# Text-guided Diffusion Model for 3D Molecule Generation

arXiv: https://arxiv.org/abs/2410.03803 · HTML: https://mlsanity.com/paper/2410.03803/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Placed in Flow matching, time series and science, one of 14 directions in Diffusion models.
- Builds on 54 of its 81 references that are in the map.
- First posted on arXiv 4 Oct 2024.

## Placed in

- Diffusion models / [Flow matching, time series and science](https://mlsanity.com/diffusion/flow-matching-time-series-and-science/)

## Builds on (most cited first, 30 of 54)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [High-Resolution Image Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2112.10752/) (2021)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Diffusion Models Beat GANs on Image Synthesis](https://mlsanity.com/paper/2105.05233/) (2021)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [DreamBooth: Fine Tuning Text-to-Image Diffusion Models for Subject-Driven Generation](https://mlsanity.com/paper/2208.12242/) (2022)
- [Image Super-Resolution via Iterative Refinement](https://mlsanity.com/paper/2104.07636/) (2021)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [DiffWave: A Versatile Diffusion Model for Audio Synthesis](https://mlsanity.com/paper/2009.09761/) (2020)
- [Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds](https://mlsanity.com/paper/1802.08219/) (2018)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [ILVR: Conditioning Method for Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2108.02938/) (2021)
- [WaveGrad: Estimating Gradients for Waveform Generation](https://mlsanity.com/paper/2009.00713/) (2020)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [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)
- [Grammar Variational Autoencoder](https://mlsanity.com/paper/1703.01925/) (2017)
- [Torsional Diffusion for Molecular Conformer Generation](https://mlsanity.com/paper/2206.01729/) (2022)
- [Equivariant Flows: Exact Likelihood Generative Learning for Symmetric Densities](https://mlsanity.com/paper/2006.02425/) (2020)
- [Generalizing Convolutional Neural Networks for Equivariance to Lie Groups on Arbitrary Continuous Data](https://mlsanity.com/paper/2002.12880/) (2020)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [Constrained Graph Variational Autoencoders for Molecule Design](https://mlsanity.com/paper/1805.09076/) (2018)
- [MoFlow: An Invertible Flow Model for Generating Molecular Graphs](https://mlsanity.com/paper/2006.10137/) (2020)

## Built on by (most cited first, 5 of 5)

- [NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation](https://mlsanity.com/paper/2502.12638/) (2025)
- [Periodic Materials Generation using Text-Guided Joint Diffusion Model](https://mlsanity.com/paper/2503.00522/) (2025)
- [Diffusion Twigs with Loop Guidance for Conditional Graph Generation](https://mlsanity.com/paper/2410.24012/) (2024)
- [GeoAda: Efficiently Finetune Geometric Diffusion Models with Equivariant Adapters](https://mlsanity.com/paper/2507.02085/) (2025)
- [Agentic Molecular Recovery via Molecule-Aware Exploration](https://mlsanity.com/paper/2606.05847/) (2026)

## Abstract (arXiv)

The de novo generation of molecules with targeted properties is crucial in biology, chemistry, and drug discovery. Current generative models are limited to using single property values as conditions, struggling with complex customizations described in detailed human language. To address this, we propose the text guidance instead, and introduce TextSMOG, a new Text-guided Small Molecule Generation Approach via 3D Diffusion Model which integrates language and diffusion models for text-guided small molecule generation. This method uses textual conditions to guide molecule generation, enhancing both stability and diversity. Experimental results show TextSMOG's proficiency in capturing and utilizing information from textual descriptions, making it a powerful tool for generating 3D molecular structures in response to complex textual customizations.