Table 1. Experimental dataset properties.

The notations $\left|\mathcal{S}\right|$, L($\mathcal{S}$), LCard($\mathcal{S}$), LDen($\mathcal{S}$), DL($\mathcal{S}$), and PDL($\mathcal{S}$) represent number of instances, number of pathway labels, pathway labels cardinality, pathway labels density, distinct pathway labels set, and proportion of distinct pathway labels set for $\mathcal{S}$, respectively. The notations R($\mathcal{S}$), RCard($\mathcal{S}$), RDen($\mathcal{S}$), DR($\mathcal{S}$), and PDR($\mathcal{S}$) have similar meanings as before but for the enzymatic reactions $\mathcal{E}$ in $\mathcal{S}$. PLR($\mathcal{S}$) represents a ratio of L($\mathcal{S}$) to R($\mathcal{S}$). The last column denotes the domain of $\mathcal{S}$.

Dataset	$\left|\mathcal{S}\right|$	L($\mathcal{S}$)	LCard($\mathcal{S}$)	LDen($\mathcal{S}$)	DL($\mathcal{S}$)	PDL($\mathcal{S}$)	R($\mathcal{S}$)	RCard($\mathcal{S}$)	RDen($\mathcal{S}$)	DR($\mathcal{S}$)	PDR($\mathcal{S}$)	PLR($\mathcal{S}$)	Domain
EcoCyc	1	307	307	1	307	307	1134	1134	1	719	719	0.2707	Escherichia coli K-12 substr.MG1655
HumanCyc	1	279	279	1	279	279	1177	1177	1	693	693	0.2370	Homo sapiens
AraCyc	1	510	510	1	510	510	2182	2182	1	1034	1034	0.2337	Arabidopsis thaliana
YeastCyc	1	229	229	1	229	229	966	966	1	544	544	0.2371	Saccharomyces cerevisiae
LeishCyc	1	87	87	1	87	87	363	363	1	292	292	0.2397	Leishmania major Friedlin
TrypanoCyc	1	175	175	1	175	175	743	743	1	512	512	0.2355	Trypanosoma brucei
SixDB	63	37295	591.9841	0.0159	944	14.9841	210080	3334.6032	0.0159	1709	27.1270	0.1775	Composed from six databases
Symbiont	3	119	39.6667	0.3333	59	19.6667	304	101.3333	0.3333	130	43.3333	0.3914	Composed of Moranella and Tremblaya
CAMI	40	6261	156.5250	0.0250	674	16.8500	14269	356.7250	0.0250	1083	27.0750	0.4388	Simulated microbiomes of low complexity
HOT	4	2178	311.1429	0.1429	781	111.5714	182675	26096.4286	0.1429	1442	206.0000	0.0119	Metagenomic Hawaii Ocean Time-series (10m, 75m, 110m, and 500m)
Synset-1	15000	6801364	453.4243	0.00007	2526	0.1684	30901554	2060.1036	0.00007	3650	0.2433	0.2201	Synthetically generated (uncorrupted)
Synset-2	15000	6806262	453.7508	0.00007	2526	0.1684	34006386	2267.0924	0.00007	3650	0.2433	0.2001	Synthetically generated (corrupted)