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T. Zhang and Franz Franchetti (Proc. SRC TECHCON, 2025)
Towards an End-to-End Processing-in-DRAM Acceleration of Spectral Library Search
Preprint (1001 KB)
Bibtex

This work explores accelerating spectral library searches, a key mass spectrometry (MS) workload, using processing-in-memory (PIM) architectures through an end-toend, co-designed approach. We apply signal processing techniques for pre-filtering MS data and implement a sum of absolute differences (SAD) algorithm optimized for PIM to compare spectral similarity. Our methodology is evaluated using a DRAMbased PIM simulator and compared against traditional CPU implementations. While initial results with small datasets favor CPUs, our analysis indicates potential benefits for PIM with larger, more realistic proteomics datasets. This work represents an initial step towards investigating PIM acceleration for MS applications.

Keywords:
Acceleration, DRAM, Spectral library search, End-to-end processing