficacious application of machine learning in the realm of biological sequence design.

Date: 2025
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1012639

DOI: 10.1371/journal.pcbi.1012639

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