# RetroXpert: Decompose Retrosynthesis Prediction like a Chemist

arXiv: https://arxiv.org/abs/2011.02893 · HTML: https://mlsanity.com/paper/2011.02893/

## Key facts

- Cited by 68 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 4 Nov 2020.

## Built on by (most cited first, 30 of 68)

- [Graph neural networks for materials science and chemistry](https://mlsanity.com/paper/2208.09481/) (2022)
- [Motif-based Graph Self-Supervised Learning for Molecular Property Prediction](https://mlsanity.com/paper/2110.00987/) (2021)
- [Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction prediction](https://mlsanity.com/paper/2110.09681/) (2021)
- [DrugOOD: Out-of-Distribution (OOD) Dataset Curator and Benchmark for AI-aided Drug Discovery -- A Focus on Affinity Prediction Problems with Noise Annotations](https://mlsanity.com/paper/2201.09637/) (2022)
- [Root-aligned SMILES: A Tight Representation for Chemical Reaction Prediction](https://mlsanity.com/paper/2203.11444/) (2022)
- [Rethinking Tokenizer and Decoder in Masked Graph Modeling for Molecules](https://mlsanity.com/paper/2310.14753/) (2023)
- [Dual-view Molecule Pre-training](https://mlsanity.com/paper/2106.10234/) (2021)
- [Re-evaluating Retrosynthesis Algorithms with Syntheseus](https://mlsanity.com/paper/2310.19796/) (2023)
- [RetroGraph: Retrosynthetic Planning with Graph Search](https://mlsanity.com/paper/2206.11477/) (2022)
- [Self-Improved Retrosynthetic Planning](https://mlsanity.com/paper/2106.04880/) (2021)
- [ReactXT: Understanding Molecular "Reaction-ship" via Reaction-Contextualized Molecule-Text Pretraining](https://mlsanity.com/paper/2405.14225/) (2024)
- [Retrosynthesis Prediction with Local Template Retrieval](https://mlsanity.com/paper/2306.04123/) (2023)
- [Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction](https://mlsanity.com/paper/2107.04119/) (2021)
- [Retrosynthetic Planning with Experience-Guided Monte Carlo Tree Search](https://mlsanity.com/paper/2112.06028/) (2021)
- [FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning](https://mlsanity.com/paper/2209.15315/) (2022)
- [Modern Hopfield Networks for Few- and Zero-Shot Reaction Template Prediction](https://mlsanity.com/paper/2104.03279/) (2021)
- [RetroComposer: Composing Templates for Template-Based Retrosynthesis Prediction](https://mlsanity.com/paper/2112.11225/) (2021)
- [SemiRetro: Semi-template framework boosts deep retrosynthesis prediction](https://mlsanity.com/paper/2202.08205/) (2022)
- [RetroGFN: Diverse and Feasible Retrosynthesis using GFlowNets](https://mlsanity.com/paper/2406.18739/) (2024)
- [DirectMultiStep: Direct Route Generation for Multistep Retrosynthesis](https://mlsanity.com/paper/2405.13983/) (2024)
- [Deep Learning Methods for Small Molecule Drug Discovery: A Survey](https://mlsanity.com/paper/2303.00313/) (2023)
- [Node-Aligned Graph-to-Graph (NAG2G): Elevating Template-Free Deep Learning Approaches in Single-Step Retrosynthesis](https://mlsanity.com/paper/2309.15798/) (2023)
- [BatGPT-Chem: A Foundation Large Model For Retrosynthesis Prediction](https://mlsanity.com/paper/2408.10285/) (2024)
- [Advancing Molecular Graph-Text Pre-training via Fine-grained Alignment](https://mlsanity.com/paper/2409.14106/) (2024)
- [Retrieval-Retro: Retrieval-based Inorganic Retrosynthesis with Expert Knowledge](https://mlsanity.com/paper/2410.21341/) (2024)
- [Retroformer: Pushing the Limits of Interpretable End-to-end Retrosynthesis Transformer](https://mlsanity.com/paper/2201.12475/) (2022)
- [MARS: A Motif-based Autoregressive Model for Retrosynthesis Prediction](https://mlsanity.com/paper/2209.13178/) (2022)
- [Equivariant Denoisers Cannot Copy Graphs: Align Your Graph Diffusion Models](https://mlsanity.com/paper/2405.17656/) (2024)
- [RetroDiff: Retrosynthesis as Multi-stage Distribution Interpolation](https://mlsanity.com/paper/2311.14077/) (2023)
- [Chemist-aligned retrosynthesis by ensembling diverse inductive bias models](https://mlsanity.com/paper/2412.05269/) (2024)

## Abstract (arXiv)

Retrosynthesis is the process of recursively decomposing target molecules into available building blocks. It plays an important role in solving problems in organic synthesis planning. To automate or assist in the retrosynthesis analysis, various retrosynthesis prediction algorithms have been proposed. However, most of them are cumbersome and lack interpretability about their predictions. In this paper, we devise a novel template-free algorithm for automatic retrosynthetic expansion inspired by how chemists approach retrosynthesis prediction. Our method disassembles retrosynthesis into two steps: i) identify the potential reaction center of the target molecule through a novel graph neural network and generate intermediate synthons, and ii) generate the reactants associated with synthons via a robust reactant generation model. While outperforming the state-of-the-art baselines by a significant margin, our model also provides chemically reasonable interpretation.