# UniPTMs: The First Unified Multi-type PTM Site Prediction Model via Master-Slave Architecture-Based Multi-Stage Fusion Strategy and Hierarchical Contrastive Loss

arXiv: https://arxiv.org/abs/2506.05443 · HTML: https://mlsanity.com/paper/2506.05443/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 11 of its 58 references that are in the map.
- First posted on arXiv 5 Jun 2025.

## Builds on (most cited first, 11 of 11)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [Knowledge Distillation: A Survey](https://mlsanity.com/paper/2006.05525/) (2020)
- [Titans: Learning to Memorize at Test Time](https://mlsanity.com/paper/2501.00663/) (2024)
- [Coordinate Attention for Efficient Mobile Network Design](https://mlsanity.com/paper/2103.02907/) (2021)
- [CrossFuse: A Novel Cross Attention Mechanism based Infrared and Visible Image Fusion Approach](https://mlsanity.com/paper/2406.10581/) (2024)
- [Dynamic Temperature Knowledge Distillation](https://mlsanity.com/paper/2404.12711/) (2024)

## Abstract (arXiv)

As a core mechanism of epigenetic regulation in eukaryotes, protein post-translational modifications (PTMs) require precise prediction to decipher dynamic life activity networks. To address the limitations of existing deep learning models in cross-modal feature fusion, domain generalization, and architectural optimization, this study proposes UniPTMs: the first unified framework for multi-type PTM prediction. The framework innovatively establishes a "Master-Slave" dual-path collaborative architecture: The master path dynamically integrates high-dimensional representations of protein sequences, structures, and evolutionary information through a Bidirectional Gated Cross-Attention (BGCA) module, while the slave path optimizes feature discrepancies and recalibration between structural and traditional features using a Low-Dimensional Fusion Network (LDFN). Complemented by a Multi-scale Adaptive convolutional Pyramid (MACP) for capturing local feature patterns and a Bidirectional Hierarchical Gated Fusion Network (BHGFN) enabling multi-level feature integration across paths, the framework employs a Hierarchical Dynamic Weighting Fusion (HDWF) mechanism to intelligently aggregate multimodal features. Enhanced by a novel Hierarchical Contrastive loss function for feature consistency optimization, UniPTMs demonstrates significant performance improvements (3.2%-11.4% MCC and 4.2%-14.3% AP increases) over state-of-the-art models across five modification types and transcends the Single-Type Prediction Paradigm. To strike a balance between model complexity and performance, we have also developed a lightweight variant named UniPTMs-mini.