SpecPCM: A Low-Power PCM-Based In-Memory Computing Accelerator for Full-Stack Mass Spectrometry Analysis

Abstract

Mass spectrometry (MS) is essential for proteomics and metabolomics but faces impending challenges in efficiently processing the vast volumes of data. This article introduces SpecPCM, an in-memory computing (IMC) accelerator designed to achieve substantial improvements in energy and delay efficiency for both MS spectral clustering and database (DB) search. SpecPCM employs analog processing with low-voltage swing and utilizes recently introduced phase change memory (PCM) devices based on superlattice materials, optimized for low-voltage and low-power programming. Our approach integrates contributions across multiple levels: application, algorithm, circuit, device, and instruction sets. We leverage a robust hyperdimensional computing (HD) algorithm with a novel dimension-packing method and develop specialized hardware for the end-to-end MS pipeline to overcome the nonideal behavior of PCM devices. We further optimize multilevel PCM devices for different tasks by using different materials. We also perform a comprehensive design exploration to improve energy and delay efficiency while maintaining accuracy, exploring various combinations of hardware and software parameters controlled by the instruction set architecture (ISA). SpecPCM, with up to three bits per cell, achieves speedups of up to $82\times $ and $143\times $ for MS clustering and DB search tasks, respectively, along with a four-orders-of-magnitude improvement in energy efficiency compared with state-of-the-art (SoA) CPU/GPU tools.