TABLE 1. Benchmarking FStitch and Vespucci.

Each algorithm, FStitch and Vespucci with default parameters (Max Edge: 500 and Density Multiplier: 10,000), and Vespucci with best parameters from a grid search, G.S. (Max Edge: 10 and Density Multiplier: 2,000), are compared on the manually annotated test set from chromosome 1. Overlap percentages are reported per base.

Method	Prediction	Truth Set Label
		Active	Inactive
FStitch	Active	98.5%	1.5%
	Inactive	0.01%	99.99%
Vespucci (default)	Active	60.7%	30.3%
	Inactive	6.03%	93.97%
Vespucci (G.S.)	Active	80.1%	19.9%
	Inactive	0.56%	99.44%