# ReactEmbed: A Plug-and-Play Module for Unifying Protein-Molecule Representations Guided by Biochemical Reaction Networks

arXiv: https://arxiv.org/abs/2501.18278 · HTML: https://mlsanity.com/paper/2501.18278/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 5 of its 31 references that are in the map.
- First posted on arXiv 30 Jan 2025.

## Builds on (most cited first, 5 of 5)

- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Evaluating Protein Transfer Learning with TAPE](https://mlsanity.com/paper/1906.08230/) (2019)
- [Protein Representation Learning by Geometric Structure Pretraining](https://mlsanity.com/paper/2203.06125/) (2022)
- [TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery](https://mlsanity.com/paper/2202.08320/) (2022)
- [DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening](https://mlsanity.com/paper/2310.06367/) (2023)

## Abstract (arXiv)

State-of-the-art models represent proteins and molecules in separate embedding manifolds, limiting the modeling of systemic biological processes. We introduce ReactEmbed, a lightweight, plug-and-play module that bridges this gap. ReactEmbed leverages biochemical reaction networks as a source of functional context, based on the principle that co-participation in reactions defines a shared functional scope. The module aligns frozen embeddings from models like ESM-3 and MolFormer into a unified space using a weighted reaction graph and a specialized sampling strategy. This process enriches unimodal embeddings and enables strong performance on cross-domain benchmarks. ReactEmbed offers a practical method to unify biological representations without costly retraining. The code and database are available for open usefootnotehttps://github.com/amitaysicherman/ReactEmbeded.