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Table 1 Benchmarking Results

From: Exploiting the pathway structure of metabolism to reveal high-order epistasis

Property

Brute-force LP (k = 2)

Random KO + Reduce (k = 10)

NetKO (k = 10)

Number of MCS found

215

223

11,706

Highest Cardinality MCS Obtained

2

3

10

Reactions included in at least one MCS

263

235

355

Number of biomass components targeted

38

41

36

Number of linear programming steps

487,670

7,221,149

113,989

  1. Comparison of our network-based genome-scale knockout design approach (NetKO) with two LP-based methods: The standard genome-scale method for MCS computation for all single and double knockouts (Brute Force LP) and a random knockout approach combined with reduction to minimality for 250,000 cardinality 10 reaction sets (Random KO + reduce).