Reason for dual TGP implementations used differently for simulations and experiments

Determine why two distinct implementations of the topological gap protocol—analyze_two (used for experimental data and figures) and analyze_2 (used for simulations and Table II)—with differing parameters were coded and applied in Aghaee et al., Phys. Rev. B 107, 245423 (2023).

Background

The paper reports that the Microsoft Quantum paper supporting its main claims applied two different analysis functions under the same protocol name: analyze_two for experimental datasets and figures, and analyze_2 for the simulation-based yield analysis. The two implementations use different parameter settings (notably average_over_cutter), leading to materially different outcomes, including the presence or absence of false positives.

Because the claim of a “high probability” of being in the topological phase relies on the assertion of “no false positives” in simulations, understanding why two different versions were used, and under what justification, is crucial for interpreting the validity of the reported conclusions.