Table 3

Run times for Ternary Dot Product Distribution algorithm

Problem size (n+)

Quartic algorithm:compute all D-values

Thresholded algorithm


8

0.05 s

0.07 s

16

0.19 s

0.15 s

32

0.92 s

0.36 s

64

6.16 s

0.61 s

128

53.15 s

2.35 s

256

689.18 s

5.93 s

512

7864.20 s

19.54 s

1024

> 1 d

85.76 s


Run time comparison of simple quartic Ternary Dot Product Distribution algorithm to thresholded version for an increasing family of problems with (n+, n-, n0, q+, q-) in the ratio (1, 1, 50, 2, 1), a typical usage scenario. Runs were performed on a 3.0 GHz Intel Xeon processor with 2 MB cache.

Chindelevitch et al. BMC Bioinformatics 2012 13:35   doi:10.1186/1471-2105-13-35

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