# Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation

arXiv: https://arxiv.org/abs/2404.16880 · HTML: https://mlsanity.com/paper/2404.16880/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 32 of its 56 references that are in the map.
- First posted on arXiv 23 Apr 2024.

## Builds on (most cited first, 30 of 32)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [Neural Machine Translation by Jointly Learning to Align and Translate](https://mlsanity.com/paper/1409.0473/) (2014)
- [BLIP: Bootstrapping Language-Image Pre-training for Unified Vision-Language Understanding and Generation](https://mlsanity.com/paper/2201.12086/) (2022)
- [Align before Fuse: Vision and Language Representation Learning with Momentum Distillation](https://mlsanity.com/paper/2107.07651/) (2021)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [Translation between Molecules and Natural Language](https://mlsanity.com/paper/2204.11817/) (2022)
- [Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing](https://mlsanity.com/paper/2212.10789/) (2022)
- [A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language](https://mlsanity.com/paper/2209.05481/) (2022)
- [MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter](https://mlsanity.com/paper/2310.12798/) (2023)
- [Not All Tokens Are Equal: Human-centric Visual Analysis via Token Clustering Transformer](https://mlsanity.com/paper/2204.08680/) (2022)
- [BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations](https://mlsanity.com/paper/2310.07276/) (2023)
- [Unifying Molecular and Textual Representations via Multi-task Language Modelling](https://mlsanity.com/paper/2301.12586/) (2023)
- [Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspective](https://mlsanity.com/paper/2306.06615/) (2023)
- [InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discovery](https://mlsanity.com/paper/2311.16208/) (2023)
- [GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text](https://mlsanity.com/paper/2308.06911/) (2023)
- [MolXPT: Wrapping Molecules with Text for Generative Pre-training](https://mlsanity.com/paper/2305.10688/) (2023)
- [Disentangled Representation Learning for Text-Video Retrieval](https://mlsanity.com/paper/2203.07111/) (2022)
- [Hierarchically Structured Meta-learning](https://mlsanity.com/paper/1905.05301/) (2019)
- [Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching](https://mlsanity.com/paper/2206.13602/) (2022)
- [Towards 3D Molecule-Text Interpretation in Language Models](https://mlsanity.com/paper/2401.13923/) (2024)
- [DrugAssist: A Large Language Model for Molecule Optimization](https://mlsanity.com/paper/2401.10334/) (2023)
- [Knowledge Graphs Meet Multi-Modal Learning: A Comprehensive Survey](https://mlsanity.com/paper/2402.05391/) (2024)
- [MolFM: A Multimodal Molecular Foundation Model](https://mlsanity.com/paper/2307.09484/) (2023)
- [Video-Text as Game Players: Hierarchical Banzhaf Interaction for Cross-Modal Representation Learning](https://mlsanity.com/paper/2303.14369/) (2023)
- [Multimodal Molecular Pretraining via Modality Blending](https://mlsanity.com/paper/2307.06235/) (2023)
- [Large Language Models are In-Context Molecule Learners](https://mlsanity.com/paper/2403.04197/) (2024)

## Built on by (most cited first, 2 of 2)

- [Exploring Optimal Transport-Based Multi-Grained Alignments for Text-Molecule Retrieval](https://mlsanity.com/paper/2411.11875/) (2024)
- [Unveiling Scaling Behaviors in Molecular Language Models: Effects of Model Size, Data, and Representation](https://mlsanity.com/paper/2601.22757/) (2026)

## Abstract (arXiv)

Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields. However, most approaches employ a global alignment approach to learn the knowledge from different modalities that may fail to capture fine-grained information, such as molecule-and-text fragments and stereoisomeric nuances, which is crucial for downstream tasks. Furthermore, it is incapable of modeling such information using a similar global alignment strategy due to the lack of annotations about the fine-grained fragments in the existing dataset. In this paper, we propose Atomas, a hierarchical molecular representation learning framework that jointly learns representations from SMILES strings and text. We design a Hierarchical Adaptive Alignment model to automatically learn the fine-grained fragment correspondence between two modalities and align these representations at three semantic levels. Atomas's end-to-end training framework supports understanding and generating molecules, enabling a wider range of downstream tasks. Atomas achieves superior performance across 12 tasks on 11 datasets, outperforming 11 baseline models thus highlighting the effectiveness and versatility of our method. Scaling experiments further demonstrate Atomas's robustness and scalability. Moreover, visualization and qualitative analysis, validated by human experts, confirm the chemical relevance of our approach. Codes are released on https://github.com/yikunpku/Atomas.