Superbubbles revisited

Table 1 Comparison of running times

Data	N	M	S	Running times [s]
Data	N	M	S	LSD	S + LSD+ f	LSD + B	S + B + f
Yeast	49,795	130,993	325	3	4	6	9
EU mail	265,214	420,045	13285	15	16	31	34
Slashdot	82,168	948,464	0	17	27	22	37
Amazon	403,394	3,387,388	3	60	86	87	158
Google	875,713	5,105,039	6477	94	127	144	254
Wikipedia	2,394,385	5,021,410	4737	147	171	385	418

The for combinations of algorithms compared here are: LSD (using the auxiliary graphs \({\hat{G}}{C}\) and the stack-based superbubble detector), S+LSD using Sung graphs with our stack-based detector plus a post-filter for the false positives, LSD+B using our graph construction with the range-query-based detector of [8], and S+B using the re-implementation of the state of the art method with the post-filter. All computations were performed on a 2.5GHz quad-core Intel Core i7 processor (Turbo Boost up to 3.7GHz) with 6MB shared L3 cache and 16GB of 1600MHz DDR3L onboard memory. Test data sets are taken from [4] and from the Stanford Large Network Dataset Collection [21]. The table lists their number N of vertices, M of edges and S of superbubbles

ISSN: 1748-7188