# G2T-LLM: Graph-to-Tree Text Encoding for Molecule Generation with Fine-Tuned Large Language Models

arXiv: https://arxiv.org/abs/2410.02198 · HTML: https://mlsanity.com/paper/2410.02198/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 23 of its 34 references that are in the map.
- First posted on arXiv 3 Oct 2024.

## Builds on (most cited first, 23 of 23)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [QLoRA: Efficient Finetuning of Quantized LLMs](https://mlsanity.com/paper/2305.14314/) (2023)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [DiGress: Discrete Denoising diffusion for graph generation](https://mlsanity.com/paper/2209.14734/) (2022)
- [GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models](https://mlsanity.com/paper/1802.08773/) (2018)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation](https://mlsanity.com/paper/2001.09382/) (2020)
- [Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations](https://mlsanity.com/paper/2202.02514/) (2022)
- [Permutation Invariant Graph Generation via Score-Based Generative Modeling](https://mlsanity.com/paper/2003.00638/) (2020)
- [Fr'echet ChemNet Distance: A metric for generative models for molecules in drug discovery](https://mlsanity.com/paper/1803.09518/) (2018)
- [MoFlow: An Invertible Flow Model for Generating Molecular Graphs](https://mlsanity.com/paper/2006.10137/) (2020)
- [GraphDF: A Discrete Flow Model for Molecular Graph Generation](https://mlsanity.com/paper/2102.01189/) (2021)
- [Talk like a Graph: Encoding Graphs for Large Language Models](https://mlsanity.com/paper/2310.04560/) (2023)
- [GraphNVP: An Invertible Flow Model for Generating Molecular Graphs](https://mlsanity.com/paper/1905.11600/) (2019)
- [Syntax-Directed Variational Autoencoder for Structured Data](https://mlsanity.com/paper/1802.08786/) (2018)
- [Grammar Prompting for Domain-Specific Language Generation with Large Language Models](https://mlsanity.com/paper/2305.19234/) (2023)
- [Graph Generation with Diffusion Mixture](https://mlsanity.com/paper/2302.03596/) (2023)
- [MolFM: A Multimodal Molecular Foundation Model](https://mlsanity.com/paper/2307.09484/) (2023)
- [MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction](https://mlsanity.com/paper/2406.12950/) (2024)
- [Exploring the Potential of Large Language Models in Graph Generation](https://mlsanity.com/paper/2403.14358/) (2024)

## Built on by (most cited first, 1 of 1)

- [KG-LLM-Bench: A Scalable Benchmark for Evaluating LLM Reasoning on Textualized Knowledge Graphs](https://mlsanity.com/paper/2504.07087/) (2025)

## Abstract (arXiv)

We introduce G2T-LLM, a novel approach for molecule generation that uses graph-to-tree text encoding to transform graph-based molecular structures into a hierarchical text format optimized for large language models (LLMs). This encoding converts complex molecular graphs into tree-structured formats, such as JSON and XML, which LLMs are particularly adept at processing due to their extensive pre-training on these types of data. By leveraging the flexibility of LLMs, our approach allows for intuitive interaction using natural language prompts, providing a more accessible interface for molecular design. Through supervised fine-tuning, G2T-LLM generates valid and coherent chemical structures, addressing common challenges like invalid outputs seen in traditional graph-based methods. While LLMs are computationally intensive, they offer superior generalization and adaptability, enabling the generation of diverse molecular structures with minimal task-specific customization. The proposed approach achieved comparable performances with state-of-the-art methods on various benchmark molecular generation datasets, demonstrating its potential as a flexible and innovative tool for AI-driven molecular design.