ProTok: Unified Protein Tokenization via Modular Multi-Codebook Quantization

ProTok introduces a unified protein tokenizer that maps protein sequence, structure, and functional annotations into a single modular discrete vocabulary using product quantization with per-modality codebook groups and modality dropout. The tokenizer supports flexible inference from any subset of modalities without retraining and achieves top performance on seven StructTokenBench benchmarks, with high reconstruction accuracy (0.939 lDDT on CATH 4.2) and superior zero‑shot functional retrieval. Additionally, a compact language model trained on ProTok tokens can jointly generate backbone and sequence, yielding a higher proportion of designable backbones compared to a GeoBPE baseline.

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• llms
• nlp
• efficiency
• multimodal
• benchmarks