Table 5. Pathway prediction performance between methods using T1 golden datasets.

mlLGPR-EN: the mlLGPR with elastic net penalty, L2: AB: abundance features, RE: reaction evidence features, and PE: pathway evidence features. For each performance metric, ‘↓’ indicates the lower score is better while ‘↑’ indicates the higher score is better.

Methods	Hamming Loss ↓
	EcoCyc	HumanCyc	AraCyc	YeastCyc	LeishCyc	TrypanoCyc	SixDB
BASELINE	0.2217	0.2486	0.3230	0.2458	0.1591	0.2526	0.3096
Naïve	0.3856	0.4113	0.4592	0.4216	0.3215	0.4319	0.4392
MinPath	0.2257	0.2530	0.3266	0.2482	0.1615	0.2561	0.3124
PathoLogic	0.0610	0.0633	0.1188	0.0424	0.0368	0.0424	0.1141
mlLGPR-EN (+AB+RE+PE)	0.0804	0.0633	0.1069	0.0550	0.0380	0.0590	0.1281
Methods	Average Precision Score ↑
	EcoCyc	HumanCyc	AraCyc	YeastCyc	LeishCyc	TrypanoCyc	SixDB
BASELINE	0.3531	0.3042	0.3832	0.2694	0.1779	0.2153	0.4145
Naïve	0.2384	0.2081	0.3035	0.1770	0.0968	0.1382	0.3357
MinPath	0.3490	0.3004	0.3806	0.2675	0.1758	0.2129	0.4124
PathoLogic	0.7230	0.6695	0.7011	0.7194	0.4803	0.5480	0.7522
mlLGPR-EN (+AB+RE+PE)	0.6187	0.6686	0.7372	0.6480	0.4731	0.5455	0.7561
Methods	Average Recall Score ↑
	EcoCyc	HumanCyc	AraCyc	YeastCyc	LeishCyc	TrypanoCyc	SixDB
BASELINE	0.9902	0.9713	0.9843	1.0000	1.0000	1.0000	0.9860
Naïve	0.9902	0.9713	0.9843	1.0000	1.0000	1.0000	0.9860
MinPath	0.9902	0.9713	0.9843	1.0000	1.0000	1.0000	0.9860
PathoLogic	0.8078	0.8423	0.7176	0.8734	0.8391	0.7829	0.7499
mlLGPR-EN (+AB+RE+PE)	0.8827	0.8459	0.7314	0.8603	0.9080	0.8914	0.6904
Methods	Average F1 Score ↑
	EcoCyc	HumanCyc	AraCyc	YeastCyc	LeishCyc	TrypanoCyc	SixDB
BASELINE	0.5205	0.4632	0.5516	0.4245	0.3021	0.3543	0.5784
Naïve	0.3843	0.3428	0.4640	0.3007	0.1765	0.2429	0.4939
MinPath	0.5161	0.4589	0.5489	0.4221	0.2990	0.3511	0.5763
PathoLogic	0.7631	0.7460	0.7093	0.7890	0.6109	0.6447	0.7479
mlLGPR-EN (+AB+RE+PE)	0.7275	0.7468	0.7343	0.7392	0.6220	0.6768	0.7098