# A Pre-trained Reaction Embedding Descriptor Capturing Bond Transformation Patterns

arXiv: https://arxiv.org/abs/2601.03689 · HTML: https://mlsanity.com/paper/2601.03689/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 6 of its 63 references that are in the map.
- First posted on arXiv 7 Jan 2026.

## Builds on (most cited first, 6 of 6)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Representation Learning on Graphs with Jumping Knowledge Networks](https://mlsanity.com/paper/1806.03536/) (2018)
- [Mapping the Space of Chemical Reactions Using Attention-Based Neural Networks](https://mlsanity.com/paper/2012.06051/) (2020)
- [DScribe: Library of Descriptors for Machine Learning in Materials Science](https://mlsanity.com/paper/1904.08875/) (2019)

## Abstract (arXiv)

With the rise of data-driven reaction prediction models, effective reaction descriptors are crucial for bridging the gap between real-world chemistry and digital representations. However, general-purpose, reaction-wise descriptors remain scarce. This study introduces RXNEmb, a novel reaction-level descriptor derived from RXNGraphormer, a model pre-trained to distinguish real reactions from fictitious ones with erroneous bond changes, thereby learning intrinsic bond formation and cleavage patterns. We demonstrate its utility by data-driven re-clustering of the USPTO-50k dataset, yielding a classification that more directly reflects bond-change similarities than rule-based categories. Combined with dimensionality reduction, RXNEmb enables visualization of reaction space diversity. Furthermore, attention weight analysis reveals the model's focus on chemically critical sites, providing mechanistic insight. RXNEmb serves as a powerful, interpretable tool for reaction fingerprinting and analysis, paving the way for more data-centric approaches in reaction analysis and discovery.