Search

DNA sequence classification is a fundamental task in computational biology with vast implications for applications such as disease prevention and drug design. Therefore, fast high-quality sequence classifiers are significantly important. This paper introduces ClaPIM, a scalable DNA sequence classification architecture based on the emerging concept of hybrid in-crossbar and near-crossbar memristive processing-in-memory (PIM). We enable efficient and high-quality classification by uniting the filter and search stages within a single algorithm. Specifically, we propose a custom filtering technique that drastically narrows the search space and a search approach that facilitates approximate string matching through a distance function. ClaPIM is the first PIM architecture for scalable approximate string matching that benefits from the high density of memristive crossbar arrays and the massive computational parallelism of PIM. Compared with Kraken2, a state-of-the-art software classifier, ClaPIM provides significantly higher classification quality (up to 20x improvement in F1 score) and also demonstrates a 1.8x throughput improvement. Compared with EDAM, a recently-proposed SRAM-based accelerator that is restricted to small datasets, we observe both a 30.4x improvement in normalized throughput per area and a 7% increase in classification precision.

Bulk-bitwise processing-in-memory (PIM), an emerging computational paradigm utilizing memory arrays as computational units, has been shown to benefit database applications. This paper demonstrates how GROUP-BY and JOIN, database operations not supported by previous works, can be performed efficiently in bulk-bitwise PIM used for relational database analytical processing. We develop a gem5 simulator and show that our hardware modifications, on the Star Schema Benchmark and compared to previous works, improve, on average, execution time by $1.83\times$, energy by $4.31\times$, and the system's lifetime by $3.21\times$. We also achieved a speedup of $4.65\times$ over MonetDB, a modern state-of-the-art in-memory database.

Processing-in-memory (PIM) architectures are emerging to reduce data movement in data-intensive applications. These architectures seek to exploit the same physical devices for both information storage and logic, thereby dwarfing the required data transfer and utilizing the full internal memory bandwidth. Whereas analog PIM utilizes the inherent connectivity of crossbar arrays for approximate matrix-vector multiplication in the analog domain, digital PIM architectures enable bitwise logic operations with massive parallelism across columns of data within memory arrays. Several recent works have extended the computational capabilities of digital PIM architectures towards the full-precision (single-precision floating-point) acceleration of convolutional neural networks (CNNs); yet, they lack a comprehensive comparison to GPUs. In this paper, we examine the potential of digital PIM for CNN acceleration through an updated quantitative comparison with GPUs, supplemented with an analysis of the overall limitations of digital PIM. We begin by investigating the different PIM architectures from a theoretical perspective to understand the underlying performance limitations and improvements compared to state-of-the-art hardware. We then uncover the tradeoffs between the different strategies through a series of benchmarks ranging from memory-bound vectored arithmetic to CNN acceleration. We conclude with insights into the general performance of digital PIM architectures for different data-intensive applications.

Stateful logic is a promising processing-in-memory (PIM) paradigm to perform logic operations using emerging nonvolatile memory cells. While most stateful logic circuits to date focused on technologies such as resistive RAM, we propose two approaches to designing stateful logic using spin orbit torque (SOT) MRAM. The first approach utilizes the separation of read and write paths in SOT devices to perform logic operations. In contrast to previous work, our method utilizes a standard memory structure, and each row can be used as input or output. The second approach uses voltage-gated SOT switching to allow stateful logic in denser memory arrays. We present array structures to support the two approaches and evaluate their functionality using SPICE simulations in the presence of process variation and device mismatch., Published in 2022 22nd IEEE International Conference on Nanotechnology (NANO)

The emerging memristive Memory Processing Unit (mMPU) overcomes the memory wall through memristive devices that unite storage and logic for real processing-in-memory (PIM) systems. At the core of the mMPU is stateful logic, which is accelerated with memristive partitions to enable logic with massive inherent parallelism within crossbar arrays. This paper vastly accelerates the fundamental operations of matrix-vector multiplication and convolution in the mMPU, with either full-precision or binary elements. These proposed algorithms establish an efficient foundation for large-scale mMPU applications such as neural-networks, image processing, and numerical methods. We overcome the inherent asymmetry limitation in the previous in-memory full-precision matrix-vector multiplication solutions by utilizing techniques from block matrix multiplication and reduction. We present the first fast in-memory binary matrix-vector multiplication algorithm by utilizing memristive partitions with a tree-based popcount reduction (39x faster than previous work). For convolution, we present a novel in-memory input-parallel concept which we utilize for a full-precision algorithm that overcomes the asymmetry limitation in convolution, while also improving latency (2x faster than previous work), and the first fast binary algorithm (12x faster than previous work).

