# Evaluating protein binding interfaces with PUMBA

arXiv: https://arxiv.org/abs/2510.16674 · HTML: https://mlsanity.com/paper/2510.16674/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Core SSM architectures for language, one of 10 directions in State-space sequence models (S4, Mamba).
- Builds on 9 of its 30 references that are in the map.
- First posted on arXiv 19 Oct 2025.

## Placed in

- State-space sequence models (S4, Mamba) / [Core SSM architectures for language](https://mlsanity.com/ssm/core-ssm-architectures-for-language/)

## Builds on (most cited first, 9 of 9)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [Supervised Contrastive Learning](https://mlsanity.com/paper/2004.11362/) (2020)
- [Vision Mamba: Efficient Visual Representation Learning with Bidirectional State Space Model](https://mlsanity.com/paper/2401.09417/) (2024)
- [Quantifying Attention Flow in Transformers](https://mlsanity.com/paper/2005.00928/) (2020)
- [This Looks Like That: Deep Learning for Interpretable Image Recognition](https://mlsanity.com/paper/1806.10574/) (2018)
- [Transformer Interpretability Beyond Attention Visualization](https://mlsanity.com/paper/2012.09838/) (2020)
- [The Hidden Attention of Mamba Models](https://mlsanity.com/paper/2403.01590/) (2024)

## Abstract (arXiv)

Protein-protein docking tools help in studying interactions between proteins, and are essential for drug, vaccine, and therapeutic development. However, the accuracy of a docking tool depends on a robust scoring function that can reliably differentiate between native and non-native complexes. PIsToN is a state-of-the-art deep learning-based scoring function that uses Vision Transformers in its architecture. Recently, the Mamba architecture has demonstrated exceptional performance in both natural language processing and computer vision, often outperforming Transformer-based models in their domains. In this study, we introduce PUMBA (Protein-protein interface evaluation with Vision Mamba), which improves PIsToN by replacing its Vision Transformer backbone with Vision Mamba. This change allows us to leverage Mamba's efficient long-range sequence modeling for sequences of image patches. As a result, the model's ability to capture both global and local patterns in protein-protein interface features is significantly improved. Evaluation on several widely-used, large-scale public datasets demonstrates that PUMBA consistently outperforms its original Transformer-based predecessor, PIsToN.