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@arrjon arrjon commented Nov 4, 2025

This pull request updates the Lotka-Volterra and SIR benchmark simulators to be in line with the benchmark of Lueckmann. The changes allow for more accurate reproduction of original benchmark tasks:

  • Added 'original' option in the subsample parameter for both lotka_volterra.py and sir.py simulators, enabling users to reproduce the exact subsampling easily.
  • Changed the construction of time vectors in both simulators by switching from np.linspace to np.arange to get the same time steps as in Lueckmann et. al.
  • In lotka_volterra.py simulations are now clipped to a minimum of 1e-10 and a maximum of 10000.0 before applying noise, instead of the log1p, which migth be nicer but deviates from the original benchmark.

@arrjon arrjon requested a review from stefanradev93 November 4, 2025 14:05
@arrjon arrjon self-assigned this Nov 4, 2025
@stefanradev93 stefanradev93 merged commit 7573a4d into dev Nov 4, 2025
2 of 8 checks passed
@stefanradev93 stefanradev93 deleted the fix_benchmark branch November 4, 2025 14:11
@arrjon arrjon restored the fix_benchmark branch November 4, 2025 14:33
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3 participants