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| Main Authors: | , , , , , , , |
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| Format: | Preprint |
| Published: |
2023
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2401.06166 |
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Table of Contents:
- We propose Adjustable Molecular Representation (AdaMR), a new large-scale uniform pre-training strategy for small-molecule drugs, as a novel unified pre-training strategy. AdaMR utilizes a granularity-adjustable molecular encoding strategy, which is accomplished through a pre-training job termed molecular canonicalization, setting it apart from recent large-scale molecular models. This adaptability in granularity enriches the model's learning capability at multiple levels and improves its performance in multi-task scenarios. Specifically, the substructure-level molecular representation preserves information about specific atom groups or arrangements, influencing chemical properties and functionalities. This proves advantageous for tasks such as property prediction. Simultaneously, the atomic-level representation, combined with generative molecular canonicalization pre-training tasks, enhances validity, novelty, and uniqueness in generative tasks. All of these features work together to give AdaMR outstanding performance on a range of downstream tasks. We fine-tuned our proposed pre-trained model on six molecular property prediction tasks (MoleculeNet datasets) and two generative tasks (ZINC250K datasets), achieving state-of-the-art (SOTA) results on five out of eight tasks.