Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: GRIM-filter: fast seed filtering in read mapping using emerging memory
  technologies   Motivation: Seed filtering is critical in DNA read mapping, a process where
billions of DNA fragments (reads) sampled from a donor are mapped onto a
reference genome to identify genomic variants of the donor. Read mappers 1)
quickly generate possible mapping locations (i.e., seeds) for each read, 2)
extract reference sequences at each of the mapping locations, and then 3) check
similarity between each read and its associated reference sequences with a
computationally expensive dynamic programming algorithm (alignment) to
determine the origin of the read. Location filters come into play before
alignment, discarding seed locations that alignment would have deemed a poor
match. The ideal location filter would discard all poor matching locations
prior to alignment such that there is no wasted computation on poor alignments.
  Results: We propose a novel filtering algorithm, GRIM-Filter, optimized to
exploit emerging 3D-stacked memory systems that integrate computation within a
stacked logic layer, enabling processing-in-memory (PIM). GRIM-Filter quickly
filters locations by 1) introducing a new representation of coarse-grained
segments of the reference genome and 2) using massively-parallel in-memory
operations to identify read presence within each coarse-grained segment. Our
evaluations show that for 5% error acceptance rates, GRIM-Filter eliminates
5.59x-6.41x more false negatives and exhibits end-to-end speedups of
1.81x-3.65x compared to mappers employing the best previous filtering
algorithm.

18
The categories of this paper are: econ
20
The categories of this paper are: acc-phys
30
The categories of this paper are: q-alg
22
The categories of this paper are: chao-dyn
11
The categories of this paper are: hep-lat
32
The categories of this paper are: atom-ph
13
The categories of this paper are: quant-ph
6
The categories of this paper are: astro-ph
34
The categories of this paper are: chem-ph
33
The categories of this paper are: plasm-ph
7
The categories of this paper are: hep-th
37
The categories of this paper are: supr-con
2
The categories of this paper are: math
9
The categories of this paper are: nlin
31
The categories of this paper are: ao-sci
17
The categories of this paper are: q-fin