We study Diffusion Schrödinger Bridge (DSB) models in the context of dynamical astrophysical systems, specifically tackling observational inverse prediction tasks within Giant Molecular Clouds (GMCs) for star formation. We introduce the AstroDSB model, a variant of DSB with the pairwise domain assumption tailored for astrophysical dynamics.

Cryo-EM is a transformational paradigm in molecular biology where computa-1 tional methods are used to infer 3D molecular structure at atomic resolution from2 extremely noisy 2D electron microscope images. At the forefront of research is3 how to model the structure when the imaged particles exhibit non-rigid conforma-4 tional flexibility and compositional variation where parts are sometimes missing.5 We introduce a novel 3D reconstruction framework with a hierarchical Gaussian6 mixture model, inspired in part by Gaussian Splatting for 4D scene reconstruction.7 In particular, the structure of the model is grounded in an initial process that infers8 a part-based segmentation of the particle, providing essential inductive bias in9 order to handle both conformational and compositional variability. The framework,10 called CryoSPIRE, is shown to reveal biologically meaningful structures on com-11 plex experimental datasets, and establishes a new state-of-the-art on CryoBench, a12 benchmark for cryo-EM heterogeneity methods.

Protein structure prediction models are now capable of generating accurate 3D structural hypotheses from sequence alone. However, they routinely fail to capture the conformational diversity of dynamic biomolecular complexes, often requiring heuristic MSA subsampling approaches for generating alternative states. In parallel, cryo-electron microscopy (cryo-EM) has emerged as a powerful tool for imaging near-native structural heterogeneity, but is challenged by arduous pipelines to transform raw experimental data into atomic models. Here, we bridge the gap between these modalities, combining cryo-EM density maps with the rich sequence and biophysical priors learned by protein structure prediction models. Our method, CryoBoltz, guides the sampling trajectory of a pretrained biomolecular structure prediction model using both global and local structural constraints derived from density maps, driving predictions towards conformational states consistent with the experimental data. We demonstrate that this flexible yet powerful inferencetime approach allows us to build atomic models into heterogeneous cryo-EM maps across a variety of dynamic biomolecular systems including transporters and antibodies.

This paper focuses on improving the reconstruction of 2D floorplans from unstructured 3D point clouds. We identify opportunities for enhancement over the existing methods in three main areas: semantic quality, efficient representation, and local geometric details. To address these, we presents SLIBO-Net, an innovative approach to reconstructing 2D floorplans from unstructured 3D point clouds. We propose a novel transformer-based architecture that employs an efficient floorplan representation, providing improved room shape supervision and allowing for manageable token numbers. By incorporating geometric priors as a regularization mechanism and post-processing step, we enhance the capture of local geometric details. We also propose a scale-independent evaluation metric, correcting the discrepancy in error treatment between varying floorplan sizes. Our approach notably achieves a new state-of-the-art on the Structured3D dataset. The resultant floorplans exhibit enhanced semantic plausibility, substantially improving the overall quality and realism of the reconstructions. Our code and dataset are available online1.

We compare our method with four competing methods in Table 1 of the main paper. We also use the score reported by [5]. We found that the corner-based methods, e.g., HEA T and RoomFormer, fail to reconstruct the correct floorplans and are easily affected by the irregular Heat: Holistic edge attention transformer for structured reconstruction. Real-world perception for embodied agents.

Cryo-electron microscopy (cryo-EM) is an experimental technique for protein structure determination that images an ensemble of macromolecules in near-physiological contexts. While recent advances enable the reconstruction of dynamic conformations of a single biomolecular complex, current methods do not adequately model samples with mixed conformational and compositional heterogeneity. In particular, datasets containing mixtures of multiple proteins require the joint inference of structure, pose, compositional class, and conformational states for 3D reconstruction.

However, both L2 and BL have two deficiencies. First, the noise in the annotation process is not considered in a principled way. L2 and BL make an assumption about per-pixel i.i.d.