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Prot2Token: A Unified Framework for Protein Modeling via Next-Token Prediction

Mahdi Pourmirzaei, Farzaneh Esmaili, Salhuldin Alqarghuli, Mohammadreza Pourmirzaei, Ye Han, Kai Chen, Mohsen Rezaei, Duolin Wang, Dong Xu

2025-05-29

Prot2Token: A Unified Framework for Protein Modeling via Next-Token
  Prediction

Summary

This paper talks about Prot2Token, a new computer model that helps scientists predict different properties of proteins using one unified approach, instead of needing separate models for each specific task.

What's the problem?

The problem is that protein modeling usually requires different specialized tools for each type of prediction, like figuring out a protein's structure or how it might interact with other molecules. This makes the process slow and complicated, since researchers have to switch between different models for different tasks.

What's the solution?

The researchers created a single model that uses a method called next-token prediction, similar to how language models predict the next word in a sentence. By using special task tokens, this model can handle many different protein prediction tasks at once, making it more efficient and accurate than using separate models for each job.

Why it matters?

This matters because it makes protein research faster and easier, helping scientists discover new medicines or understand diseases more quickly. By having one powerful tool for many tasks, researchers can get better results without as much hassle.

Abstract

Prot2Token unifies protein prediction tasks using an autoregressive decoder with task tokens, improving efficiency and accuracy across different benchmarks compared to specialized models.