Related papers: AlignOT: An optimal transport based algorithm for …
Unbalanced optimal transport (UOT) provides a flexible way to match or compare nonnegative finite Radon measures. However, UOT requires a predefined ground transport cost, which may misrepresent the data's underlying geometry. Choosing such…
Cryogenic electron microscopy (cryo-EM) provides images from different copies of the same biomolecule in arbitrary orientations. Here, we present an end-to-end unsupervised approach that learns individual particle orientations from cryo-EM…
We present a new approach for Neural Optimal Transport (NOT) training procedure, capable of accurately and efficiently estimating optimal transportation plan via specific regularization on dual Kantorovich potentials. The main bottleneck of…
The current best practice for computing optimal transport (OT) is via entropy regularization and Sinkhorn iterations. This algorithm runs in quadratic time as it requires the full pairwise cost matrix, which is prohibitively expensive for…
In machine learning, Optimal Transport (OT) theory is extensively utilized to compare probability distributions across various applications, such as graph data represented by node distributions and image data represented by pixel…
Cryo-EM is an increasingly popular method for determining the atomic resolution 3D structure of macromolecular complexes (eg, proteins) from noisy 2D images captured by an electron microscope. The computational task is to reconstruct the 3D…
Cryo-electron tomography (Cryo-ET) is a 3D imaging technique that enables the systemic study of shape, abundance, and distribution of macromolecular structures in single cells in near-atomic resolution. However, the systematic and efficient…
Enhancing cryogenic electron microscopy (cryo-EM) 3D density maps at intermediate resolution (4-8 {\AA}) is crucial in protein structure determination. Recent advances in deep learning have led to the development of automated approaches for…
Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the…
Finding node correspondence across networks, namely multi-network alignment, is an essential prerequisite for joint learning on multiple networks. Despite great success in aligning networks in pairs, the literature on multi-network…
Accurate pose estimation and shift correction are key challenges in cryo-EM due to the very low SNR, which directly impacts the fidelity of 3D reconstructions. We present an approach for pose estimation in cryo-EM that leverages…
Alignment plays a fundamental role in many machine learning problems, such as multi-network analysis, multimodal learning, and point cloud registration. Recent works increasingly leverage optimal transport (OT) for distributional alignment,…
Dataset distillation seeks to synthesize a compact distilled dataset, enabling models trained on it to achieve performance comparable to models trained on the full dataset. Recent methods for large-scale datasets focus on matching global…
Accurate orientation estimation is a crucial component of 3D molecular structure reconstruction, both in single-particle cryo-electron microscopy (cryo-EM) and in the increasingly popular field of cryo-electron tomography (cryo-ET). The…
Cryogenic electron microscopy (cryo-EM) has become an enabling technology in drug discovery and in understanding molecular bases of disease by producing near-atomic resolution (less than 0.4 nm) 3D reconstructions of biological…
Lidar data can be used to generate point clouds for the navigation of autonomous vehicles or mobile robotics platforms. Scan matching, the process of estimating the rigid transformation that best aligns two point clouds, is the basis for…
Optimal transport (OT) is a central framework for modeling distribution shifts. Because OT compares distributions directly in input space, a well-designed ground metric between observations is essential to ensure that the optimizer does not…
In this work, we propose a novel machine learning approach to compute the optimal transport map between two continuous distributions from their unpaired samples, based on the DeepParticle methods. The proposed method leads to a min-min…
Cryo-electron tomography (cryoET) is a technique that captures images of biological samples at different tilts, preserving their native state as much as possible. Along with the partial tilt series and noise, one of the major challenges in…
We presented a new 3D refinement method for Cryo-EM single particle analysis which can improve the resolution of final electron density map in this paper. We proposed to enforce both sparsity and smoothness to improve the regularity of…