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Some focus on floor plan reconstruction as a simplified problem to better analyze connectivity between planes of floors and walls. However, the connectivity analysis is still challenging and ill-posed with incomplete point clouds as input. We propose ArrangementNet to estimate scene arrangements from an incomplete point cloud, which we can easily convert into a BIM model. ArrangementNet is a novel graph neural network that consumes noisy over-partitioned initial arrangements extracted through non-learning techniques and outputs high-quality scene arrangement. The core of ArrangementNet is an extended graph convolution that leverages co-linear and co-face relationships in the arrangement and improves the quality of prediction in complex scenes. We apply ArrangementNet to improve floor plan and ceiling arrangements and enrich them with semantic objects as scene arrangements for scene generation. Our approach faithfully models challenging scenes obtained from laser scans or multiview stereo and shows significant improvement in BIM model reconstruction compared to the state-of-the-art. 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