flowEMMi: an automated model-based clustering tool for microbial cytometric data

BMC Bioinformatics

Table 4 Running times and F ₁ score aggregated over experiments with different ε stopping criteria

Label	ε≤	Time (mean)	Time (sd)	F ₁ score (mean)	F ₁ (sd)
flowEMMi	1.0	528	53	0.56	0.18
flowEMMi	0.01	1 080	214	0.59	0.17
flowEMMi	10⁻⁵	1 445	182	0.56	0.17
flowMerge	1.0	8 391	3 239	0.54	0.24
flowMerge	0.01	8 951	3 597	0.51	0.17
flowMerge	10⁻⁵	56 652	53 379	0.54	0.17

Times and F ₁ scores (and their standard deviation (sd)) are aggregated over four experiments and 5 expert user gatings, each. Note that the default flowMerge stopping criterion of 10⁻⁵ yields running times in excess of 1 day. flowEMMi consistently yields better F ₁ measures with an average improvement of 4% to 16% over flowMerge, with much better running times, easily yielding speed improvements of ×8 – ×15 or better. For both algorithms, having a more stringent EM stopping criterion tends to increase the F ₁ score, however especially for flowMerge at prohibitive running time costs

ISSN: 1471-2105