compatibilityDistance.js

function compatibilityDistance(network1, network2, c1 = 1, c2 = 1, c3 = 0.4) {
  const i1 = new Set(network1.connections.map((c) => c.innovation));
  const i2 = new Set(network2.connections.map((c) => c.innovation));

  const disjoint =
    [...i1].filter((i) => !i1.has(i)).length +
    [...i2].filter((i) => !i2.has(i)).length;

  const excess = Math.max(i1.size, i2.size) - Math.min(i1.size, i2.size);
  const matching = network1.connections.filter((c1) => i2.has(c1.innovation));

  const avgWeightDiff =
    matching.reduce((sum, c1) => {
      const c2 = network2.connections.find(
        (c) => c.innovation === c1.innovation
      );
      return sum + Math.abs(c1.weight - c2.weight);
    }, 0) / matching.length;

  const N = Math.min(i1.size, i2.size) > 20 ? Math.min(i1.size, i2.size) : 1;

  return (c1 * excess) / N + (c2 * disjoint) / N + c3 * avgWeightDiff;
}

c1: This coefficient assigns importance to the excess genes. Excess genes are those that have higher innovation numbers in one genome compared to the other. A larger c1 value means that genomes with more excess genes are considered more dissimilar.

c2: This coefficient assigns importance to the disjoint genes. Disjoint genes are those with innovation numbers present in one genome but not in the other. A larger c2 value means that genomes with more disjoint genes are considered more dissimilar.

c3: This coefficient assigns importance to the average weight differences between matching genes (i.e., genes with the same innovation numbers in both genomes). A larger c3 value means that genomes with greater weight differences are considered more dissimilar.