Digital memristive processing-in-memory overcomes the memory wall through a fundamental storage device capable of stateful logic within crossbar arrays. Dynamically dividing the crossbar arrays by adding memristive partitions further increases parallelism, thereby overcoming an inherent trade-off in memristive processing-in-memory. The algorithmic topology of partitions is highly unique, and was recently exploited to accelerate multiplication (11x with 32 partitions) and sorting (14x with 16 partitions). Yet, the physical implementation of memristive partitions, such as the peripheral decoders and the control message, has never been considered and may lead to vast impracticality. This paper overcomes that challenge with several novel techniques, presenting efficient practical designs of memristive partitions. We begin by formalizing the algorithmic properties of memristive partitions into serial, parallel, and semi-parallel operations. Peripheral overhead is addressed via a novel technique of half-gates that enables efficient decoding with negligible overhead. Control overhead is addressed by carefully reducing the operation set of memristive partitions, while resulting in negligible performance impact, by utilizing techniques such as shared indices and pattern generators. Ultimately, these efficient practical solutions, combined with the vast algorithmic potential, may revolutionize digital memristive processing-in-memory.

Bulk-bitwise processing-in-memory (PIM), where large bitwise operations are performed in parallel by the memory array itself, is an emerging form of computation with the potential to mitigate the memory wall problem. This paper examines the capabilities of bulk-bitwise PIM by constructing PIMDB, a fully-digital system based on memristive stateful logic, utilizing and focusing on in-memory bulk-bitwise operations, designed to accelerate a real-life workload: analytical processing of relational databases. We introduce a host processor programming model to support bulk-bitwise PIM in virtual memory, develop techniques to efficiently perform in-memory filtering and aggregation operations, and present the mapping of the application into the memory. When tested against an equivalent in-memory database on the same host system, our approach substantially lowers the number of required memory read operations, thus accelerating TPC-H filter operations by 1.6$\times$--18$\times$ and full queries by 56$\times$--608$\times$, while reducing the energy consumption by 1.7$\times$--18.6$\times$ and 0.81$\times$--12$\times$ for these benchmarks, respectively. Our extensive evaluation uses the gem5 full-system simulation environment.

Processing-in-memory (PIM) solutions vastly accelerate systems by reducing data transfer between computation and memory. Memristors possess a unique property that enables storage and logic within the same device, which is exploited in the memristive Memory Processing Unit (mMPU). The mMPU expands fundamental stateful logic techniques, such as IMPLY, MAGIC and FELIX, to high-throughput parallel logic and arithmetic operations within the memory. Unfortunately, memristive processing-in-memory is highly vulnerable to soft errors and this massive parallelism is not compatible with traditional reliability techniques, such as error-correcting-code (ECC). In this paper, we discuss reliability techniques that efficiently support the mMPU by utilizing the same principles as the mMPU computation. We detail ECC techniques that are based on the unique properties of the mMPU to efficiently utilize the massive parallelism. Furthermore, we present novel solutions for efficiently implementing triple modular redundancy (TMR). The short-term and long-term reliability of large-scale applications, such as neural-network acceleration, are evaluated. The analysis clearly demonstrates the importance of high-throughput reliability mechanisms for memristive processing-in-memory., Accepted to 28th International Conference on Electronics Circuits and Systems (ICECS) 2021

Quantized neural networks (QNNs) are being actively researched as a solution for the computational complexity and memory intensity of deep neural networks. This has sparked efforts to develop algorithms that support both inference and training with quantized weight and activation values without sacrificing accuracy. A recent example is the GXNOR framework for stochastic training of ternary and binary neural networks. In this paper, we introduce a novel hardware synapse circuit that uses magnetic tunnel junction (MTJ) devices to support the GXNOR training. Our solution enables processing near memory (PNM) of QNNs, therefore can further reduce the data movements from and into the memory. We simulated MTJ-based stochastic training of a TNN over the MNIST and SVHN datasets and achieved an accuracy of 98.61% and 93.99%, respectively.