# AdaMR: Adaptable Molecular Representation for Unified Pre-training Strategy

arXiv: https://arxiv.org/abs/2401.06166 · HTML: https://mlsanity.com/paper/2401.06166/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 3 of its 10 references that are in the map.
- First posted on arXiv 28 Dec 2023.

## Builds on (most cited first, 3 of 3)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [Regression Transformer: Concurrent sequence regression and generation for molecular language modeling](https://mlsanity.com/paper/2202.01338/) (2022)

## Abstract (arXiv)

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.