Euclidean distance geometry and applications

Euclidean distance geometry is the study of Euclidean geometry based on the concept of distance. This is useful in several applications where the input data consists of an incomplete set of distances, and the output is a set of points in Euclidean space that realizes the given distances. We survey some of the theory of Euclidean distance geometry and some of the most important applications: molecular conformation, localization of sensor networks and statics.Comment: 64 pages, 21 figure

Eigenvector Synchronization, Graph Rigidity and the Molecule Problem

The graph realization problem has received a great deal of attention in recent years, due to its importance in applications such as wireless sensor networks and structural biology. In this paper, we extend on previous work and propose the 3D-ASAP algorithm, for the graph realization problem in $\mathbb{R}^3$, given a sparse and noisy set of distance measurements. 3D-ASAP is a divide and conquer, non-incremental and non-iterative algorithm, which integrates local distance information into a global structure determination. Our approach starts with identifying, for every node, a subgraph of its 1-hop neighborhood graph, which can be accurately embedded in its own coordinate system. In the noise-free case, the computed coordinates of the sensors in each patch must agree with their global positioning up to some unknown rigid motion, that is, up to translation, rotation and possibly reflection. In other words, to every patch there corresponds an element of the Euclidean group Euc(3) of rigid transformations in $\mathbb{R}^3$, and the goal is to estimate the group elements that will properly align all the patches in a globally consistent way. Furthermore, 3D-ASAP successfully incorporates information specific to the molecule problem in structural biology, in particular information on known substructures and their orientation. In addition, we also propose 3D-SP-ASAP, a faster version of 3D-ASAP, which uses a spectral partitioning algorithm as a preprocessing step for dividing the initial graph into smaller subgraphs. Our extensive numerical simulations show that 3D-ASAP and 3D-SP-ASAP are very robust to high levels of noise in the measured distances and to sparse connectivity in the measurement graph, and compare favorably to similar state-of-the art localization algorithms.Comment: 49 pages, 8 figure

Riemannian Optimization for Distance-Geometric Inverse Kinematics

Solving the inverse kinematics problem is a fundamental challenge in motion planning, control, and calibration for articulated robots. Kinematic models for these robots are typically parametrized by joint angles, generating a complicated mapping between the robot configuration and the end-effector pose. Alternatively, the kinematic model and task constraints can be represented using invariant distances between points attached to the robot. In this paper, we formalize the equivalence of distance-based inverse kinematics and the distance geometry problem for a large class of articulated robots and task constraints. Unlike previous approaches, we use the connection between distance geometry and low-rank matrix completion to find inverse kinematics solutions by completing a partial Euclidean distance matrix through local optimization. Furthermore, we parametrize the space of Euclidean distance matrices with the Riemannian manifold of fixed-rank Gram matrices, allowing us to leverage a variety of mature Riemannian optimization methods. Finally, we show that bound smoothing can be used to generate informed initializations without significant computational overhead, improving convergence. We demonstrate that our inverse kinematics solver achieves higher success rates than traditional techniques, and substantially outperforms them on problems that involve many workspace constraints.Comment: 20 pages, 14 figure

GPU-based Iterative Cone Beam CT Reconstruction Using Tight Frame Regularization

X-ray imaging dose from serial cone-beam CT (CBCT) scans raises a clinical concern in most image guided radiation therapy procedures. It is the goal of this paper to develop a fast GPU-based algorithm to reconstruct high quality CBCT images from undersampled and noisy projection data so as to lower the imaging dose. For this purpose, we have developed an iterative tight frame (TF) based CBCT reconstruction algorithm. A condition that a real CBCT image has a sparse representation under a TF basis is imposed in the iteration process as regularization to the solution. To speed up the computation, a multi-grid method is employed. Our GPU implementation has achieved high computational efficiency and a CBCT image of resolution 512\times512\times70 can be reconstructed in ~5 min. We have tested our algorithm on a digital NCAT phantom and a physical Catphan phantom. It is found that our TF-based algorithm is able to reconstrct CBCT in the context of undersampling and low mAs levels. We have also quantitatively analyzed the reconstructed CBCT image quality in terms of modulation-transfer-function and contrast-to-noise ratio under various scanning conditions. The results confirm the high CBCT image quality obtained from our TF algorithm. Moreover, our algorithm has also been validated in a real clinical context using a head-and-neck patient case. Comparisons of the developed TF algorithm and the current state-of-the-art TV algorithm have also been made in various cases studied in terms of reconstructed image quality and computation efficiency.Comment: 24 pages, 8 figures, accepted by Phys. Med. Bio

Computing quasiconformal folds

We propose a novel way of computing surface folding maps via solving a linear PDE. This framework is a generalization to the existing quasiconformal methods and allows manipulation of the geometry of folding. Moreover, the crucial quantity that characterizes the geometry occurs as the coefficient of the equation, namely the Beltrami coefficient. This allows us to solve an inverse problem of parametrizing the folded surface given only partial data but with known folding topology. Various interesting applications such as fold sculpting on 3D models and self-occlusion reasoning are demonstrated to show the effectiveness of our method