Preserving Clusters in Error-Bounded Lossy Compression of Particle Data

Abstract: Lossy compression is widely used to reduce storage and I/O costs for large-scale particle datasets in scientific applications such as cosmology, molecular dynamics, and fluid dynamics, where clustering structures (e.g., single-linkage or Friends-of-Friends) are critical for downstream analysis; however, existing compressors typically provide only pointwise error bounds on particle positions and offer no guarantees on preserving clustering outcomes, and even small perturbations can alter cluster connectivity and compromise scientific validity. We propose a correction-based technique to preserve single-linkage clustering under lossy compression, operating on decompressed data from off-the-shelf compressors such as SZ3 and Draco. Our key contributions are threefold: (1) a clustering-aware correction algorithm that identifies vulnerable particle pairs via spatial partitioning and local neighborhood search; (2) an optimization-based formulation that enforces clustering consistency using projected gradient descent with a loss that encodes pairwise distance violations; and (3) a scalable GPU-accelerated and distributed implementation for large-scale datasets. Experiments on cosmology and molecular dynamics datasets show that our method effectively preserves clustering results while maintaining competitive compression performance compared with SZ3, ZFP, Draco, LCP, and space-filling-curve-based schemes.