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Table 3 Comparison of runtime and clustering accuracy (measured by adjusted rand index) between CIDR and four other algorithms on a simulation data set with 10,000 cells

From: CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data

Simulation (10K) CIDR CIDR (L) prcomp t-SNE RaceID ZIFA
Time 44.5 min 1.5 h 3.1 h 21.8 h >14 day 1.6 daya
Adjusted rand index 0.99 1.00 0.99 0.00 N/Ab 0.09
  1. CIDR is the default CIDR algorithm implementation with step function simplification, while CIDR (L) is the implementation with the non-simplified logistic function. The algorithms except ZIFA were run on an AWS ec2 r3.2xlarge instance
  2. aZIFA ran out of memory on the AWS ec2 r3.2xlarge instance, and its runtime was recorded from a run on an AWS ec2 r3.8xlarge instance
  3. bRaceID did not complete after 14 days