Dataset Information

Device quantization policy in variation-aware in-memory computing design.

ABSTRACT: Device quantization of in-memory computing (IMC) that considers the non-negligible variation and finite dynamic range of practical memory technology is investigated, aiming for quantitatively co-optimizing system performance on accuracy, power, and area. Architecture- and algorithm-level solutions are taken into consideration. Weight-separate mapping, VGG-like algorithm, multiple cells per weight, and fine-tuning of the classifier layer are effective for suppressing inference accuracy loss due to variation and allow for the lowest possible weight precision to improve area and energy efficiency. Higher priority should be given to developing low-conductance and low-variability memory devices that are essential for energy and area-efficiency IMC whereas low bit precision (< 3b) and memory window (< 10) are less concerned.

SUBMITTER: Chang CC

PROVIDER: S-EPMC8741899 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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Device quantization policy in variation-aware in-memory computing design.

Chang Chih-Cheng CC Li Shao-Tzu ST Pan Tong-Lin TL Tsai Chia-Ming CM Wang I-Ting IT Chang Tian-Sheuan TS Hou Tuo-Hung TH

Scientific reports 20220107 1

Device quantization of in-memory computing (IMC) that considers the non-negligible variation and finite dynamic range of practical memory technology is investigated, aiming for quantitatively co-optimizing system performance on accuracy, power, and area. Architecture- and algorithm-level solutions are taken into consideration. Weight-separate mapping, VGG-like algorithm, multiple cells per weight, and fine-tuning of the classifier layer are effective for suppressing inference accuracy loss due t ...[more]

PMID: 34997104

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Project description:MotivationThe completion of the genome has paved the way for genome-wide association studies (GWAS), which explained certain proportions of heritability. GWAS are not optimally suited to detect non-linear effects in disease risk, possibly hidden in non-additive interactions (epistasis). Alternative methods for epistasis detection using, e.g. deep neural networks (DNNs) are currently under active development. However, DNNs are constrained by finite computational resources, which can be rapidly depleted due to increasing complexity with the sheer size of the genome. Besides, the curse of dimensionality complicates the task of capturing meaningful genetic patterns for DNNs; therefore necessitates dimensionality reduction.ResultsWe propose a method to compress single nucleotide polymorphism (SNP) data, while leveraging the linkage disequilibrium (LD) structure and preserving potential epistasis. This method involves clustering correlated SNPs into haplotype blocks and training per-block autoencoders to learn a compressed representation of the block's genetic content. We provide an adjustable autoencoder design to accommodate diverse blocks and bypass extensive hyperparameter tuning. We applied this method to genotyping data from Project MinE, and achieved 99% average test reconstruction accuracy-i.e. minimal information loss-while compressing the input to nearly 10% of the original size. We demonstrate that haplotype-block based autoencoders outperform linear Principal Component Analysis (PCA) by approximately 3% chromosome-wide accuracy of reconstructed variants. To the extent of our knowledge, our approach is the first to simultaneously leverage haplotype structure and DNNs for dimensionality reduction of genetic data.Availability and implementationData are available for academic use through Project MinE at https://www.projectmine.com/research/data-sharing/, contingent upon terms and requirements specified by the source studies. Code is available at https://github.com/gizem-tas/haploblock-autoencoders.

Dataset Information

Device quantization policy in variation-aware in-memory computing design.

Publications

Device quantization policy in variation-aware in-memory computing design.

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