# PTransIPs: Identification of phosphorylation sites enhanced by protein PLM embeddings

arXiv: https://arxiv.org/abs/2308.05115 · HTML: https://mlsanity.com/paper/2308.05115/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 10 of its 54 references that are in the map.
- First posted on arXiv 8 Aug 2023.

## Builds on (most cited first, 10 of 10)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Very Deep Convolutional Networks for Large-Scale Image Recognition](https://mlsanity.com/paper/1409.1556/) (2014)
- [Neural Machine Translation by Jointly Learning to Align and Translate](https://mlsanity.com/paper/1409.0473/) (2014)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing](https://mlsanity.com/paper/2007.06225/) (2020)
- [Structured Attention Networks](https://mlsanity.com/paper/1702.00887/) (2017)
- [Transductive Information Maximization For Few-Shot Learning](https://mlsanity.com/paper/2008.11297/) (2020)

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

- [REACT: Representation Extraction And Controllable Tuning to Overcome Overfitting in LLM Knowledge Editing](https://mlsanity.com/paper/2505.18933/) (2025)

## Abstract (arXiv)

Phosphorylation is pivotal in numerous fundamental cellular processes and plays a significant role in the onset and progression of various diseases. The accurate identification of these phosphorylation sites is crucial for unraveling the molecular mechanisms within cells and during viral infections, potentially leading to the discovery of novel therapeutic targets. In this study, we develop PTransIPs, a new deep learning framework for the identification of phosphorylation sites. Independent testing results demonstrate that PTransIPs outperforms existing state-of-the-art (SOTA) methods, achieving AUCs of 0.9232 and 0.9660 for the identification of phosphorylated S/T and Y sites, respectively. PTransIPs contributes from three aspects. 1) PTransIPs is the first to apply protein pre-trained language model (PLM) embeddings to this task. It utilizes ProtTrans and EMBER2 to extract sequence and structure embeddings, respectively, as additional inputs into the model, effectively addressing issues of dataset size and overfitting, thus enhancing model performance; 2) PTransIPs is based on Transformer architecture, optimized through the integration of convolutional neural networks and TIM loss function, providing practical insights for model design and training; 3) The encoding of amino acids in PTransIPs enables it to serve as a universal framework for other peptide bioactivity tasks, with its excellent performance shown in extended experiments of this paper. Our code, data and models are publicly available at https://github.com/StatXzy7/PTransIPs.