The vast potential of memristor-based computation-in-memory (CIM) engines has mainly triggered the mapping of best-suited applications. Nevertheless, with additional support, existing applications can also benefit from CIM. In particular, this paper proposes an energy and area-efficient CIM-based methodology to perform arithmetic signed matrix multiplications. Our approach combines a) the mapping of the signed operands on the 1T1R crossbar, and b) the augmentation of the periphery with customized circuits to support the execution of shift and accumulate needed for the arithmetic operations. The operand mapping is performed without the need for sign extension; hence, reducing the required memory size. To demonstrate the superiority of our scheme as compared with the state-of-the-art, simulations are performed for different case studies including a neural network and two kernels which are taken from the Polybench/C benchmark suite. The results show that our approach achieves up to 8× energy-saving and 3× area-saving compared with other CIM-based prior works.

The high execution time of DNA sequence alignment negatively affects many genomic studies that rely on sequence alignment results. Pre-alignment filtering was introduced as a step before alignment to reduce the execution time of short-read sequence alignment greatly. With its success, i.e., achieving high accuracy and thus removing unnecessary alignments, the filtering itself now constitutes the larger portion of the execution time. A significant contributing factor entails the movement of sequences from the memory to the processing units, while a majority will filter out as they do not result in an acceptable alignment. State-of-the-art (SotA) pre-alignment filtering accelerators suffer from the same overhead for data movements. Furthermore, these accelerators lack support for future pre-alignment filtering algorithms using the same operations and underlying hardware. This paper addresses these shortcomings by introducing SieveMem. SieveMem is an architecture that exploits the Computation-in-Memory paradigm with memristive-based devices to support shared kernels of pre-alignment filters and algorithms inside the memory (i.e., preventing data movements). SieveMem architecture also provides support for future algorithms. SieveMem supports more than 47.6% of shared operations among all top 5 SotA filters. Moreover, SieveMem includes a hardware-friendly pre-alignment filtering algorithm called BandedKrait, inspired by a combination of mentioned kernels. Our evaluations show that SieveMem provides up to 331.1 x and 446.8 × improvement in the execution time of the two most-common kernels. Our evaluations also show that BandedKrait provides accuracy at the SotA level. Using BandedKrait on SieveMem, a design we call Mem-BandedKrait, one can improve the execution time of end-to-end sequence alignment irrespective of the dataset, which can go up to 91.4 × compared to the SotA accelerator on GPU.

In recent years, we are witnessing a trend toward in-memory computing for future generations of computers that differs from traditional von-Neumann architecture in which there is a clear distinction between computing and memory units. Considering that data movements between the central processing unit (CPU) and memory consume several orders of magnitude more energy compared to simple arithmetic operations in the CPU, in-memory computing will lead to huge energy savings as data no longer needs to be moved around between these units. In an initial step toward this goal, new non-volatile memory technologies, e.g., resistive RAM (ReRAM) and phase-change memory (PCM), are being explored. This has led to a large body of research that mainly focuses on the design of the memory array and its peripheral circuitry. In this article, we mainly focus on the tile architecture (comprising a memory array and peripheral circuitry) in which storage and compute operations are performed in the (analog) memory array and the results are produced in the (digital) periphery. Such an architecture is termed compute-in-memory-periphery (CIM-P). More precisely, we derive an abstract CIM-tile architecture and define its main building blocks. To bridge the gap between higher-level programming languages and the underlying (analog) circuit designs, an instruction-set architecture is defined that is intended to control and, in turn, sequence the operations within this CIM tile to perform higher-level more complex operations. Moreover, we define a procedure to pipeline the CIM-tile operations to further improve the performance. To simulate the tile and perform design space exploration considering different technologies and parameters, we introduce the fully parameterized first-of-its-kind CIM tile simulator and compiler. Furthermore, the compiler is technology-aware when scheduling the CIM-tile instructions. Finally, using the simulator, we perform several preliminary design space explorations regarding the three competing technologies, ReRAM, PCM, and STT-MRAM concerning CIM-tile parameters, e.g., the number of ADCs. Additionally, we investigate the effect of pipelining in relation to the clock speeds of the digital periphery assuming the three technologies. In the end, we demonstrate that our simulator is also capable of reporting energy consumption for each building block within the CIM tile after the execution of in-memory kernels considering the data-dependency on the energy consumption of the memory array. All the source codes are publicly available.

State-of-the-art taxonomic profilers that comprise the first step in larger-context metagenomic studies have proven to be computationally intensive, i.e., while accurate, they come at the cost of high latency and energy consumption. Table Lookup operation is a primary bottleneck of today's profilers. In this paper, we first propose TL-PIM, a hardware accelerator based on the processing-in-memory (PIM) paradigm to accelerate Table Lookup. TL-PIM leverages the in-memory compute capability of emerging memory technologies along with intelligent data mapping. Then, we integrate TL-PIM into Kraken2, a state-of-the-art metagenomic profiler, and build an HW/SW co-designed profiler, called KrakenOnMem. Results from a silicon-based prototype of our emerging memory validate the design and required operations on a smaller scale. Our large-scale calibrated simulations show that KrakenOnMem can provide an average of 61.3% speedup compared to original Kraken2 for end-to-end profiling. Additionally, our design improves the energy consumption by orders of magnitude compared to the original Kraken2 while incurring a negligible area overhead.

Spin-transfer torque magnetic random access memory (STT-MRAM) based computation-in-memory (CIM) architectures have shown great prospects for an energy-efficient computing. However, device variations and non-idealities narrow down the sensing margin that severely impacts the computing accuracy. In this work, we propose an adaptive referencing mechanism to improve the sensing margin of a CIM architecture for boolean binary logic (BBL) operations. We generate reference signals using multiple STT-MRAM devices and place them strategically into the array such that these signals can address the variations and trace the wire parasitics effectively. We have demonstrated this behavior using an STT-MRAM model, which is calibrated using 1Mbit characterized array. Results show that our proposed architecture for binary neural networks (BNN) achieves up to 17.8 TOPS/W on the MNIST dataset and 130× performance improvement for the text encryption compared to the software implementation on Intel Haswell processor.

Von Neumann-based architectures suffer from costly communication between CPU and memory. This communication imposes several orders of magnitude more power and performance overheads compared to the arithmetic operations performed by the processor. This overhead becomes critical for applications that require processing a large amount of data. Computation-in-Memory (CIM) leveraging memristor devices in the crossbar structure offers a potential solution to tackle this challenge. However, support for the integer data type is lacking in CIM approaches as most solutions operate on a single/few bits only. This paper proposes a new organization of the periphery (next to memristor crossbar) to compute matrix-matrix multiplication (MMM) at the tile level. More precisely, the analog additions performed in the crossbar is complemented with additions performed in the digital periphery. In this mixed analog-digital system, digital additions are performed in a way that only the minimum size of adders are required-this is to reduce the latency of the digital periphery as much as possible. In addition, the design is customized to the number of ADCs as well as datatype sizes to support different possible scenarios. The results show that our organization reduces energy and latency up to 50x and 3x, respectively, compared to the reference design.