SEDD: Scalable and Efficient Dataset Deduplication with GPUs

Abstract

Dataset deduplication is widely recognized as a crucial preprocessing step that enhances data quality and improves the performance of large language models. A commonly used method for this process is the MinHash Locality-Sensitive Hashing (LSH) algorithm. Recently, GPU-accelerated frameworks such as NVIDIA NeMo Curator have been introduced to handle large-scale corpora; however, they remain suboptimal due to high communication overhead from physical data shuffling and underutilization of GPU resources. In this paper, we propose SEDD, a high-performance GPU-accelerated deduplication framework optimized for distributed cluster environments. SEDD introduces a computationally efficient, partially reusable hash function, alongside highly optimized GPU kernels and a hardware-aware automatic parameter selection mechanism. By replacing traditional data shuffling with a streaming-based approach, SEDD significantly mitigates communication bottlenecks. Our framework outperforms the CPU-based deduplication tool in SlimPajama by up to 158$\times$ and the GPU-based tool in NVIDIA NeMo Curator by up to 7.8$\times$ when processing 30 million documents on a node with four GPUs. Notably, SEDD dramatically accelerates the previously time-consuming MinHash signature generation phase, achieving speedups of up to 375$\times$ over the CPU baseline. Despite these gains in efficiency, SEDD maintains high deduplication fidelity, with duplicate document sets achieving Jaccard similarities of over 0.95 compared to those identified by the standard MinHash algorithm. In large-scale experiments, the deduplication of 1.2 trillion tokens is completed in just 3 hours on an 8-node 32-GPU V100 cluster. The related code is publicly available on GitHub (https://github.com/mcrl/SEDD).