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Genome analysis has revolutionized fields such as personalized medicine and forensics. Modern sequencing machines generate vast amounts of fragmented strings of genome data called reads. The alignment of these reads into a complete DNA sequence of an organism (the read mapping process) requires extensive data transfer between processing units and memory, leading to execution bottlenecks. Prior studies have primarily focused on accelerating specific stages of the read-mapping task. Conversely, this paper introduces a holistic framework called DART-PIM that accelerates the entire read-mapping process. DART-PIM facilitates digital processing-in-memory (PIM) for an end-to-end acceleration of the entire read-mapping process, from indexing using a unique data organization schema to filtering and read alignment with an optimized Wagner Fischer algorithm. A comprehensive performance evaluation with real genomic data shows that DART-PIM achieves a 5.7x and 257x improvement in throughput and a 92x and 27x energy efficiency enhancement compared to state-of-the-art GPU and PIM implementations, respectively.

The von Neumann architecture, in which the memory and the computation units are separated, demands massive data traffic between the memory and the CPU. To reduce data movement, new technologies and computer architectures have been explored. The use of memristors, which are devices with both memory and computation capabilities, has been considered for different processing-in-memory (PIM) solutions, including using memristive stateful logic for a programmable digital PIM system. Nevertheless, all previous work has focused on a specific stateful logic family, and on optimizing the execution for a certain target machine. These solutions require new compiler and compilation when changing the target machine, and provide no backward compatibility with other target machines. In this chapter, we present abstractPIM, a new compilation concept and flow which enables executing any function within the memory, using different stateful logic families and different instruction set architectures (ISAs). By separating the code generation into two independent components, intermediate representation of the code using target independent ISA and then microcode generation for a specific target machine, we provide a flexible flow with backward compatibility and lay foundations for a PIM compiler. Using abstractPIM, we explore various logic technologies and ISAs and how they impact each other, and discuss the challenges associated with it, such as the increase in execution time., Comment: Link to the book chapter in Springer: https://link.springer.com/chapter/10.1007/978-3-030-81641-4_16

Aligning the entire genome of an organism is a compute-intensive task. Pre-alignment filters substantially reduce computation complexity by filtering potential alignment locations. The base-count filter successfully removes over 68% of the potential locations through a histogram-based heuristic. This paper presents FiltPIM, an efficient design of the basecount filter that is based on memristive processing-in-memory. The in-memory design reduces CPU-to-memory data transfer and utilizes both intra-crossbar and inter-crossbar memristive stateful-logic parallelism. The reduction in data transfer and the efficient stateful-logic computation together improve filtering time by 100x compared to a CPU implementation of the filter., Comment: Published in 2021 28th IEEE International Conference on Electronics, Circuits, and Systems (ICECS)