Meta-Learning Initializations for Low-Resource Drug Discovery

Building in silico models to predict chemical properties and activities is a crucial step in drug discovery. However, drug discovery projects are often characterized by limited labeled data, hindering the applications of deep learning in this setting. Meanwhile advances in meta-learning have enabled state-of-the-art performances in few-shot learning benchmarks, naturally prompting the question: Can meta-learning improve deep learning performance in low-resource drug discovery projects? In this work, we assess the efficiency of the Model-Agnostic Meta-Learning (MAML) algorithm – along with its variants FO-MAML and ANIL – at learning to predict chemical properties and activities. Using the ChEMBL20 dataset to emulate low-resource settings, our benchmark shows that meta-initializations perform comparably to or outperform multi-task pre-training baselines on 16 out of 20 in-distribution tasks and on all out-of-distribution tasks, providing an average improvement in AUPRC of 7. 2% and 14. 9% respectively. Finally, we observe that meta-initializations consistently result in the best performing models across fine-tuning sets with k ∈ 16, 32, 64, 128, 256 instances.