Pointwise Distance Distributions for detecting near-duplicates in large materials databases

Abstract

Many real objects are modeled as discrete sets of points, such as corners or other salient features. For our main applications in chemistry, points represent atomic centers in a molecule or a solid material. We study the problem of classifying discrete (finite and periodic) sets of unordered points under isometry, which is any transformation preserving distances in a metric space. Experimental noise motivates the new practical requirement to make such invariants Lipschitz continuous so that perturbing every point in its epsilon-neighborhood changes the invariant up to a constant multiple of epsilon in a suitable distance satisfying all metric axioms. Since the given points are unordered, the key challenge is to compute all invariants and metrics in a near-linear time of the input size. We define the Pointwise Distance Distribution (PDD) for any discrete set and prove, in addition to the properties above, the completeness of PDD for all periodic sets in general position. The PDD can compare nearly 2 million crystals from the world's five largest databases within 2 hours on a modest desktop computer. The impact is upholding data integrity in crystallography because the PDD will not allow anyone to claim a `new' material as a noisy disguise of a known crystal.