# LDMol: A Text-to-Molecule Diffusion Model with Structurally Informative Latent Space Surpasses AR Models

arXiv: https://arxiv.org/abs/2405.17829 · HTML: https://mlsanity.com/paper/2405.17829/

## Key facts

- Cited by 11 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 53 of its 73 references that are in the map.
- First posted on arXiv 28 May 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 53)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [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)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [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)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Classifier-Free Diffusion Guidance](https://mlsanity.com/paper/2207.12598/) (2022)
- [Flamingo: a Visual Language Model for Few-Shot Learning](https://mlsanity.com/paper/2204.14198/) (2022)
- [Generative Modeling by Estimating Gradients of the Data Distribution](https://mlsanity.com/paper/1907.05600/) (2019)
- [DreamBooth: Fine Tuning Text-to-Image Diffusion Models for Subject-Driven Generation](https://mlsanity.com/paper/2208.12242/) (2022)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [SDEdit: Guided Image Synthesis and Editing with Stochastic Differential Equations](https://mlsanity.com/paper/2108.01073/) (2021)
- [Consistency Models](https://mlsanity.com/paper/2303.01469/) (2023)
- [Structured Denoising Diffusion Models in Discrete State-Spaces](https://mlsanity.com/paper/2107.03006/) (2021)
- [Image Super-Resolution via Iterative Refinement](https://mlsanity.com/paper/2104.07636/) (2021)
- [Diffusion Posterior Sampling for General Noisy Inverse Problems](https://mlsanity.com/paper/2209.14687/) (2022)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [Diffusion-LM Improves Controllable Text Generation](https://mlsanity.com/paper/2205.14217/) (2022)
- [What Makes for Good Views for Contrastive Learning?](https://mlsanity.com/paper/2005.10243/) (2020)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Score-based Generative Modeling in Latent Space](https://mlsanity.com/paper/2106.05931/) (2021)
- [Understanding the Behaviour of Contrastive Loss](https://mlsanity.com/paper/2012.09740/) (2020)
- [Your Diffusion Model is Secretly a Zero-Shot Classifier](https://mlsanity.com/paper/2303.16203/) (2023)
- [Molecular De Novo Design through Deep Reinforcement Learning](https://mlsanity.com/paper/1704.07555/) (2017)

## Built on by (most cited first, 11 of 11)

- [The Superposition of Diffusion Models Using the Ito Density Estimator](https://mlsanity.com/paper/2412.17762/) (2024)
- [mCLM: A Modular Chemical Language Model that Generates Functional and Makeable Molecules](https://mlsanity.com/paper/2505.12565/) (2025)
- [DrugR: Optimizing Molecular Drugs through LLM-based Explicit Reasoning](https://mlsanity.com/paper/2602.08213/) (2026)
- [LLM-Guided Dynamic Action Spaces for Synthesizable Molecular Optimization](https://mlsanity.com/paper/2604.07669/) (2026)
- [Training Text-to-Molecule Models with Context-Aware Tokenization](https://mlsanity.com/paper/2509.04476/) (2025)
- [Cross-Modality Controlled Molecule Generation with Diffusion Language Model](https://mlsanity.com/paper/2508.14748/) (2025)
- [BadGraph: A Backdoor Attack Against Latent Diffusion Model for Text-Guided Graph Generation](https://mlsanity.com/paper/2510.20792/) (2025)
- [SiDGen: Structure-informed Diffusion for Generative modeling of Ligands for Proteins](https://mlsanity.com/paper/2511.09529/) (2025)
- [BiMol-Diff: A Unified Diffusion Framework for Molecular Generation and Captioning](https://mlsanity.com/paper/2604.24089/) (2026)
- [Divide-and-Denoise: A Game-Theoretic Method for Fairly Composing Diffusion Models](https://mlsanity.com/paper/2606.14756/) (2026)
- [MolGVR: A Chemistry-Grounded Framework for Text-to-Molecule Generation](https://mlsanity.com/paper/2607.29479/) (2026)

## Abstract (arXiv)

With the emergence of diffusion models as a frontline generative model, many researchers have proposed molecule generation techniques with conditional diffusion models. However, the unavoidable discreteness of a molecule makes it difficult for a diffusion model to connect raw data with highly complex conditions like natural language. To address this, here we present a novel latent diffusion model dubbed LDMol for text-conditioned molecule generation. By recognizing that the suitable latent space design is the key to the diffusion model performance, we employ a contrastive learning strategy to extract novel feature space from text data that embeds the unique characteristics of the molecule structure. Experiments show that LDMol outperforms the existing autoregressive baselines on the text-to-molecule generation benchmark, being one of the first diffusion models that outperforms autoregressive models in textual data generation with a better choice of the latent domain. Furthermore, we show that LDMol can be applied to downstream tasks such as molecule-to-text retrieval and text-guided molecule editing, demonstrating its versatility as a diffusion model.