# Towards 3D Molecule-Text Interpretation in Language Models

arXiv: https://arxiv.org/abs/2401.13923 · HTML: https://mlsanity.com/paper/2401.13923/

## Key facts

- Cited by 66 papers in the map (data through 14 Oct 2026).
- Builds on 38 of its 59 references that are in the map.
- First posted on arXiv 25 Jan 2024.

## Builds on (most cited first, 30 of 38)

- [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)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [Flamingo: a Visual Language Model for Few-Shot Learning](https://mlsanity.com/paper/2204.14198/) (2022)
- [Prefix-Tuning: Optimizing Continuous Prompts for Generation](https://mlsanity.com/paper/2101.00190/) (2021)
- [Scaling Instruction-Finetuned Language Models](https://mlsanity.com/paper/2210.11416/) (2022)
- [InstructBLIP: Towards General-purpose Vision-Language Models with Instruction Tuning](https://mlsanity.com/paper/2305.06500/) (2023)
- [A Survey of Large Language Models](https://mlsanity.com/paper/2303.18223/) (2023)
- [PaLM-E: An Embodied Multimodal Language Model](https://mlsanity.com/paper/2303.03378/) (2023)
- [Video-LLaMA: An Instruction-tuned Audio-Visual Language Model for Video Understanding](https://mlsanity.com/paper/2306.02858/) (2023)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Conceptual 12M: Pushing Web-Scale Image-Text Pre-Training To Recognize Long-Tail Visual Concepts](https://mlsanity.com/paper/2102.08981/) (2021)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [The Flan Collection: Designing Data and Methods for Effective Instruction Tuning](https://mlsanity.com/paper/2301.13688/) (2023)
- [Multimodal Few-Shot Learning with Frozen Language Models](https://mlsanity.com/paper/2106.13884/) (2021)
- [Supervision Exists Everywhere: A Data Efficient Contrastive Language-Image Pre-training Paradigm](https://mlsanity.com/paper/2110.05208/) (2021)
- [PointLLM: Empowering Large Language Models to Understand Point Clouds](https://mlsanity.com/paper/2308.16911/) (2023)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [Translation between Molecules and Natural Language](https://mlsanity.com/paper/2204.11817/) (2022)
- [Macaw-LLM: Multi-Modal Language Modeling with Image, Audio, Video, and Text Integration](https://mlsanity.com/paper/2306.09093/) (2023)
- [Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing](https://mlsanity.com/paper/2212.10789/) (2022)
- [Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models](https://mlsanity.com/paper/2306.08018/) (2023)
- [A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language](https://mlsanity.com/paper/2209.05481/) (2022)

