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However, that's what's most common in notebooks anyway and, therefore, the benchmarks below are a good indication of real world results.
While, as described above, ChaNGa is capable of handling hydrodynamics and star formation, in the benchmarks below we show the performance of dark matter only simulations.
We examine 40 transcription factors in yeast (that are further studied in the benchmarks below), each of which has at least 32 predicted targets in MacIsaac et al. [20].
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We used three categories: above the benchmark, below the benchmark, or indeterminate.
We classified individual sites in one of three categories: above the benchmark, below the benchmark, and indeterminate.
Determining a lower acceptable value of alpha is not straightforward but the accepted minimum value for alpha in an examination has traditionally been 0.8, which it has been said that, "remains the benchmark below which an exam or elements within it should not fall.
Some factors deviate more from PWM values than others, and in many cases, these are the same factors that perform well in the yeast benchmark below, as described there.
In fact, based on the benchmark results below, I argue that this approach would be particularly useful in analysing binding data from high-throughput experiments (ChIP-chip or ChIP-seq): these yield thousands of putative binding sites, of which hundreds may be sufficiently high-confidence for this purpose.
We considered these 24 known targets as "true positives" for the phenotypes of interest in one of the benchmarks described below (see section Validation of predicted therapeutic targets in Results and discussion).
We used the third category when 85% of site average measurements were below the MDL and the benchmark was below the MDL.
Given that ReliefF generated high quality AD for the benchmark dataset (discussed below), we propose this technique is, in principle, particularly well-suited for AD mapping.
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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