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

• URL: http://arxiv.org/abs/2505.20589v1
• Date: Mon, 26 May 2025 23:50:36 GMT
• Title: Prot2Token: A Unified Framework for Protein Modeling via Next-Token Prediction
• Authors: Mahdi Pourmirzaei, Farzaneh Esmaili, Salhuldin Alqarghuli, Mohammadreza Pourmirzaei, Ye Han, Kai Chen, Mohsen Rezaei, Duolin Wang, Dong Xu,
• Abstract summary: We introduce Prot2Token, a unified framework that overcomes challenges by converting a wide spectrum of protein-related predictions.<n>At its core, Prot2Token employs an autoregressive decoder, conditioned on embeddings from pre-trained protein encoders and guided by learnable task tokens.<n>We present extensive experimental validation across a variety of benchmarks, demonstrating Prot2Tokens strong predictive power in different types of protein-prediction tasks.
• Score: 19.164841536081568
• License: http://creativecommons.org/licenses/by-nc-nd/4.0/
• Abstract: The diverse nature of protein prediction tasks has traditionally necessitated specialized models, hindering the development of broadly applicable and computationally efficient Protein Language Models (PLMs). In this work, we introduce Prot2Token, a unified framework that overcomes these challenges by converting a wide spectrum of protein-related predictions, from sequence-level properties and residue-specific attributes to complex inter-protein interactions, into a standardized next-token prediction format. At its core, Prot2Token employs an autoregressive decoder, conditioned on embeddings from pre-trained protein encoders and guided by learnable task tokens, to perform diverse predictions. This architecture uniquely facilitates multi-task learning, enabling a single model to master numerous tasks with improved efficiency. We present extensive experimental validation across a variety of benchmarks, demonstrating Prot2Tokens strong predictive power in different types of protein-prediction tasks. Key results include significant speedups (e.g., near 1000x over AlphaFold2 with MSA) and performance often matching or exceeding specialized approaches. Beyond that, we introduce an auxiliary self-supervised decoder pre-training approach to improve spatially sensitive task performance. Prot2Token thus offers a significant step towards a versatile, high-throughput paradigm for protein modeling, promising to accelerate biological discovery and the development of novel therapeutics. The code is available at https://github.com/mahdip72/prot2token .

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