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We needed to apply a boundary condition to the outlet; applying a standard "outlet" condition resulted in slower runtime and program warnings due to the methods the program uses to apply an outlet condition.
Multiple iterations of HHblits would have resulted in slower runtime performance.
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This is important, as slow runtime is often a limitation of stochastic methods.
Both COLONY and the HS-MSC cannot estimate half-sibling groups for large populations due to slow runtimes.
Specifically, Tables 2 5 show, as general trend, that the higher the error ratio the slower the runtime performances of the model.
We found other string kernels (Leslie et al., 2004; Lodhi et al., 2002) either slower in runtime or worse in performance (Supplementary Table S4).
However, we perceive that there are applications where a slower but deterministic runtime is preferable to a faster but data-dependent runtime.
The GATK-based VCF to PED conversion for ADMIXTURE is also slower, with a runtime of over 10 min. > Clustering the samples is also fastest in VARIANTSPARK (1 min and 20 sec, see Table 1), despite VARIANTSPARK and ADAM both using SPARK's MLlib k-means implementation.
As we increase accuracy further in Smoldyn with 10 times more iterations the runtime slows to 726 seconds (not plotted), and with approximately 10 times more subvolumes in STEPS (4520) and MesoRD (4096) STEPS slows to 109 seconds compared to 169 seconds for MesoRD.
This is a large burden, because claiming a release runs on "Linux x86" requires compatibility with extremely old libraries and forces a lot of checks to happen at runtime which slows down Mozilla.
In the Methods section, we show that complete probabilistic shape analysis has a "slow" exponential term in its runtime requirements.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com