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In Fig. 1S we show that when the E-value cutoff in the fly dataset was changed from a less conservative 10-10 to a more conservative 10-30 value, the shape of the histogram above 40% remained virtually unchanged.
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We find that their results are not being reproduced when alternative software packages are used or when the variables' ordering within the dataset is changed.
We argue that, given two models (A) and (B), where (A) learns to predict continuous values and model (B) learns to predict binary values, and the performance of model (A) in terms of (AUC) and (AUPR) is as good as the performance of model (B), model (A) is advantageous because it does not need to be retrained when the threshold for the dataset is changed.
The datasets were changed to log2 scale and to each individual value the population mean was subtracted.
Third, missing values in the Seoul datasets were changed to random values to evaluate the model's tolerance against missing values (missing value analysis).
Finally, before they were used, the training, testing, and Sørlie datasets' annotation was changed from clone ID to UniGene Cluster ID.
The number of releases was changed from 3 to 5 and 8 for dataset-1 and dataset-2, respectively.
Even with the same dataset it may be changed to satisfy a particular research objective.
After data files have been uploaded, the color of the dataset name will be changed from red to yellow to indicate the pipeline is processing the data.
MERCI software compares positive and negative dataset and motifs provided will be changed as we change the input dataset.
Some minor syntax comments are: In Page 1 : "AGRIS database, together with other related resources extracted from other preselected datasets"… "together with" should be changed to "combined with".
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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