# TransMA: an explainable multi-modal deep learning model for predicting properties of ionizable lipid nanoparticles in mRNA delivery

arXiv: https://arxiv.org/abs/2407.05736 · HTML: https://mlsanity.com/paper/2407.05736/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 8 of its 50 references that are in the map.
- First posted on arXiv 8 Jul 2024.

## Builds on (most cited first, 8 of 8)

- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [CBAM: Convolutional Block Attention Module](https://mlsanity.com/paper/1807.06521/) (2018)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [BAM: Bottleneck Attention Module](https://mlsanity.com/paper/1807.06514/) (2018)
- [Drug discovery with explainable artificial intelligence](https://mlsanity.com/paper/2007.00523/) (2020)
- [Weak-Mamba-UNet: Visual Mamba Makes CNN and ViT Work Better for Scribble-based Medical Image Segmentation](https://mlsanity.com/paper/2402.10887/) (2024)

## Built on by (most cited first, 1 of 1)

- [Mamba in Vision: A Comprehensive Survey of Techniques and Applications](https://mlsanity.com/paper/2410.03105/) (2024)

## Abstract (arXiv)

As the primary mRNA delivery vehicles, ionizable lipid nanoparticles (LNPs) exhibit excellent safety, high transfection efficiency, and strong immune response induction. However, the screening process for LNPs is time-consuming and costly. To expedite the identification of high-transfection-efficiency mRNA drug delivery systems, we propose an explainable LNPs transfection efficiency prediction model, called TransMA. TransMA employs a multi-modal molecular structure fusion architecture, wherein the fine-grained atomic spatial relationship extractor named molecule 3D Transformer captures three-dimensional spatial features of the molecule, and the coarse-grained atomic sequence extractor named molecule Mamba captures one-dimensional molecular features. We design the mol-attention mechanism block, enabling it to align coarse and fine-grained atomic features and captures relationships between atomic spatial and sequential structures. TransMA achieves state-of-the-art performance in predicting transfection efficiency using the scaffold and cliff data splitting methods on the current largest LNPs dataset, including Hela and RAW cell lines. Moreover, we find that TransMA captures the relationship between subtle structural changes and significant transfection efficiency variations, providing valuable insights for LNPs design. Additionally, TransMA's predictions on external transfection efficiency data maintain a consistent order with actual transfection efficiencies, demonstrating its robust generalization capability. The code, model and data are made publicly available at https://github.com/wklix/TransMA/tree/master. We hope that high-accuracy transfection prediction models in the future can aid in LNPs design and initial screening, thereby assisting in accelerating the mRNA design process.