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Updated: Feb 10, 2026

Air-sampled Filter Analysis for Endotoxins and DNA Content

Air-sampled Filter Analysis for Endotoxins and DNA Content

Published on: March 7, 2016

GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.

Jeremie S Kim^1,2, Damla Senol Cali³, Hongyi Xin⁴

¹Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. jeremiekim123@gmail.com.

|May 17, 2018

Summary

This summary is machine-generated.

GRIM-Filter enhances DNA read mapping by using processing-in-memory on 3D-stacked systems. This novel seed location filter significantly speeds up read mappers and reduces errors.

Keywords:

3D-stacked DRAM Emerging memory technologies Genome sequencing High throughput sequencing Processing-in-memory Seed location filtering

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Area of Science:

Bioinformatics
Computer Architecture
Genomics

Background:

Seed location filtering is crucial for efficient DNA read mapping to identify genomic variants.
Current methods rely on computationally expensive sequence alignment after initial seed location generation.
An ideal filter would eliminate incorrect seed locations before alignment to save computational resources.

Purpose of the Study:

To introduce GRIM-Filter, a novel seed location filtering algorithm.
To optimize GRIM-Filter for 3D-stacked memory systems using processing-in-memory (PIM).
To improve the efficiency and speed of DNA read mapping.

Main Methods:

Developed a new representation for coarse-grained segments of the reference genome.
Utilized massively-parallel in-memory operations for rapid seed location filtering.
Integrated computation within 3D-stacked memory layers for processing-in-memory.

Main Results:

GRIM-Filter reduced the false negative rate of seed location filtering by 5.59x-6.41x (for 0.05 error tolerance).
Achieved an end-to-end read mapper speedup of 1.81x-3.65x compared to state-of-the-art methods.
Demonstrated GRIM-Filter's effectiveness in overcoming memory bandwidth limitations.

Conclusions:

GRIM-Filter leverages 3D-stacked memory and PIM to enhance DNA read mapping performance.
The algorithm significantly boosts the speed of state-of-the-art read mappers.
GRIM-Filter is a universal solution applicable to any read mapper, encouraging future research in PIM for bioinformatics.