An In-Storage Processing Architecture with 3D NAND Heterogeneous Integration for Spectra Open Modification Search
Po-Kai Hsu, Weihong Xu, Tajana Rosing, Shimeng Yu · Proceedings of the International Symposium on Memory Systems · 2023
Spectra open modification search (OMS) is the critical step in mass spectrometry (MS) analysis and proteomics to identify peptides underlying protein samples. However, large-scale spectra OMS is a data-intensive workload that takes hours to days. In this work, we propose a reconfigurable architecture based on 3D NAND ISP with heterogeneous integration to accelerate the mass spectrum data processing. We present two types of encoding designs for optimization. Then we design scalable and reconfigurable 3D NAND ISP tiles to further optimize the performance. The experiments show that the 3D NAND ISP architecture with proper hardware configuration achieves 14.3 × to 24.2 × speedup over the GPU baseline [10]. The energy consumption is also improved by four orders of magnitude without data movements. The proposed design is an energy-efficient and high-performance ISP solution for the emerging large-scale spectra OMS.