We present SceneNAT, a masked non-autoregressive Transformer for 3D indoor scene synthesis from natural language instructions. It generates complete scenes in a few parallel decoding passes, improving both quality and efficiency over prior methods. SceneNAT is trained via masked modeling over fully discretized representations of both semantic and spatial attributes. By applying a masking strategy at both the attribute level and the instance level, the model can better capture intra-object and inter-object structure. To boost relational reasoning, SceneNAT employs a relational reasoning module (RRM) that captures implicit spatial constraints. By formulating relation modeling as a set prediction task, it extracts structure-aware features to guide the layout generation without explicit sequential parsing. Extensive experiments on 3D-FRONT show that SceneNAT outperforms state-of-the-art autoregressive and diffusion baselines in both semantic compliance and spatial arrangement accuracy while using substantially lower computational cost, enabling high-throughput generation of diverse scenes at scale.

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