## Built on by (most cited first, 30 of 66)

- [LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset](https://mlsanity.com/paper/2402.09391/) (2024)
- [A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery](https://mlsanity.com/paper/2406.10833/) (2024)
- [SciLitLLM: How to Adapt LLMs for Scientific Literature Understanding](https://mlsanity.com/paper/2408.15545/) (2024)
- [ProtT3: Protein-to-Text Generation for Text-based Protein Understanding](https://mlsanity.com/paper/2405.12564/) (2024)
- [Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generation](https://mlsanity.com/paper/2412.14642/) (2024)
- [MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction](https://mlsanity.com/paper/2406.12950/) (2024)
- [UniMoT: Unified Molecule-Text Language Model with Discrete Token Representation](https://mlsanity.com/paper/2408.00863/) (2024)
- [MolTC: Towards Molecular Relational Modeling In Language Models](https://mlsanity.com/paper/2402.03781/) (2024)
- [Prospect Personalized Recommendation on Large Language Model-based Agent Platform](https://mlsanity.com/paper/2402.18240/) (2024)
- [ReactXT: Understanding Molecular "Reaction-ship" via Reaction-Contextualized Molecule-Text Pretraining](https://mlsanity.com/paper/2405.14225/) (2024)
- [Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey](https://mlsanity.com/paper/2403.01528/) (2024)
- [HIGHT: Hierarchical Graph Tokenization for Molecule-Language Alignment](https://mlsanity.com/paper/2406.14021/) (2024)
- [NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation](https://mlsanity.com/paper/2502.12638/) (2025)
- [Mol-LLaMA: Towards General Understanding of Molecules in Large Molecular Language Model](https://mlsanity.com/paper/2502.13449/) (2025)
- [ChemDFM-X: Towards Large Multimodal Model for Chemistry](https://mlsanity.com/paper/2409.13194/) (2024)
- [LLM/Agent-as-Data-Analyst: A Survey](https://mlsanity.com/paper/2509.23988/) (2025)
- [PRESTO: Progressive Pretraining Enhances Synthetic Chemistry Outcomes](https://mlsanity.com/paper/2406.13193/) (2024)
- [MolReasoner: Toward Effective and Interpretable Reasoning for Molecular LLMs](https://mlsanity.com/paper/2508.02066/) (2025)
- [Learning Multi-view Molecular Representations with Structured and Unstructured Knowledge](https://mlsanity.com/paper/2406.09841/) (2024)
- [From Generalist to Specialist: A Survey of Large Language Models for Chemistry](https://mlsanity.com/paper/2412.19994/) (2024)
- [3D-MolT5: Leveraging Discrete Structural Information for Molecule-Text Modeling](https://mlsanity.com/paper/2406.05797/) (2024)
- [Advancing Molecular Graph-Text Pre-training via Fine-grained Alignment](https://mlsanity.com/paper/2409.14106/) (2024)
- [OCSU: Optical Chemical Structure Understanding for Molecule-centric Scientific Discovery](https://mlsanity.com/paper/2501.15415/) (2025)
- [mCLM: A Modular Chemical Language Model that Generates Functional and Makeable Molecules](https://mlsanity.com/paper/2505.12565/) (2025)
- [MolBind: Multimodal Alignment of Language, Molecules, and Proteins](https://mlsanity.com/paper/2403.08167/) (2024)
- [Language-Enhanced Representation Learning for Single-Cell Transcriptomics](https://mlsanity.com/paper/2503.09427/) (2025)
- [KnowMol: Advancing Molecular Large Language Models with Multi-Level Chemical Knowledge](https://mlsanity.com/paper/2510.19484/) (2025)
- [Mol-LLM: Multimodal Generalist Molecular LLM with Improved Graph Utilization](https://mlsanity.com/paper/2502.02810/) (2025)
- [How to Detect and Defeat Molecular Mirage: A Metric-Driven Benchmark for Hallucination in LLM-based Molecular Comprehension](https://mlsanity.com/paper/2504.12314/) (2025)
- [Flex-Judge: Text-Only Reasoning Unleashes Zero-Shot Multimodal Evaluators](https://mlsanity.com/paper/2505.18601/) (2025)

## Abstract (arXiv)

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus on 3D molecule-text interpretation, and propose 3D-MoLM: 3D-Molecular Language Modeling. Specifically, 3D-MoLM enables an LM to interpret and analyze 3D molecules by equipping the LM with a 3D molecular encoder. This integration is achieved by a 3D molecule-text projector, bridging the 3D molecular encoder's representation space and the LM's input space. Moreover, to enhance 3D-MoLM's ability of cross-modal molecular understanding and instruction following, we meticulously curated a 3D molecule-centric instruction tuning dataset -- 3D-MoIT. Through 3D molecule-text alignment and 3D molecule-centric instruction tuning, 3D-MoLM establishes an integration of 3D molecular encoder and LM. It significantly surpasses existing baselines on downstream tasks, including molecule-text retrieval, molecule captioning, and more challenging open-text molecular QA tasks, especially focusing on 3D-dependent properties. We release our codes and datasets at https://github.com/lsh0520/3D-MoLM.