JuliaCon 2023

AdaptiveHierarchicalRegularBinning
07-26, 15:30–16:00 (US/Eastern), 32-124

AdaptiveHierarchicalRegularBinning.jl computes a hierarchical space-partitioning tree for a given set of points of arbitrary dimensions, that divides the space and stores the reordered points offering efficient access. Space-partitioning data structures are vital for algorithms that exploit spatial distance to reduce computational complexity, see for example the Fast Multipole Method and Nearest Neighbors.


Model

Assuming a set of n points V in a d-dimensional space, we partition the space into regular hierarchical bins. The resulting data structure is a sparse tree T with, at most, 2^d child nodes per node and a maximum depth of L.

Normalization

The given set of points V is mapped into a d-dimensional unit hypercube via an affine transformation that scales and translates V resulting in Vn.

Binning

We split each dimension of the unit hypercube in half and recursively continue splitting each resulting hypercube in the same manner. Each partition is called a bin. The subdivision stops at a maximum depth L or when a bin contains k or fewer points. The recursive splitting process is recorded as a hierarchical tree data structure.

1D Encoding

We use Morton encoding to map the d-dimensional set Vn to a one-dimensional space-filling curve. Each point in Vn is assigned an index in the reduced space resulting in R. Elements of R are bit-fields, each one consisting of L groups of d bits. These groups describe the position of the point in the corresponding level of the tree T. Points described by morton indices with equal most signifficant digits belong in the same bin. Thus, sorting R results in Rs which defines the sparse tree.

Implementation

Cache-locality and parallel programming are some of the techniques we used, to make our implementation performant.

Cache locality

Cache locality offers fast memory access that greatly improves the performance of our algorithm.

  • The set of points V, and by extension Vn, is defined as a Matrix of size (d, n). The leading dimension describes the number of dimensions in the hyperspace resulting in an access pattern that is more friendly to the cache since all points of V have their corresponding coordinates densely packed in memory.

  • Sorting R and Vn offers a memory layout that is cache-friendly. Since we access V through the T tree, we only access points that are in the same bin. Rs describes a bin of T with a contiguous block of memory, thus preserving cache-locality.

  • T is not a linked-tree. T is a tree stored densely in memory as a Vector{Node}. Each Node of T is aware of their children and parent using their indices in this dense Vector{Node}.

Parallel Partial Sorting

The Morton curve bit-field denotes the tree node of each point. The partial sorting using the Most Significant Digit (MSD) radix-sort, places the points to the corresponding bins. Points that fall within the same leaf node do not get sorted. The radix-sort runs in parallel: the partition of digits is done with a parallel count-sort, and then each digit subset is processed independently in parallel.

Adaptive Tree

Empty bins, that is, nodes that do not contain any points, are not stored or referenced explicitly.

References

  • Sun, X., & Pitsianis, N. P. (2001). A Matrix Version of the Fast Multipole Method. In SIAM Review (Vol. 43, Issue 2, pp. 289–300). Society for Industrial & Applied Mathematics (SIAM). https://doi.org/10.1137/s0036144500370835

  • Curtin, R., March, W., Ram, P., Anderson, D., Gray, A. & Isbell, C.. (2013). Tree-Independent Dual-Tree Algorithms. Proceedings of the 30th International Conference on Machine Learning, in Proceedings of Machine Learning Research 28(3):1435-1443 Available from https://proceedings.mlr.press/v28/curtin13.html.

  • Carrier, J., Greengard, L., & Rokhlin, V. (1988). A Fast Adaptive Multipole Algorithm for Particle Simulations. In SIAM Journal on Scientific and Statistical Computing (Vol. 9, Issue 4, pp. 669–686). Society for Industrial & Applied Mathematics (SIAM). https://doi.org/10.1137/0909044

  • Yokota, R. (2013). An FMM Based on Dual Tree Traversal for Many-Core Architectures. In Journal of Algorithms & Computational Technology (Vol. 7, Issue 3, pp. 301–324). SAGE Publications. https://doi.org/10.1260/1748-3018.7.3.301

  • Curtin, R.R. (2015). Faster Dual-Tree Traversal for Nearest Neighbor Search. In: Amato, G., Connor, R., Falchi, F., Gennaro, C. (eds) Similarity Search and Applications. SISAP 2015. Lecture Notes in Computer Science(), vol 9371. Springer, Cham. https://doi.org/10.1007/978-3-319-25087-8_7

  • Greengard, L. (1990). The numerical solution of the n‐body problem. Computers in physics, 4(2), 142-152.

  • Cho, M., Brand, D., Bordawekar, R., Finkler, U., Kulandaisamy, V., & Puri, R. (2015). PARADIS: An efficient parallel algorithm for in-place radix sort. Proceedings of the VLDB Endowment, 8(12), 1518-1529.

  • Zagha, M., & Blelloch, G. E. (1991, August). Radix sort for vector multiprocessors. In Proceedings of the 1991 ACM/IEEE conference on Supercomputing (pp. 712-721).

  • Morton, G. M. (1966). A computer oriented geodetic data base and a new technique in file sequencing.