2026/01/01 by Sumukh Pinge, Chang Eun Song, Po-Kai Hsu +11
Computer Science · #Advanced Data Storage Technologies #Parallel Computing and Optimization Techniques #Software System Performance and Reliability
paper · pdf · doi:10.1109/jetcas.2026.3701551
Open modification search (OMS) in mass spectrometry (MS) is a data-intensive workload whose performance is dominantly limited by reference data movement rather than computation. Prior OMS accelerators have largely been evaluated in isolation, making it difficult to understand system-level trade-offs across platforms. This paper presents the first workload-driven, cross-platform survey of accelerators for MS search by studying not only commodity platforms, but also emerging memory- and storage-centric architectures, including GPUs, near-storage FPGAs, DRAM near-memory processing, ReRAM/PCM in-memory processing, and 3D NAND/FeNAND in-storage processing, under consistent algorithmic and accuracy assumptions. Leveraging a binary hyperdimensional computing (HDC)–based OMS formulation that reduces similarity evaluation to lightweight bitwise primitives and tolerates device-level non-idealities, we enable a robust execution on memory-centric architectures despite device-level non-idealities and limited computing capability. Overall, this study identifies memory- and storage-centric architectures as a key architectural breakthrough for large-scale, high-speed search acceleration, delivering up to >100× speedup and >40, 000× improvement in energy efficiency.