# GDiffRetro: Retrosynthesis Prediction with Dual Graph Enhanced Molecular Representation and Diffusion Generation

arXiv: https://arxiv.org/abs/2501.08001 · HTML: https://mlsanity.com/paper/2501.08001/

## Key facts

- Cited by 7 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 14 Jan 2025.

## Built on by (most cited first, 7 of 7)

- [FutureSightDrive: Thinking Visually with Spatio-Temporal CoT for Autonomous Driving](https://mlsanity.com/paper/2505.17685/) (2025)
- [Order Matters in Retrosynthesis: Structure-aware Generation via Reaction-Center-Guided Discrete Flow Matching](https://mlsanity.com/paper/2602.13136/) (2026)
- [RS-WorldModel: a Unified Model for Remote Sensing Understanding and Future Sense Forecasting](https://mlsanity.com/paper/2603.14941/) (2026)
- [DiffER: Categorical Diffusion for Chemical Retrosynthesis](https://mlsanity.com/paper/2505.23721/) (2025)
- [Enhanced Pre-training of Graph Neural Networks for Million-Scale Heterogeneous Graphs](https://mlsanity.com/paper/2510.12401/) (2025)
- [Learning Transferable Reaction Mechanisms from Visual Chemical Knowledge](https://mlsanity.com/paper/2609.33608/) (2026)
- [Salvation Lies Within: Eliciting Inherent Style Transfer in Step-Distilled Diffusion Models](https://mlsanity.com/paper/2610.05066/) (2026)

## Abstract (arXiv)

Retrosynthesis prediction focuses on identifying reactants capable of synthesizing a target product. Typically, the retrosynthesis prediction involves two phases: Reaction Center Identification and Reactant Generation. However, we argue that most existing methods suffer from two limitations in the two phases: (i) Existing models do not adequately capture the ``face'' information in molecular graphs for the reaction center identification. (ii) Current approaches for the reactant generation predominantly use sequence generation in a 2D space, which lacks versatility in generating reasonable distributions for completed reactive groups and overlooks molecules' inherent 3D properties. To overcome the above limitations, we propose GDiffRetro. For the reaction center identification, GDiffRetro uniquely integrates the original graph with its corresponding dual graph to represent molecular structures, which helps guide the model to focus more on the faces in the graph. For the reactant generation, GDiffRetro employs a conditional diffusion model in 3D to further transform the obtained synthon into a complete reactant. Our experimental findings reveal that GDiffRetro outperforms state-of-the-art semi-template models across various evaluative metrics.