ProTok: Unified Protein Tokenization via Modular Multi-Codebook Quantization
Protein sequence, structure, and functional annotations each capture complementary aspects of protein biology, yet existing tokenizers encode each modality independently, limiting the expressiveness of discrete protein representations. We present ProTok, a unified protein tokenizer that maps all three modalities into a modular discrete vocabulary via product quantization with per-modality codebook groups and modality dropout. A single ProTok checkpoint supports flexible inference from any modality subset without retraining. On seven StructTokenBench benchmarks spanning 14 tasks and 28 test splits, ProTok achieves an average rank of 1.4 across all structure-only tokenizers, placing first o...
| Authors | Romain Hardy, Xiaoman Zhang, Pranav Rajpurkar |
|---|---|
| Primary category | cs.LG |
| Published | 13 October 2026 |
| Last updated at source | 13 October 2026 |
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