Pre-training (PT) followed by fine-tuning (FT) is an effective method for training neural networks, and has led to significant performance improvements in many domains. PT can incorporate various design choices such as task and data reweighting strategies, augmentation policies, and noise models, all of which can significantly impact the quality of representations learned. The hyperparameters introduced by these strategies therefore must be tuned appropriately. However, setting the values of these hyperparameters is challenging. Most existing methods either struggle to scale to high dimensions, are too slow and memory-intensive, or cannot be directly applied to the two-stage PT and FT learning process. In this work, we propose an efficient, gradient-based algorithm to meta-learn PT hyperparameters. We formalize the PT hyperparameter optimization problem and propose a novel method to obtain PT hyperparameter gradients by combining implicit differentiation and backpropagation through unrolled optimization. We demonstrate that our method improves predictive performance on two real-world domains. First, we optimize high-dimensional task weighting hyperparameters for multitask pre-training on protein-protein interaction graphs and improve AUROC by up to 3.9%. Second, we optimize a data augmentation neural network for self-supervised PT with SimCLR on electrocardiography data and improve AUROC by up to 1.9%.The PT & FT paradigm introduces high-dimensional, complex PT hyperparameters, such as parameterized data augmentation policies used in contrastive representation learning [8,22] or the use of task, class, or instance weighting variables in multi-task PT to avoid negative transfer [70]. These hyperparameters can significantly affect the quality of pre-trained models [8], and thus finding techniques to set their values optimally is an important area of research.Choosing optimal PT hyperparameter values is challenging, and existing methods do not work well. Simple approaches such as random or grid search are inefficient since evaluating a hyperparameter setting requires performing the full, two-stage PT & FT optimization, which may be prohibitively computationally expensive. Gradient-free approaches, such as Bayesian optimization or evolutionary algorithms [33,61,47], are also limited in how well they scale to this setting. Gradient-based 35th Conference on Neural Information Processing Systems (NeurIPS 2021).