Trion-1: Unifying Language, Protein Sequence, and Structure with Diffusion Language Models

Abstract

We envision a general-purpose protein foundation model as a unified, interactive model of sequence, structure, and function, capable of understanding, generation, and cross-modal translation while retaining the instruction-following and reasoning capabilities of modern LLMs. Toward this vision, we introduce Trion-1, the first native, unified, multimodal diffusion language model (dLLM) for proteins. Trion-1 is built on two key design choices: (1) a unified discrete token space that jointly represents sequence, structure, and natural language; (2) a dLLM backbone that replaces strict left-to-right factorization with bidirectional or semi-bidirectional token interactions, enabling global residue communication and long-range contact modeling that are naturally suited to structure modeling. This formulation unifies six core capabilities: folding, inverse folding, sequence understanding, structure understanding, sequence design, and structure design, while retaining the native language capabilities of general-purpose LLMs. On established benchmarks, Trion-1 achieves broadly competitive performance. In folding, Trion-1 achieves a TM-score above 0.8 with a single sample under strict homology control, matching or exceeding the existing tri-modal model using 200 samples. For sequence understanding, Trion-1 performs on par with top-tier LLMs such as Claude Opus 4.7 (62.37%). These results support well-aligned sequence-structure-language representations and strong cross-modal generative capabilities.